Mark A Beilstein

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• Beilstein, M. A., & Szymanski, D. B. (2018). Cytoskeletal Requirements during Arabidopsis Trichome Development. In Annual Plant Reviews online. John Wiley & Sons, LTD. doi:10.1002/9781119312994.APR0099
• Beilstein, M. A., Shippen, D. E., & Nelson, A. C. (2014). Plant telomeres and telomerase. In Molecular Biology, The Plant Sciences 2,. Springer New York. doi:10.1007/978-1-4614-7570-5_4
• Nelson, A. D., Beilstein, M. A., & Shippen, D. E. (2013). Plant Telomeres and Telomerase: Evolution in the Field. In The Plant Sciences; Molecular Biology. Springer.
• Kellogg, E. A., Beilstein, M. A., & Al-shehbaz, I. A. (2012). Tribu DESCURAINIEAE Al-Shehbaz, Beilstein & E.A. Kellogg. In Flora of North America. Instituto de Botánica Darwinion. doi:10.2307/J.CTT16VJ2G8.14
• Kellogg, E. A., Beilstein, M. A., & Al-shehbaz, I. A. (2012). Tribu HALIMOLOBEAE Al-Shehbaz, Beilstein & E.A. Kellogg. In Flora of North America. Instituto de Botánica Darwinion. doi:10.2307/J.CTT16VJ2G8.18

Journals/Publications

• Dew-Budd, K. J., Chow, H. T., Kendall, T., David, B. C., Rozelle, J. A., Mosher, R. A., & Beilstein, M. A. (2023). Mating system is associated with seed phenotypes upon loss of RNA-directed DNA methylation in Brassicaceae. Plant Physiology.
• Kramer, M. C., Kim, H. J., Palos, K. R., Garcia, B. A., Lyons, E., Beilstein, M. A., Nelson, A. D., & Gregory, B. D. (2022). A Conserved Long Intergenic Non-coding RNA Containing snoRNA Sequences, , Affects Arabidopsis Germination and Development. Frontiers in plant science, 13, 906603.
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  Long non-coding RNAs (lncRNAs) are an increasingly studied group of non-protein coding transcripts with a wide variety of molecular functions gaining attention for their roles in numerous biological processes. Nearly 6,000 lncRNAs have been identified in but many have yet to be studied. Here, we examine a class of previously uncharacterized lncRNAs termed BRASSICA RAPA () transcripts that were previously identified for their high level of sequence conservation in the related crop species , their nuclear-localization and protein-bound nature. In particular, we focus on and demonstrate that its abundance is highly tissue and developmental specific, with particularly high levels early in germination. contains two snoRNAs domains within it, making it the first sno-lincRNA example in a non-mammalian system. However, we find that it is processed differently than its mammalian counterparts. We further show that plants lacking display patterns of delayed germination and are overall smaller than wild-type plants. Lastly, we identify the proteins that interact with and propose a novel mechanism of lincRNA action in which it may act as a scaffold with the RACK1A protein to regulate germination and development, possibly through a role in ribosome biogenesis.
• Noble, J. A., Bielski, N. V., Liu, M. J., DeFalco, T. A., Stegmann, M., Nelson, A. D., McNamara, K., Sullivan, B., Dinh, K. K., Khuu, N., Hancock, S., Shiu, S. H., Zipfel, C., Cheung, A. Y., Beilstein, M. A., & Palanivelu, R. (2022). Evolutionary analysis of the LORELEI gene family in plants reveals regulatory subfunctionalization. Plant physiology, 190(4), 2539-2556.
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  A signaling complex comprising members of the LORELEI (LRE)-LIKE GPI-anchored protein (LLG) and Catharanthus roseus RECEPTOR-LIKE KINASE 1-LIKE (CrRLK1L) families perceive RAPID ALKALINIZATION FACTOR (RALF) peptides and regulate growth, reproduction, immunity, and stress responses in Arabidopsis (Arabidopsis thaliana). Genes encoding these proteins are members of multigene families in most angiosperms and could generate thousands of signaling complex variants. However, the links between expansion of these gene families and the functional diversification of this critical signaling complex as well as the evolutionary factors underlying the maintenance of gene duplicates remain unknown. Here, we investigated LLG gene family evolution by sampling land plant genomes and explored the function and expression of angiosperm LLGs. We found that LLG diversity within major land plant lineages is primarily due to lineage-specific duplication events, and that these duplications occurred both early in the history of these lineages and more recently. Our complementation and expression analyses showed that expression divergence (i.e. regulatory subfunctionalization), rather than functional divergence, explains the retention of LLG paralogs. Interestingly, all but one monocot and all eudicot species examined had an LLG copy with preferential expression in male reproductive tissues, while the other duplicate copies showed highest levels of expression in female or vegetative tissues. The single LLG copy in Amborella trichopoda is expressed vastly higher in male compared to in female reproductive or vegetative tissues. We propose that expression divergence plays an important role in retention of LLG duplicates in angiosperms.
• Palos, K., Nelson Dittrich, A. C., Yu, L., Brock, J. R., Railey, C. E., Wu, H. L., Sokolowska, E., Skirycz, A., Hsu, P. Y., Gregory, B. D., Lyons, E., Beilstein, M. A., & Nelson, A. D. (2022). Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae. The Plant cell, 34(9), 3233-3260.
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  Long intergenic noncoding RNAs (lincRNAs) are a large yet enigmatic class of eukaryotic transcripts that can have critical biological functions. The wealth of RNA-sequencing (RNA-seq) data available for plants provides the opportunity to implement a harmonized identification and annotation effort for lincRNAs that enables cross-species functional and genomic comparisons as well as prioritization of functional candidates. In this study, we processed >24 Tera base pairs of RNA-seq data from >16,000 experiments to identify ∼130,000 lincRNAs in four Brassicaceae: Arabidopsis thaliana, Camelina sativa, Brassica rapa, and Eutrema salsugineum. We used nanopore RNA-seq, transcriptome-wide structural information, peptide data, and epigenomic data to characterize these lincRNAs and identify conserved motifs. We then used comparative genomic and transcriptomic approaches to highlight lincRNAs in our data set with sequence or transcriptional conservation. Finally, we used guilt-by-association analyses to assign putative functions to lincRNAs within our data set. We tested this approach on a subset of lincRNAs associated with germination and seed development, observing germination defects for Arabidopsis lines harboring T-DNA insertions at these loci. LincRNAs with Brassicaceae-conserved putative miRNA binding motifs, small open reading frames, or abiotic-stress modulated expression are a few of the annotations that will guide functional analyses into this cryptic portion of the transcriptome.
