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1. Genomes of multicellular algal sisters to land plants illuminate signaling network evolution

Author

Feng, Xuehuan, Zheng, Jinfang, Irisarri, Iker, Yu, Huihui, Zheng, Bo, Ali, Zahin, de Vries, Sophie, Keller, Jean, Fürst-Jansen, Janine MR, Dadras, Armin, Zegers, Jaccoline MS, Rieseberg, Tim P, Dhabalia Ashok, Amra, Darienko, Tatyana, Bierenbroodspot, Maaike J, Gramzow, Lydia, Petroll, Romy, Haas, Fabian B, Fernandez-Pozo, Noe, Nousias, Orestis, Li, Tang, Fitzek, Elisabeth, Grayburn, W Scott, Rittmeier, Nina, Permann, Charlotte, Rümpler, Florian, Archibald, John M, Theißen, Günter, Mower, Jeffrey P, Lorenz, Maike, Buschmann, Henrik, von Schwartzenberg, Klaus, Boston, Lori, Hayes, Richard D, Daum, Chris, Barry, Kerrie, Grigoriev, Igor V, Wang, Xiyin, Li, Fay-Wei, Rensing, Stefan A, Ben Ari, Julius, Keren, Noa, Mosquna, Assaf, Holzinger, Andreas, Delaux, Pierre-Marc, Zhang, Chi, Huang, Jinling, Mutwil, Marek, de Vries, Jan, and Yin, Yanbin

Subjects
Plant Biology, Biological Sciences, Genetics, Life on Land, Signal Transduction, Embryophyta, Evolution, Molecular, Phylogeny, Gene Regulatory Networks, Genome, Genome, Plant, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.

Published
2024

2. JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom

Author

Sreedasyam, Avinash, Plott, Christopher, Hossain, Shakhawat, Lovell, John T, Grimwood, Jane, Jenkins, Jerry W, Daum, Christopher, Barry, Kerrie, Carlson, Joseph, Shu, Shengqiang, Phillips, Jeremy, Amirebrahimi, Mojgan, Zane, Matthew, Wang, Mei, Goodstein, David, Haas, Fabian B, Hiss, Manuel, Perroud, Pierre-François, Jawdy, Sara S, Yang, Yongil, Hu, Rongbin, Johnson, Jenifer, Kropat, Janette, Gallaher, Sean D, Lipzen, Anna, Shakirov, Eugene V, Weng, Xiaoyu, Torres-Jerez, Ivone, Weers, Brock, Conde, Daniel, Pappas, Marilia R, Liu, Lifeng, Muchlinski, Andrew, Jiang, Hui, Shyu, Christine, Huang, Pu, Sebastian, Jose, Laiben, Carol, Medlin, Alyssa, Carey, Sankalpi, Carrell, Alyssa A, Chen, Jin-Gui, Perales, Mariano, Swaminathan, Kankshita, Allona, Isabel, Grattapaglia, Dario, Cooper, Elizabeth A, Tholl, Dorothea, Vogel, John P, Weston, David J, Yang, Xiaohan, Brutnell, Thomas P, Kellogg, Elizabeth A, Baxter, Ivan, Udvardi, Michael, Tang, Yuhong, Mockler, Todd C, Juenger, Thomas E, Mullet, John, Rensing, Stefan A, Tuskan, Gerald A, Merchant, Sabeeha S, Stacey, Gary, and Schmutz, Jeremy

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Generic health relevance, Gene Expression Regulation, Plant, Genes, Plant, Genome, Plant, Phylogeny, Software, Transcriptome, Atlases as Topic, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

Published
2023

4. Gene-rich UV sex chromosomes harbor conserved regulators of sexual development

Author

Carey, Sarah B, Jenkins, Jerry, Lovell, John T, Maumus, Florian, Sreedasyam, Avinash, Payton, Adam C, Shu, Shengqiang, Tiley, George P, Fernandez-Pozo, Noe, Healey, Adam, Barry, Kerrie, Chen, Cindy, Wang, Mei, Lipzen, Anna, Daum, Chris, Saski, Christopher A, McBreen, Jordan C, Conrad, Roth E, Kollar, Leslie M, Olsson, Sanna, Huttunen, Sanna, Landis, Jacob B, Burleigh, J Gordon, Wickett, Norman J, Johnson, Matthew G, Rensing, Stefan A, Grimwood, Jane, Schmutz, Jeremy, and McDaniel, Stuart F