• Dew-Budd, K., Cheung, J., Palos, K., Forsythe, E. S., & Beilstein, M. A. (2020). Evolutionary and biochemical analyses reveal conservation of the Brassicaceae telomerase ribonucleoprotein complex. PloS one, 15(4), e0222687.
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  The telomerase ribonucleoprotein complex (RNP) is essential for genome stability and performs this role through the addition of repetitive DNA to the ends of chromosomes. The telomerase enzyme is composed of a reverse transcriptase (TERT), which utilizes a template domain in an RNA subunit (TER) to reiteratively add telomeric DNA at the ends of chromosomes. Multiple TERs have been identified in the model plant Arabidopsis thaliana. Here we combine a phylogenetic and biochemical approach to understand how the telomerase RNP has evolved in Brassicaceae, the family that includes A. thaliana. Because of the complex phylogenetic pattern of template domain loss and alteration at the previously characterized A. thaliana TER loci, TER1 and TER2, across the plant family Brassicaceae, we bred double mutants from plants with a template deletion at AtTER1 and T-DNA insertion at AtTER2. These double mutants exhibited no telomere length deficiency, a definitive indication that neither of these loci encode a functional telomerase RNA. Moreover, we determined that the telomerase components TERT, Dyskerin, and the KU heterodimer are under strong purifying selection, consistent with the idea that the TER with which they interact is also conserved. To test this hypothesis further, we analyzed the substrate specificity of telomerase from species across Brassicaceae and determined that telomerase from close relatives bind and extend substrates in a similar manner, supporting the idea that TERs in different species are highly similar to one another and are likely encoded from an orthologous locus. Lastly, TERT proteins from across Brassicaceae were able to complement loss of function tert mutants in vivo, indicating TERTs from other species have the ability to recognize the native TER of A. thaliana. Finally, we immunoprecipitated the telomerase complex and identified associated RNAs via RNA-seq. Using our evolutionary data we constrained our analyses to conserved RNAs within Brassicaceae that contained a template domain. These analyses revealed a highly expressed locus whose disruption by a T-DNA resulted in a telomeric phenotype similar to the loss of other telomerase core proteins, indicating that the RNA has an important function in telomere maintenance.
• Forsythe, E. S., Nelson, A. D., & Beilstein, M. A. (2020). Biased Gene Retention in the Face of Introgression Obscures Species Relationships. Genome biology and evolution, 12(9), 1646-1663.
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  Phylogenomic analyses are recovering previously hidden histories of hybridization, revealing the genomic consequences of these events on the architecture of extant genomes. We applied phylogenomic techniques and several complementary statistical tests to show that introgressive hybridization appears to have occurred between close relatives of Arabidopsis, resulting in cytonuclear discordance and impacting our understanding of species relationships in the group. The composition of introgressed and retained genes indicates that selection against incompatible cytonuclear and nuclear-nuclear interactions likely acted during introgression, whereas linkage also contributed to genome composition through the retention of ancient haplotype blocks. We also applied divergence-based tests to determine the species branching order and distinguish donor from recipient lineages. Surprisingly, these analyses suggest that cytonuclear discordance arose via extensive nuclear, rather than cytoplasmic, introgression. If true, this would mean that most of the nuclear genome was displaced during introgression whereas only a small proportion of native alleles were retained.
• Forsythe, E. S., Sloan, D. B., & Beilstein, M. A. (2020). Divergence-Based Introgression Polarization. Genome biology and evolution, 12(4), 463-478.
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  Introgressive hybridization results in the transfer of genetic material between species, often with fitness implications for the recipient species. The development of statistical methods for detecting the signatures of historical introgression in whole-genome data has been a major area of focus. Although existing techniques are able to identify the taxa that exchanged genes during introgression using a four-taxon system, most methods do not explicitly distinguish which taxon served as donor and which as recipient during introgression (i.e., polarization of introgression directionality). Existing methods that do polarize introgression are often only able to do so when there is a fifth taxon available and that taxon is sister to one of the taxa involved in introgression. Here, we present divergence-based introgression polarization (DIP), a method for polarizing introgression using patterns of sequence divergence across whole genomes, which operates in a four-taxon context. Thus, DIP can be applied to infer the directionality of introgression when additional taxa are not available. We use simulations to show that DIP can polarize introgression and identify potential sources of bias in the assignment of directionality, and we apply DIP to a well-described hominin introgression event.
• Kramer, M. C., Janssen, K. A., Palos, K., Nelson, A. D., Vandivier, L. E., Garcia, B. A., Lyons, E., Beilstein, M. A., & Gregory, B. D. (2020). N-methyladenosine and RNA secondary structure affect transcript stability and protein abundance during systemic salt stress in Arabidopsis. Plant direct, 4(7), e00239.
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  After transcription, a messenger RNA (mRNA) is further post-transcriptionally regulated by several features including RNA secondary structure and covalent RNA modifications (specifically N-methyladenosine, mA). Both RNA secondary structure and mA have been demonstrated to regulate mRNA stability and translation and have been independently linked to plant responses to soil salinity levels. However, the effect of mA on regulating RNA secondary structure and the combinatorial interplay between these two RNA features during salt stress response has yet to be studied. Here, we globally identify RNA-protein interactions and RNA secondary structure during systemic salt stress. This analysis reveals that RNA secondary structure changes significantly during salt stress, and that it is independent of global changes in RNA-protein interactions. Conversely, we find that mA is anti-correlated with RNA secondary structure in a condition-dependent manner, with salt-specific mA correlated with a decrease in mRNA secondary structure during salt stress. Taken together, we suggest that salt-specific mA deposition and the associated loss of RNA secondary structure results in increases in mRNA stability for transcripts encoding abiotic stress response proteins and ultimately increases in protein levels from these stabilized transcripts. In total, our comprehensive analyses reveal important post-transcriptional regulatory mechanisms involved in plant long-term salt stress response and adaptation.
• Monihan, S. M., Magness, C. A., Ryu, C. H., McMahon, M. M., Beilstein, M. A., & Schumaker, K. S. (2020). Duplication and functional divergence of a calcium sensor in the Brassicaceae. Journal of experimental botany, 71(9), 2782-2795.
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  The presence of varied numbers of CALCINEURIN B-LIKE10 (CBL10) calcium sensor genes in species across the Brassicaceae and the demonstrated role of CBL10 in salt tolerance in Arabidopsis thaliana and Eutrema salsugineum provided a unique opportunity to determine if CBL10 function is modified in different species and linked to salt tolerance. Salinity effects on species growth and cross-species complementation were used to determine the extent of conservation and divergence of CBL10 function in four species representing major lineages within the core Brassicaceae (A. thaliana, E. salsugineum, Schrenkiella parvula, and Sisymbrium irio) as well as the first diverging lineage (Aethionema arabicum). Evolutionary and functional analyses indicate that CBL10 duplicated within expanded lineage II of the Brassicaceae and that, while portions of CBL10 function are conserved across the family, there are species-specific variations in CBL10 function. Paralogous CBL10 genes within a species diverged in expression and function probably contributing to the maintenance of the duplicated gene pairs. Orthologous CBL10 genes diverged in function in a species-specific manner, suggesting that functions arose post-speciation. Multiple CBL10 genes and their functional divergence may have expanded calcium-mediated signaling responses and contributed to the ability of certain members of the Brassicaceae to maintain growth in salt-affected soils.
• Anderson, S. J., Kramer, M. C., Gosai, S. J., Yu, X., Vandivier, L. E., Nelson, A., Anderson, Z. D., Beilstein, M. A., Fray, R. G., Lyons, E., & Gregory, B. D. (2018). N-6-Methyladenosine Inhibits Local Ribonucleolytic Cleavage to Stabilize mRNAs in Arabidopsis. CELL REPORTS, 25(5), 1146-+.
• Brock, J. R., Dönmez, A. A., Beilstein, M. A., & Olsen, K. M. (2018). Phylogenetics of Camelina Crantz. (Brassicaceae) and insights on the origin of gold-of-pleasure (Camelina sativa). Molecular phylogenetics and evolution, 127, 834-842.
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  Camelina sativa (false flax or gold-of-pleasure) is an Old World oilseed crop that fell out of use in the mid 20th Century but has recently gained renewed interest as a biofuel source. The crop is hexaploid, and its relationship to its diploid and polyploid congeners has remained unresolved. Using 54 accessions representing five species sampled across Camelina's center of diversity in Turkey and the Caucasus, we performed phylogenetic and genetic diversity analyses using RADseq genotyping and ITS sequencing. Flow cytometry was performed to assess relationships between genome size and phylogenetic groupings. Accessions fell into distinct, highly-supported clades that accord with named species, indicating that morphological characters can reliably distinguish members of the genus. A phylogenetically distinct lineage from Turkey may represent a currently unrecognized diploid species. In most analyses, C. sativa accessions nest within those of C. microcarpa, suggesting that the crop is descended from this wild hexaploid species. This inference is further supported by their similar genome size, and by lower genetic diversity in C. sativa, which is consistent with a domestication bottleneck. These analyses provide the first definitive phylogeny of C. sativa and its wild relatives, and they point to C. microcarpa as the crop's wild ancestor.
• Francois-Moutal, L., Jahanbakhsh, S., Nelson, A., Ray, D., Scott, D. D., Hennefarth, M. R., Moutal, A., Perez-Miller, S., Ambrose, A. J., Al-Shamari, A., Coursodon, P., Meechoovet, B., Reiman, R., Lyons, E., Beilstein, M., Chapman, E., Morris, Q. D., Van, K. K., Hughes, T. R., , Khanna, R., et al. (2018). A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B). ACS CHEMICAL BIOLOGY, 13(10), 3000-3010.
• Trujillo, J. T., Seetharam, A. S., Hufford, M. B., Beilstein, M. A., & Mosher, R. A. (2018). Evidence for a Unique DNA-Dependent RNA Polymerase in Cereal Crops. MOLECULAR BIOLOGY AND EVOLUTION, 35(10), 2454-2462.
• Nelson, A., Devisetty, U. K., Palos, K., Haug-Baltzell, A. K., Lyons, E., & Beilstein, M. A. (2017). Evolinc:A Tool for the Identification and Evolutionary Comparison of Long Intergenic Non-coding RNAs. FRONTIERS IN GENETICS, 8.
• Arora, A., Beilstein, M. A., & Shippen, D. E. (2016). Evolution of Arabidopsis protection of telomeres 1 alters nucleic acid recognition and telomerase regulation. Nucleic acids research, 44(20), 9821-9830.
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  Protection of telomeres (POT1) binds chromosome ends, recognizing single-strand telomeric DNA via two oligonucleotide/oligosaccharide binding folds (OB-folds). The Arabidopsis thaliana POT1a and POT1b paralogs are atypical: they do not exhibit telomeric DNA binding, and they have opposing roles in regulating telomerase activity. AtPOT1a stimulates repeat addition processivity of the canonical telomerase enzyme, while AtPOT1b interacts with a regulatory lncRNA that represses telomerase activity. Here, we show that OB1 of POT1a, but not POT1b, has an intrinsic affinity for telomeric DNA. DNA binding was dependent upon a highly conserved Phe residue (F65) that in human POT1 directly contacts telomeric DNA. F65A mutation of POT1aOB1 abolished DNA binding and diminished telomerase repeat addition processivity. Conversely, AtPOT1b and other POT1b homologs from Brassicaceae and its sister family, Cleomaceae, naturally bear a non-aromatic amino acid at this position. By swapping Val (V63) with Phe, AtPOT1bOB1 gained the capacity to bind telomeric DNA and to stimulate telomerase repeat addition processivity. We conclude that, in the context of DNA binding, variation at a single amino acid position promotes divergence of the AtPOT1b paralog from the ancestral POT1 protein.
• Liu, Z., Tavares, R., Forsythe, E. S., André, F., Lugan, R., Jonasson, G., Boutet-Mercey, S., Tohge, T., Beilstein, M. A., Werck-Reichhart, D., & Renault, H. (2016). Evolutionary interplay between sister cytochrome P450 genes shapes plasticity in plant metabolism. Nature communications, 7, 13026.