Subjects
Biological Sciences, Genetics, Biotechnology, Human Genome, 1.1 Normal biological development and functioning, Animals, DNA Transposable Elements, Evolution, Molecular, Female, Male, Mammals, Sex Chromosomes, Sexual Development
Abstract

Nonrecombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration. The correlation between suppressed recombination and degeneration is clear in animal XY systems, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions. Here, we generate nearly gapless female and male chromosome-scale reference genomes of the moss Ceratodon purpureus to test for degeneration in the bryophyte UV sex chromosomes. We show that the moss sex chromosomes evolved over 300 million years ago and expanded via two chromosomal fusions. Although the sex chromosomes exhibit weaker purifying selection than autosomes, we find that suppressed recombination alone is insufficient to drive degeneration. Instead, the U and V sex chromosomes harbor thousands of broadly expressed genes, including numerous key regulators of sexual development across land plants.

Published
2021

5. Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet

Author

Hu, Ruoyang, Li, Xuedong, Hu, Yong, Zhang, Runjie, Lv, Qiang, Zhang, Min, Sheng, Xianyong, Zhao, Feng, Chen, Zhijia, Ding, Yuhan, Yuan, Huan, Wu, Xiaofeng, Xing, Shuang, Yan, Xiaoyu, Bao, Fang, Wan, Ping, Xiao, Lihong, Wang, Xiaoqin, Xiao, Wei, Decker, Eva L., van Gessel, Nico, Renault, Hugues, Wiedemann, Gertrud, Horst, Nelly A., Haas, Fabian B., Wilhelmsson, Per K.I., Ullrich, Kristian K., Neumann, Eva, Lv, Bin, Liang, Chengzhi, Du, Huilong, Lu, Hongwei, Gao, Qiang, Cheng, Zhukuan, You, Hanli, Xin, Peiyong, Chu, Jinfang, Huang, Chien-Hsun, Liu, Yang, Dong, Shanshan, Zhang, Liangsheng, Chen, Fei, Deng, Lei, Duan, Fuzhou, Zhao, Wenji, Li, Kai, Li, Zhongfeng, Li, Xingru, Cui, Hengjian, Zhang, Yong E., Ma, Chuan, Zhu, Ruiliang, Jia, Yu, Wang, Meizhi, Hasebe, Mitsuyasu, Fu, Jinzhong, Goffinet, Bernard, Ma, Hong, Rensing, Stefan A., Reski, Ralf, and He, Yikun

Published
2023
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6. Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts

Author

Li, Fay-Wei, Nishiyama, Tomoaki, Waller, Manuel, Frangedakis, Eftychios, Keller, Jean, Li, Zheng, Fernandez-Pozo, Noe, Barker, Michael S, Bennett, Tom, Blázquez, Miguel A, Cheng, Shifeng, Cuming, Andrew C, de Vries, Jan, de Vries, Sophie, Delaux, Pierre-Marc, Diop, Issa S, Harrison, C Jill, Hauser, Duncan, Hernández-García, Jorge, Kirbis, Alexander, Meeks, John C, Monte, Isabel, Mutte, Sumanth K, Neubauer, Anna, Quandt, Dietmar, Robison, Tanner, Shimamura, Masaki, Rensing, Stefan A, Villarreal, Juan Carlos, Weijers, Dolf, Wicke, Susann, Wong, Gane K-S, Sakakibara, Keiko, and Szövényi, Péter

Subjects
Plant Biology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Anthocerotophyta, Biological Evolution, Embryophyta, Genome, Plant, Life History Traits, Crop and Pasture Production, Ecology, Plant biology
Abstract

Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.

Published
2020

7. One thousand plant transcriptomes and the phylogenomics of green plants

Author

Leebens-Mack, James H, Barker, Michael S, Carpenter, Eric J, Deyholos, Michael K, Gitzendanner, Matthew A, Graham, Sean W, Grosse, Ivo, Li, Zheng, Melkonian, Michael, Mirarab, Siavash, Porsch, Martin, Quint, Marcel, Rensing, Stefan A, Soltis, Douglas E, Soltis, Pamela S, Stevenson, Dennis W, Ullrich, Kristian K, Wickett, Norman J, DeGironimo, Lisa, Edger, Patrick P, Jordon-Thaden, Ingrid E, Joya, Steve, Liu, Tao, Melkonian, Barbara, Miles, Nicholas W, Pokorny, Lisa, Quigley, Charlotte, Thomas, Philip, Villarreal, Juan Carlos, Augustin, Megan M, Barrett, Matthew D, Baucom, Regina S, Beerling, David J, Benstein, Ruben Maximilian, Biffin, Ed, Brockington, Samuel F, Burge, Dylan O, Burris, Jason N, Burris, Kellie P, Burtet-Sarramegna, Valerie, Caicedo, Ana L, Cannon, Steven B, Cebi, Zehra, Chang, Ying, Chater, Caspar, Cheeseman, John M, Chen, Tao, Clarke, Neil D, Clayton, Harmony, Covshoff, Sarah, Crandall-Stotler, Barbara J, Cross, Hugh, dePamphilis, Claude W, Der, Joshua P, Determann, Ron, Dickson, Rowan C, Di Stilio, Veronica S, Ellis, Shona, Fast, Eva, Feja, Nicole, Field, Katie J, Filatov, Dmitry A, Finnegan, Patrick M, Floyd, Sandra K, Fogliani, Bruno, Garcia, Nicolas, Gateble, Gildas, Godden, Grant T, Goh, Falicia Qi Yun, Greiner, Stephan, Harkess, Alex, Heaney, James Mike, Helliwell, Katherine E, Heyduk, Karolina, Hibberd, Julian M, Hodel, Richard GJ, Hollingsworth, Peter M, Johnson, Marc TJ, Jost, Ricarda, Joyce, Blake, Kapralov, Maxim V, Kazamia, Elena, Kellogg, Elizabeth A, Koch, Marcus A, Von Konrat, Matt, Konyves, Kalman, Kutchan, Toni M, Lam, Vivienne, Larsson, Anders, Leitch, Andrew R, Lentz, Roswitha, Li, Fay-Wei, Lowe, Andrew J, Ludwig, Martha, Manos, Paul S, Mavrodiev, Evgeny, McCormick, Melissa K, McKain, Michael, McLellan, Tracy, and McNeal, Joel R

Subjects
Biotechnology, Genetics, Human Genome, Biological Evolution, Databases, Genetic, Evolution, Molecular, Genome, Plant, Phylogeny, Transcriptome, Viridiplantae, One Thousand Plant Transcriptomes Initiative, General Science & Technology
Abstract

Green plants (Viridiplantae) include around 450,000-500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.

Published
2019

12. Fern genomes elucidate land plant evolution and cyanobacterial symbioses.

Author

Li, Fay-Wei, Brouwer, Paul, Carretero-Paulet, Lorenzo, Cheng, Shifeng, de Vries, Jan, Delaux, Pierre-Marc, Eily, Ariana, Koppers, Nils, Kuo, Li-Yaung, Li, Zheng, Simenc, Mathew, Small, Ian, Wafula, Eric, Angarita, Stephany, Barker, Michael S, Bräutigam, Andrea, dePamphilis, Claude, Gould, Sven, Hosmani, Prashant S, Huang, Yao-Moan, Huettel, Bruno, Kato, Yoichiro, Liu, Xin, Maere, Steven, McDowell, Rose, Mueller, Lukas A, Nierop, Klaas GJ, Rensing, Stefan A, Robison, Tanner, Rothfels, Carl J, Sigel, Erin M, Song, Yue, Timilsena, Prakash R, Van de Peer, Yves, Wang, Hongli, Wilhelmsson, Per KI, Wolf, Paul G, Xu, Xun, Der, Joshua P, Schluepmann, Henriette, Wong, Gane K-S, and Pryer, Kathleen M

Subjects
Cyanobacteria, Ferns, Phylogeny, Symbiosis, Gene Duplication, Genes, Plant, Genome, Plant, Biological Evolution, Genes, Plant, Genome
Abstract

Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns-one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.

Published
2018

13. The Physcomitrella patens gene atlas project: large‐scale RNA‐seq based expression data

Author

Perroud, Pierre‐François, Haas, Fabian B, Hiss, Manuel, Ullrich, Kristian K, Alboresi, Alessandro, Amirebrahimi, Mojgan, Barry, Kerrie, Bassi, Roberto, Bonhomme, Sandrine, Chen, Haodong, Coates, Juliet C, Fujita, Tomomichi, Guyon‐Debast, Anouchka, Lang, Daniel, Lin, Junyan, Lipzen, Anna, Nogué, Fabien, Oliver, Melvin J, de León, Inés Ponce, Quatrano, Ralph S, Rameau, Catherine, Reiss, Bernd, Reski, Ralf, Ricca, Mariana, Saidi, Younousse, Sun, Ning, Szövényi, Péter, Sreedasyam, Avinash, Grimwood, Jane, Stacey, Gary, Schmutz, Jeremy, and Rensing, Stefan A