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  Expansion of the cytochrome P450 gene family is often proposed to have a critical role in the evolution of metabolic complexity, in particular in microorganisms, insects and plants. However, the molecular mechanisms underlying the evolution of this complexity are poorly understood. Here we describe the evolutionary history of a plant P450 retrogene, which emerged and underwent fixation in the common ancestor of Brassicales, before undergoing tandem duplication in the ancestor of Brassicaceae. Duplication leads first to gain of dual functions in one of the copies. Both sister genes are retained through subsequent speciation but eventually return to a single copy in two of three diverging lineages. In the lineage in which both copies are maintained, the ancestral functions are split between paralogs and a novel function arises in the copy under relaxed selection. Our work illustrates how retrotransposition and gene duplication can favour the emergence of novel metabolic functions.
• Nelson, A. D., Forsythe, E. S., Devisetty, U. K., Clausen, D. S., Haug-Batzell, A. K., Meldrum, A. M., Frank, M. R., Lyons, E., & Beilstein, M. A. (2016). A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants. G3 (Bethesda, Md.), 6(9), 2881-91.
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  Transcriptomic analyses from across eukaryotes indicate that most of the genome is transcribed at some point in the developmental trajectory of an organism. One class of these transcripts is termed long intergenic noncoding RNAs (lincRNAs). Recently, attention has focused on understanding the evolutionary dynamics of lincRNAs, particularly their conservation within genomes. Here, we take a comparative genomic and phylogenetic approach to uncover factors influencing lincRNA emergence and persistence in the plant family Brassicaceae, to which Arabidopsis thaliana belongs. We searched 10 genomes across the family for evidence of > 5000 lincRNA loci from A. thaliana From loci conserved in the genomes of multiple species, we built alignments and inferred phylogeny. We then used gene tree/species tree reconciliation to examine the duplication history and timing of emergence of these loci. Emergence of lincRNA loci appears to be linked to local duplication events, but, surprisingly, not whole genome duplication events (WGD), or transposable elements. Interestingly, WGD events are associated with the loss of loci for species having undergone relatively recent polyploidy. Lastly, we identify 1180 loci of the 6480 previously annotated A. thaliana lincRNAs (18%) with elevated levels of conservation. These conserved lincRNAs show higher expression, and are enriched for stress-responsiveness and cis-regulatory motifs known as conserved noncoding sequences (CNSs). These data highlight potential functional pathways and suggest that CNSs may regulate neighboring genes at both the genomic and transcriptomic level. In sum, we provide insight into processes that may influence lincRNA diversification by providing an evolutionary context for previously annotated lincRNAs.
• Trujillo, J. T., Beilstein, M. A., & Mosher, R. A. (2016). The Argonaute-binding platform of NRPE1 evolves through modulation of intrinsically disordered repeats. The New phytologist, 212(4), 1094-1105.
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  Argonaute (Ago) proteins are important effectors in RNA silencing pathways, but they must interact with other machinery to trigger silencing. Ago hooks have emerged as a conserved motif responsible for interaction with Ago proteins, but little is known about the sequence surrounding Ago hooks that must restrict or enable interaction with specific Argonautes. Here we investigated the evolutionary dynamics of an Ago-binding platform in NRPE1, the largest subunit of RNA polymerase V. We compared NRPE1 sequences from > 50 species, including dense sampling of two plant lineages. This study demonstrates that the Ago-binding platform of NRPE1 retains Ago hooks, intrinsic disorder, and repetitive character while being highly labile at the sequence level. We reveal that loss of sequence conservation is the result of relaxed selection and frequent expansions and contractions of tandem repeat arrays. These factors allow a complete restructuring of the Ago-binding platform over 50-60 million yr. This evolutionary pattern is also detected in a second Ago-binding platform, suggesting it is a general mechanism. The presence of labile repeat arrays in all analyzed NRPE1 Ago-binding platforms indicates that selection maintains repetitive character, potentially to retain the ability to rapidly restructure the Ago-binding platform.
• Beilstein, M. A., Renfrew, K. B., Song, X., Shakirov, E. V., Zanis, M. J., & Shippen, D. E. (2015). Evolution of the telomere-associated protein POT1a in Arabidopsis thaliana is characterized by positive selection to reinforce protein-protein interaction. Molecular Biology and Evolution, 32(5), 1329–1341. doi:10.1093/molbev/msv025
• Gosai, S. J., Foley, S. W., Wang, D., Silverman, I. M., Selamoglu, N., Nelson, A. D., Beilstein, M. A., Daldal, F., Deal, R. B., & Gregory, B. D. (2015). Global Analysis of the RNA-Protein Interaction and RNA Secondary Structure Landscapes of the Arabidopsis Nucleus. Molecular cell, 57(2), 376-88.
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  Posttranscriptional regulation in eukaryotes requires cis- and trans-acting features and factors including RNA secondary structure and RNA-binding proteins (RBPs). However, a comprehensive view of the structural and RBP interaction landscape of nuclear RNAs has yet to be compiled for any organism. Here, we use our ribonuclease-mediated structure and RBP-binding site mapping approaches to globally profile these features in Arabidopsis seedling nuclei in vivo. We reveal anticorrelated patterns of secondary structure and RBP binding throughout nuclear mRNAs that demarcate sites of alternative splicing and polyadenylation. We also uncover a collection of protein-bound sequence motifs, and identify their structural contexts, co-occurrences in transcripts encoding functionally related proteins, and interactions with putative RBPs. Finally, using these motifs, we find that the chloroplast RBP CP29A also interacts with nuclear mRNAs. In total, we provide a simultaneous view of the RNA secondary structure and RBP interaction landscapes in a eukaryotic nucleus.
• Huang, Y., Kendall, T., Forsythe, E. S., Dorantes-Acosta, A., Li, S., Caballero-Perez, J., Chen, C., Arteaga-Vazquez, M., Beilstein, M. A., & Mosher, R. A. (2015). Ancient origin and recent innovations of RNA Plymerase IV and V. Molecular Biology and Evolution, 32(7), 1788–1799. doi:10.1093/molbev/msv060
• Arias, T., Beilstein, M. A., Tang, M., McKain, M. R., & Pires, J. C. (2014). Diversification times among Brassica (Brassicaceae) crops suggest hybrid formation after 20 million years of divergence. American Journal of Botany, 101(1), 86-91.
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  Abstract: Premise of the study: Cruciferous vegetables, many of which are in the genus Brassica (Brassicaceae), are prized for their nutritive value and have been cultivated for thousands of years. There are numerous wild northwestern Mediterranean species in the tribe Brassiceae, and it is therefore assumed this center of diversity is also the region of origin. Within the tribe, the Nigra and Oleracea clades contain the three diploid Brassica crops, B. oleracea, B. rapa, and B. nigra. These three species hybridized in the past to form the tetraploid crop species B. juncea, B. carinata, and B. napus. Collectively, these crop Brassicas have been thought to be closely related because they can still hybridize. Methods: Using a combination of molecular phylogenetics, diversification analysis, and historical biogeography, we evaluated the relationships and origins of four nested clades: the tribe Brassiceae, the Nigra-Oleracea clade, the core Oleracea (includes B. oleracea + B. rapa and their respective wild relatives), and Brassica oleracea and relatives. Key results: We found evidence that the tribe originated around the intersection forming between the Arabian Peninsula and Saharan Africa approximately 24 million years ago (Mya). Our data also suggest that the maternal genomes of the three diploid crop Brassicas are not closely related and that the Nigra-Oleracea clade diverged 20 Mya. Finally, our analyses indicate that the core Oleracea lineage giving rise to B. oleracea + B. rapa originated ~3 Mya in the northeastern Mediterranean, from where ancestors of B. oleracea spread through Europe and B. rapa to Asia. Conclusions: These results challenge previous hypotheses about the biogeographic origins of the tribe Brassiceae and the crop Brassica species and appear to be correlated with major geological and climatic events in the Mediterranean basin. © 2014 Botanical Society of America.
• Jarvis, D. E., Ryu, C., Beilstein, M. A., & Schumaker, K. S. (2014). Distinct roles of SOS1 in the convergent evolution of salt tolerance in Eutrema salsugineum and Schrenkiella parvula. Molecular Biology and Evolution.
• Nelson, A. D., Forsythe, E. S., Gan, X., Tsiantis, M., & Beilstein, M. A. (2014). Extending the model of Arabidopsis telomere length and composition across Brassicaceae. Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology, 22(2), 153-66.
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  Telomeres are repetitive TG-rich DNA elements essential for maintaining the stability of genomes and replicative capacity of cells in almost all eukaryotes. Most of what is known about telomeres in plants comes from the angiosperm Arabidopsis thaliana, which has become an important comparative model for telomere biology. Arabidopsis tolerates numerous insults to its genome, many of which are catastrophic or lethal in other eukaryotic systems such as yeast and vertebrates. Despite the importance of Arabidopsis in establishing a model for the structure and regulation of plant telomeres, only a handful of studies have used this information to assay components of telomeres from across land plants, or even among the closest relatives of Arabidopsis in the plant family Brassicaceae. Here, we determined how well Arabidopsis represents Brassicaceae by comparing multiple aspects of telomere biology in species that represent major clades in the family tree. Specifically, we determined the telomeric repeat sequence, measured bulk telomere length, and analyzed variation in telomere length on syntenic chromosome arms. In addition, we used a phylogenetic approach to infer the evolutionary history of putative telomere-binding proteins, CTC1, STN1, TEN1 (CST), telomere repeat-binding factor like (TRFL), and single Myb histone (SMH). Our analyses revealed conservation of the telomeric DNA repeat sequence, but considerable variation in telomere length among the sampled species, even in comparisons of syntenic chromosome arms. We also found that the single-stranded and double-stranded telomeric DNA-binding complexes CST and TRFL, respectively, differ in their pattern of gene duplication and loss. The TRFL and SMH gene families have undergone numerous duplication events, and these duplicate copies are often retained in the genome. In contrast, CST components occur as single-copy genes in all sampled genomes, even in species that experienced recent whole genome duplication events. Taken together, our results place the Arabidopsis model in the context of other species in Brassicaceae, making the family the best characterized plant group in regard to telomere architecture.
• Arias, T., Beilstein, M. A., Tang, M., McKain, M., & Pires, J. C. (2014). Diversification times among Brassica (Brassicaceae) crops suggest hybrid formation after 20 million years of divergence. American Journal of Botany, 86–91.
• Yang, R., Jarvis, D. E., Chen, H., Beilstein, M. A., Grimwood, J., Jenkins, J., Shu, S., Prochnik, S., Xin, M., Ma, C., Schmutz, J., Wing, R. A., Mitchell-Olds, T., Schumaker, K. S., & Wang, X. -. (2013). The reference genome of the halophytic plant Eutrema salsugineum. Frontiers in Plant Genetics and Genomics, doi: 10.3389/fpls.2013.00046.
• Beilstein, M. A., Brinegar, A. E., & Shippen, D. E. (2012). Evolution of the Arabidopsis telomerase RNA. Frontiers in Genetics, 3(SEP).
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  Abstract: The telomerase reverse transcriptase promotes genome integrity by continually synthesizing a short telomere repeat sequence on chromosome ends. Telomerase is a ribonucleoprotein complex whose integral RNA subunitTER contains a template domain with a sequence complementary to the telomere repeat that is reiteratively copied by the catalytic subunit. Although TER harbors well-conserved secondary structure elements, its nucleotide sequence is highly divergent, even among closely related organisms. Thus, it has been extremely challenging to identify TER orthologs by bioinformatics strategies. Recently, TER was reported in the flowering plant, Arabidopsis thaliana. In contrast to other model organisms, A. thaliana encodes two TER subunits, only one of which is required to maintain telomere tracts in vivo. Here we investigate the evolution of the loci that encode TER in Arabidopsis by comparison to the same locus in its close relatives. We employ a combination of PCR and bioinformatics approaches to identify putative TER loci based on syntenic regions flanking theTERI andTER2 loci of A. thaliana. Unexpectedly, we discovered that the genomic regions encoding the two A. thalianaJEHs occur as a single locus in other Brassicaceae. Moreover, we find striking sequence divergence within the telomere template domain of putativeTERs from Brassicaceae, including some orthologous loci that completely lack a template domain. Finally, evolution of the locus is characterized by lineage-specific events rather than changes shared among closely related species. We conclude that the ArabidopsisTER duplication occurred very recently, and further that changes at this locus in other Brassicaceae indicate the process of TER evolution may be different in plants compared with vertebrates and yeast. © 2012 Beilstein, Brinegar and Shippen.