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, 1.1 Normal biological development and functioning, Bryopsida, Chromosome Mapping, Datasets as Topic, Genes, Plant, Genome, Plant, High-Throughput Nucleotide Sequencing, Transcriptome, developmental stage, differential expression, Physcomitrella patens, RNA-seq, stress, transcriptome analysis, Biochemistry and Cell Biology, Plant Biology, Plant Biology & Botany, Biochemistry and cell biology, Plant biology
Abstract

High-throughput RNA sequencing (RNA-seq) has recently become the method of choice to define and analyze transcriptomes. For the model moss Physcomitrella patens, although this method has been used to help analyze specific perturbations, no overall reference dataset has yet been established. In the framework of the Gene Atlas project, the Joint Genome Institute selected P. patens as a flagship genome, opening the way to generate the first comprehensive transcriptome dataset for this moss. The first round of sequencing described here is composed of 99 independent libraries spanning 34 different developmental stages and conditions. Upon dataset quality control and processing through read mapping, 28 509 of the 34 361 v3.3 gene models (83%) were detected to be expressed across the samples. Differentially expressed genes (DEGs) were calculated across the dataset to permit perturbation comparisons between conditions. The analysis of the three most distinct and abundant P. patens growth stages - protonema, gametophore and sporophyte - allowed us to define both general transcriptional patterns and stage-specific transcripts. As an example of variation of physico-chemical growth conditions, we detail here the impact of ammonium supplementation under standard growth conditions on the protonemal transcriptome. Finally, the cooperative nature of this project allowed us to analyze inter-laboratory variation, as 13 different laboratories around the world provided samples. We compare differences in the replication of experiments in a single laboratory and between different laboratories.

Published
2018

14. The Physcomitrella patens chromosome‐scale assembly reveals moss genome structure and evolution

Author

Lang, Daniel, Ullrich, Kristian K, Murat, Florent, Fuchs, Jörg, Jenkins, Jerry, Haas, Fabian B, Piednoel, Mathieu, Gundlach, Heidrun, Van Bel, Michiel, Meyberg, Rabea, Vives, Cristina, Morata, Jordi, Symeonidi, Aikaterini, Hiss, Manuel, Muchero, Wellington, Kamisugi, Yasuko, Saleh, Omar, Blanc, Guillaume, Decker, Eva L, van Gessel, Nico, Grimwood, Jane, Hayes, Richard D, Graham, Sean W, Gunter, Lee E, McDaniel, Stuart F, Hoernstein, Sebastian NW, Larsson, Anders, Li, Fay‐Wei, Perroud, Pierre‐François, Phillips, Jeremy, Ranjan, Priya, Rokshar, Daniel S, Rothfels, Carl J, Schneider, Lucas, Shu, Shengqiang, Stevenson, Dennis W, Thümmler, Fritz, Tillich, Michael, Aguilar, Juan C Villarreal, Widiez, Thomas, Wong, Gane Ka‐Shu, Wymore, Ann, Zhang, Yong, Zimmer, Andreas D, Quatrano, Ralph S, Mayer, Klaus FX, Goodstein, David, Casacuberta, Josep M, Vandepoele, Klaas, Reski, Ralf, Cuming, Andrew C, Tuskan, Gerald A, Maumus, Florian, Salse, Jérome, Schmutz, Jeremy, and Rensing, Stefan A

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Biological Evolution, Bryopsida, Centromere, Chromatin, Chromosomes, Plant, DNA Methylation, DNA Transposable Elements, Genetic Variation, Genome, Plant, Polymorphism, Single Nucleotide, Recombination, Genetic, Synteny, evolution, genome, chromosome, plant, moss, methylation, duplication, synteny, Physcomitrella patens, Biochemistry and Cell Biology, Plant Biology, Plant Biology & Botany, Biochemistry and cell biology, Plant biology
Abstract

The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.