• Beilstein, M., Brinegar, A., & Shippen, D. (2012). Evolution of the Arabidopsis telomerase RNA. Frontiers in Genetics, 3, 188.
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  doi:10.3389/fgene.2012.00188
• Beilstein, M. A., Nagalingum, N. S., Clements, M. D., Manchester, S. R., & Mathews, S. (2010). Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America, 107(43), 18724-18728.
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  PMID: 20921408;PMCID: PMC2973009;Abstract: Dated molecular phylogenies are the basis for understanding species diversity and for linking changes in rates of diversification with historical events such as restructuring in developmental pathways, genome doubling, or dispersal onto a new continent. Valid fossil calibration points are essential to the accurate estimation of divergence dates, but for many groups of flowering plants fossil evidence is unavailable or limited. Arabidopsis thaliana, the primary genetic model in plant biology and the first plant to have its entire genome sequenced, belongs to one such group, the plant family Brassicaceae. Thus, the timing of A. thaliana evolution and the history of its genome have been controversial. We bring previously overlooked fossil evidence to bear on these questions and find the split between A. thaliana and Arabidopsis lyrata occurred about 13 Mya, and that the split between Arabidopsis and the Brassica complex (broccoli, cabbage, canola) occurred about 43 Mya. These estimates, which are two- to threefold older than previous estimates, indicate that gene, genomic, and developmental evolution occurred much more slowly than previously hypothesized and that Arabidopsis evolved during a period of warming rather than of cooling. We detected a 2- to 10-fold shift in species diversification rates on the branch uniting Brassicaceae with its sister families. The timing of this shift suggests a possible impact of the Cretaceous-Paleogene mass extinction on their radiation and that Brassicales codiversified with pierid butterflies that specialize on mustard-oil-producing plants.
• Hutcheon, C., Ditt, R. F., Beilstein, M., Comai, L., Schroeder, J., Goldstein, E., Shewmaker, C. K., Nguyen, T., Rocher, J. D., & Kiser, J. (2010). Polyploid genome of Camelina sativa revealed by isolation of fatty acid synthesis genes. BMC Plant Biology, 10.
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  PMID: 20977772;PMCID: PMC3017853;Abstract: Background: Camelina sativa, an oilseed crop in the Brassicaceae family, has inspired renewed interest due to its potential for biofuels applications. Little is understood of the nature of the C. sativa genome, however. A study was undertaken to characterize two genes in the fatty acid biosynthesis pathway, fatty acid desaturase (FAD) 2 and fatty acid elongase (FAE) 1, which revealed unexpected complexity in the C. sativa genome.Results: In C. sativa, Southern analysis indicates the presence of three copies of both FAD2 and FAE1 as well as LFY, a known single copy gene in other species. All three copies of both CsFAD2 and CsFAE1 are expressed in developing seeds, and sequence alignments show that previously described conserved sites are present, suggesting that all three copies of both genes could be functional. The regions downstream of CsFAD2 and upstream of CsFAE1 demonstrate co-linearity with the Arabidopsis genome. In addition, three expressed haplotypes were observed for six predicted single-copy genes in 454 sequencing analysis and results from flow cytometry indicate that the DNA content of C. sativa is approximately three-fold that of diploid Camelina relatives. Phylogenetic analyses further support a history of duplication and indicate that C. sativa and C. microcarpa might share a parental genome.Conclusions: There is compelling evidence for triplication of the C. sativa genome, including a larger chromosome number and three-fold larger measured genome size than other Camelina relatives, three isolated copies of FAD2, FAE1, and the KCS17-FAE1 intergenic region, and three expressed haplotypes observed for six predicted single-copy genes. Based on these results, we propose that C. sativa be considered an allohexaploid. The characterization of fatty acid synthesis pathway genes will allow for the future manipulation of oil composition of this emerging biofuel crop; however, targeted manipulations of oil composition and general development of C. sativa should consider and, when possible take advantage of, the implications of polyploidy. © 2010 Hutcheon et al; licensee BioMed Central Ltd.
• Mathews, S., Clements, M. D., & Beilstein, M. A. (2010). A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1539), 383-395.
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  PMID: 20047866;PMCID: PMC2838261;Abstract: Flowering plants represent the most significant branch in the tree of land plants, with respect to the number of extant species, their impact on the shaping of modern ecosystems and their economic importance. However, unlike so many persistent phylogenetic problems that have yielded to insights from DNA sequence data, the mystery surrounding the origin of angiosperms has deepened with the advent and advance of molecular systematics. Strong statistical support for competing hypotheses and recent novel trees from molecular data suggest that the accuracy of current molecular trees requires further testing. Analyses of phytochrome amino acids using a duplicate gene-rooting approach yield trees that unite cycads and angiosperms in a clade that is sister to a clade in which Gingko and Cupressophyta are successive sister taxa to gnetophytes plus Pinaceae. Application of a cycads + angiosperms backbone constraint in analyses of a morphological dataset yields better resolved trees than do analyses in which extant gymnosperms are forced to be monophyletic. The results have implications both for our assessment of uncertainty in trees from sequence data and for our use of molecular constraints as a way to integrate insights from morphological and molecular evidence. © 2010 The Royal Society.
• Price, C. M., Boltz, K. A., Chaiken, M. F., Stewart, J. A., Beilstein, M. A., & Shippen, D. E. (2010). Evolution of CST function in telomere maintenance. Cell Cycle, 9(16), 3157-3165.
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  PMID: 20697207;PMCID: PMC3041159;Abstract: Telomeres consist of an elaborate, higher-order DNA architecture, and a suite of proteins that provide protection for the chromosome terminus by blocking inappropriate recombination and nucleolytic attack. In addition, telomeres facilitate telomeric DNA replication by physical interactions with telomerase and the lagging strand replication machinery. The prevailing view has been that two distinct telomere capping complexes evolved, shelterin in vertebrates and a trimeric complex comprised of Cdc13, Stn1 and Ten1 (CST) in yeast. The recent discovery of a CST-like complex in plants and humans raises new questions about the composition of telomeres and their regulatory mechanisms in multicellular eukaryotes. In this review we discuss the evolving functions and interactions of CST components and their contributions to chromosome end protection and DNA replication. © 2010 Landes Bioscience.
• Beilstein, M. A., Al-Shehbaz, I. A., Mathews, S., & Kellogg, E. A. (2008). Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: Tribes and trichomes revisited. American Journal of Botany, 95(10), 1307-1327.
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  PMID: 21632335;Abstract: The family Brassicaceae comprises 3710 species in 338 genera, 25 recently delimited tribes, and three major lineages based on phylogenetic results from the chloroplast gene ndhF. To assess the credibility of the lineages and newly delimited tribes, we sequenced an approximately 1.8-kb region of the nuclear phytochrome A (PHYA) gene for taxa previously sampled for the chloroplast gene ndhF. Using parsimony, likelihood, and Bayesian methods, we reconstructed the phylogeny of the gene and used the approximately unbiased (AU) test to compare phylogenetic results from PHYA with findings from ndhF. We also combined ndhF and PHYA data and used a Bayesian mixed model approach to infer phylogeny. PHYA and combined analyses recovered the same three large lineages as those recovered in ndhF trees, increasing confidence in these lineages. The combined tree confirms the monophyly of most of the recently delimited tribes (only Alysseae, Anchonieae, and Descurainieae are not monophyletic), while 13 of the 23 sampled tribes are monophyletic in PHYA trees. In addition to phylogenetic results, we documented the trichome branching morphology of species across the phylogeny and explored the evolution of different trichome morphologies using the AU test. Our results indicate that dendritic, medifixed, and stellate trichomes likely evolved independently several times in the Brassicaceae.
• Al-Shehbaz, I., Beilstein, M. A., & Kellogg, E. A. (2006). Systematics and phylogeny of the Brassicaceae (Cruciferae): An overview. Plant Systematics and Evolution, 259(2-4), 89-120.
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  Abstract: A critical review of characters used in the systematics of the Brassicaceae is given, and aspects of the origin, classification, and generic delimitation of the family discussed. Molecular phylogenetic studies of the family were reviewed, and major clades identified. Based on molecular studies, especially from the ndhF chloroplast gene, and careful evaluation of morphology and generic circumscriptions, a new tribal alignment of the Brassicaceae is proposed. In all, 25 tribes are recognized, of which seven (Aethionemeae, Boechereae, Descurainieae, Eutremeae, Halimolobeae, Noccaeeae, and Smelowskieae) are described as new. For each tribe, the center(s) of distribution, morphology, and number of taxa are given. Of the 338 genera currently recognized in the Brassicaceae, about 260 genera (or about 77%) were either assigned or tentatively assigned to the 25 tribes. Some problems relating to various genera and tribes are discussed, and future research developments are briefly covered. © Springer-Verlag 2006.
• Beilstein, M. A., Al-Shehbaz, I. A., & Kellogg, E. A. (2006). Brassicaceae phylogeny and trichome evolution. American Journal of Botany, 93(4), 607-619.
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  PMID: 21646222;Abstract: To estimate the evolutionary history of the mustard family (Brassicaceae or Cruciferae), we sampled 113 species, representing 101 of the roughly 350 genera and 17 of the 19 tribes of the family, for the chloroplast gene ndhF. The included accessions increase the number of genera sampled over previous phylogenetic studies by four-fold. Using parsimony, likelihood, and Bayesian methods, we reconstructed the phylogeny of the gene and used the Shimodaira-Hasegawa test (S-H test) to compare the phylogenetic results with the most recent tribal classification for the family. The resultant phylogeny allowed a critical assessment of variations in fruit morphology and seed anatomy, upon which the current classification is based. We also used the S-H test to examine the utility of trichome branching patterns for describing monophyletic groups in the ndhF phylogeny. Our phylogenetic results indicate that 97 of 114 ingroup accessions fall into one of 21 strongly supported clades. Some of these clades can themselves be grouped into strongly to moderately supported monophyletic groups. One of these lineages is a novel grouping overlooked in previous phylogenetic studies. Results comparing 30 different scenarios of evolution by the S-H test indicate that five of 12 tribes represented by two or more genera in the study are clearly polyphyletic, although a few tribes are not sampled well enough to establish para- or polyphyly. In addition, branched trichomes likely evolved independently several times in the Brassicaceae, although malpighiaceous and stellate trichomes may each have a single origin.
• Beilstein, M., & Al-Shehbaz, I. A. (2005). Pennellia brachycarpa (Brassicaceae), a new species from Jujuy, Argentina. Novon, 15(2), 267-269.
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  Abstract: Pennellia brachycarpa (Brassicaceae), a new species from the province of Jujuy in northern Argentina, is described and illustrated. The new species is distinguished from other members of the genus by having corymbose rather than lax racemes and forked and Y-shaped instead of dendritic trichomes.
• Beilstein, M. A., & Windham, M. D. (2003). A phylogenetic analysis of western North American Draba (Brassicaceae) based on nuclear ribosomal DNA sequences from the ITS region. Systematic Botany, 28(3), 584-592.
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  Abstract: To clarify relationships among western North American members of the genus Draba, we produced a molecular phylogeny using nucleotide sequences from both internal transcribed spacers of nuclear ribosomal DNA and the 5.8S rRNA gene (collectively, ITS). Sequence data from 17 Draba taxa and two outgroups were subjected to both parsimony and maximum likelihood analyses. The phylogenetic results support previously proposed informal groupings for the sampled species. Western North American Draba are divided into two well-supported clades: 1) all taxa with a chromosome number based on x = 8, and 2) taxa whose chromosome base numbers appear to be aneuploid, deviating from x = 8. The resulting phylogenetic framework also reveals the taxonomic limitations of flower color, chromosome base number, and growth habit for predicting relationships within the genus.

Presentations

• Beilstein, M. A. (2017, January). Brassicaceae Genome Evolution. Department of Plant Sciences University of California, Davis.
• Forsythe, E. S., Beilstein, M. A., & Nelson, A. D. (2017, October). Phylogenomic analysis of Arabidopsis, Capsella, Camelina, and Boechera reveals ancient introgression. Plant Genome Evolution. Sitges, Spain: Elsevier.
• Nelson, A. D., & Beilstein, M. A. (2017, October). Comparative genomic and transcriptomic analysis of lincRNA evolution across angiosperms. Plant Genome Evolution. Sitges, Spain: Elsevier.
• Beilstein, M. A. (2016, July). Evolution of the telomerase RNA in plants. Plant Genome Stability and Change. Tokyo, Japan: EMBO.
• Beilstein, M. A. (2016, October). Evolution of the telomerase RNA in plants. Southwest Regional Meeting for the Society of Developmental Biology. Salt Lake City, UT, USA: Society of Developmental Biology.
• Beilstein, M. A., & Lyons, E. H. (2016, January). Evolution of Plant lincRNAs. Plant and Animal Genomes. San Diego, CA, USA: Scherago International.
• Beilstein, M. A. (2015, February). Evolution of the telomerase RNA in plants. University of Utah, Departmental Seminar. Salt Lake City, Utah: University of Utah, Department of Biology.
• Forsythe, E. S., Nelson, A. D., & Beilstein, M. A. (2015, March). Phylogenetic analysis of lincRNA origins and evolution in the plant family Brassicaceae. Long non-coding RNAS: from evolution to function. Keystone, CO: Keystone Symposia.
• Nelson, A. D., Forsythe, E. S., Lyons, E. H., & Beilstein, M. A. (2015, September). Identification of long non-coding RNAs using a comparative genomic approach: lessons from Brassicaceae. Plant Genome Evolution. Amsterdam, Netherlands: Current Opinion Conferences - Elsevier.
• Nelson, A. D., Forsythe, E. S., & Beilstein, M. A. (2014, Jun). The Continuing Evolution of the Telomerase RNA in the Plant Family Brassicaceae.. Plant Genome Stability and Change.
• Noble, J., Noble, J., Beilstein, M. A., Beilstein, M. A., Palanivelu, R., & Palanivelu, R. (2014, November). Is LORELEI, a Putative Glycosylphosphatidylinositol-Anchored Membrane Protein Involved in Pollen Tube Reception in Arabidopsis thaliana, Undergoing Selection?. 2014 SACNAS National Conference. Los Angeles, CA: SACNAS (Society for Advancing Hispanics, Chicanos, Native Americans in Science).
• Beilstein, M. A. (2013, May). Evolutionary history of Brassicaceae with special emphasis on the emerging biofuel Camelina sativa. Invited Seminar. Royal Botanic Garden, Sydney, Australia: Royal Botanic Garden.
• Beilstein, M. A. (2013, October). Evolution of telomerase in plants. Invited Seminar. University of Vermont, Burlington, VT: Department of Plant Science.
• Nelson, A. D., Forsythe, E. S., & Beilstein, M. A. (2013, May). Molecular Evolution of Plant Telomeres and Telomerase. Cold Spring Harbor meeting on Telomeres and Telomerase. Cold Spring Harbor Labs.
• Beilstein, M. A. (2012). Evolution of the Arabidopsis telomerase RNP. Abstract selected for oral presentation, EMBO workshop: Genetic Stability and Change. Roscoff, France.
• Beilstein, M. A. (2012). Mining for Gold-of-Pleasure (Camelina sativa) in Arizona. Agriculture Research Service, U.S. Arid Land Agricultural Research Center (Invited Seminar). Maricopa, AZ, USA.
• Beilstein, M. A. (2012). The Age of Arabidopsis: a focus on fossils. Symposium on Brassicaceae (Invited Speaker), Annual Meeting of the Botanical Society of America. Columbus, OH, USA.

Poster Presentations

• Dew-Budd, K., Harris, R. A., & Beilstein, M. A. (2018, July). Identifying the genomic factors that influence the impact of RNA-directed DNA during seed development. American Society of Plant Biologists Annual Meeting (ASPB 2018). Montreal, Canada: American Society of Plant Biologists.
• Forsythe, E. S., Nelson, A. D., & Beilstein, M. A. (2018, June). Phylogenomic analyses reveal the hidden hybridization history of Arabidopsis. International Conference on Arabisopsis Research (ICAR 2018). Turku, Finland.
• Palos, K. A., & Beilstein, M. A. (2018, June). Molecular and Phenotypic Characterization of a Conserved Long Intergenic Non-Coding RNA in Brassicaceae. International Conference on Arabidopsis Research. Turku, Finland.
• Grover, J. W., Dew-Budd, K., Beilstein, M. A., & Mosher, R. A. (2017, Sept). Deciphering the link between RNA-directed DNA Methylation and reproduction in Brassicaceae. National Science Foundation Plant Genome Research Program. Washington, DC: NSF.
• Trujillo, J. T., Beilstein, M. A., & Mosher, R. A. (2017, June). Understanding molecular variation in the RNA polymerase V Ago-binding platform. 28th International Conference on Arabidopsis Research.
• Noble, J., Beilstein, M. A., & Palanivelu, R. (2016, March). Evolutionary and Functional Analysis of LORELEI, a GPI-Anchored Membrane Protein Involved in Pollen Tube Reception in Arabidopsis thaliana. Plant Reproduction 2016. Tucson, Arizona: International Association of Sexual Plant Reproduction.
• Trujillo, J. T., Beilstein, M. A., & Mosher, R. A. (2016, June). The Argonaute-binding platform of NRPE1 Evolves through Modulation of Intrinsically Disordered Repeats. Odd Pols 2016: International Conference on Transcription by RNA Polymerases I, III, IV, and V. Ann Arbor, MI, USA.
• Nelson, A. D., Forsythe, E. S., & Beilstein, M. A. (2015, March). Evolution of Plant lncRNAs. Long non-coding RNAS: from evolution to function. Keystone, CO: Keystone Symposia.
• Forsythe, E. S., Nelson, A. D., & Beilstein, M. A. (2014, Jul). Molecular Evolution of Brassicaceae Telomerase. Annual Meeting of the American Society of Plant Biology. Portland, OR: American Society of Plant Biology.
• Noble, J., Beilstein, M. A., & Palanivelu, R. (2014, July). Is LORELEI, a Putative Glycosylphosphatidylinositol-Anchored Membrane Protein Involved in Pollen Tube Reception in Arabidopsis thaliana, Undergoing Selection?. Plant Biology 2014. Portland, OR: American Society of Plant Biologists.
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  Poster Presentation
• Palanivelu, R., Beilstein, M. A., & Noble, J. (2014, April). Is LORELEI, a Putative Glycosylphosphatidylinositol-Anchored Membrane Protein Involved in Pollen Tube Reception in Arabidopsis thaliana, Undergoing Selection?. Deep Genomics Symposium. Tucson, AZ: UA IGERT program in comparative genomics.
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  Authors: Jennifer Noble, Mark Beilstein, and Ravishankar Palanivelu