Published
2018

18. Genetic Analysis of Physcomitrella patens Identifies ABSCISIC ACID NON-RESPONSIVE, a Regulator of ABA Responses Unique to Basal Land Plants and Required for Desiccation Tolerance

Author

Stevenson, Sean R, Kamisugi, Yasuko, Trinh, Chi H, Schmutz, Jeremy, Jenkins, Jerry W, Grimwood, Jane, Muchero, Wellington, Tuskan, Gerald A, Rensing, Stefan A, Lang, Daniel, Reski, Ralf, Melkonian, Michael, Rothfels, Carl J, Li, Fay-Wei, Larsson, Anders, Wong, Gane K-S, Edwards, Thomas A, and Cuming, Andrew C

Subjects
Plant Biology, Biological Sciences, Genetics, Abscisic Acid, Bryopsida, Crystallography, X-Ray, Desiccation, Droughts, Gene Expression Regulation, Plant, Mutation, Osmotic Pressure, Phylogeny, Plant Proteins, Protein Structure, Secondary, Biochemistry and Cell Biology, Plant Biology & Botany, Plant biology
Abstract

The anatomically simple plants that first colonized land must have acquired molecular and biochemical adaptations to drought stress. Abscisic acid (ABA) coordinates responses leading to desiccation tolerance in all land plants. We identified ABA nonresponsive mutants in the model bryophyte Physcomitrella patens and genotyped a segregating population to map and identify the ABA NON-RESPONSIVE (ANR) gene encoding a modular protein kinase comprising an N-terminal PAS domain, a central EDR domain, and a C-terminal MAPKKK-like domain. anr mutants fail to accumulate dehydration tolerance-associated gene products in response to drought, ABA, or osmotic stress and do not acquire ABA-dependent desiccation tolerance. The crystal structure of the PAS domain, determined to 1.7-Å resolution, shows a conserved PAS-fold that dimerizes through a weak dimerization interface. Targeted mutagenesis of a conserved tryptophan residue within the PAS domain generates plants with ABA nonresponsive growth and strongly attenuated ABA-responsive gene expression, whereas deleting this domain retains a fully ABA-responsive phenotype. ANR orthologs are found in early-diverging land plant lineages and aquatic algae but are absent from more recently diverged vascular plants. We propose that ANR genes represent an ancestral adaptation that enabled drought stress survival of the first terrestrial colonizers but were lost during land plant evolution.

Published
2016

19. Genomic imprints of unparalleled growth

Author

Murik, Omer, primary, Geffen, Or, additional, Shotland, Yoram, additional, Fernandez‐Pozo, Noe, additional, Ullrich, Kristian Karsten, additional, Walther, Dirk, additional, Rensing, Stefan Andreas, additional, and Treves, Haim, additional

Published
2023
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20. Aethionema arabicum dimorphic seed trait resetting during transition to seedlings.

Author

Arshad, Waheed, Steinbrecher, Tina, Wilhelmsson, Per K. I., Fernandez-Pozo, Noe, Pérez, Marta, Mérai, Zsuzsanna, Rensing, Stefan A., Chandler, Jake O., and Leubner-Metzger, Gerhard

Subjects
PLANT life cycles, FRUIT seeds, PHASE transitions, SEEDLINGS, SEED dispersal, ROOT growth, SEEDS, OATS
Abstract

The transition from germinating seeds to emerging seedlings is one of the most vulnerable plant life cycle stages. Heteromorphic diaspores (seed and fruit dispersal units) are an adaptive bet-hedging strategy to cope with spatiotemporally variable environments. While the roles and mechanisms of seedling traits have been studied in monomorphic species, which produce one type of diaspore, very little is known about seedlings in heteromorphic species. Using the dimorphic diaspore model Aethionema arabicum (Brassicaceae), we identified contrasting mechanisms in the germination responses to different temperatures of the mucilaginous seeds (M+ seed morphs), the dispersed indehiscent fruits (IND fruit morphs), and the bare non-mucilaginous M-seeds obtained from IND fruits by pericarp (fruit coat) removal. What follows the completion of germination is the pre-emergence seedling growth phase, which we investigated by comparative growth assays of early seedlings derived from the M+ seeds, bare M- seeds, and IND fruits. The dimorphic seedlings derived from M+ and M- seeds did not differ in their responses to ambient temperature and water potential. The phenotype of seedlings derived from IND fruits differed in that they had bent hypocotyls and their shoot and root growth was slower, but the biomechanical hypocotyl properties of 15-day-old seedlings did not differ between seedlings derived from germinated M+ seeds, M- seeds, or IND fruits. Comparison of the transcriptomes of the natural dimorphic diaspores, M+ seeds and IND fruits, identified 2,682 differentially expressed genes (DEGs) during late germination. During the subsequent 3 days of seedling preemergence growth, the number of DEGs was reduced 10-fold to 277 root DEGs and 16-fold to 164 shoot DEGs. Among the DEGs in early seedlings were hormonal regulators, in particular for auxin, ethylene, and gibberellins. Furthermore, DEGs were identified for water and ion transporters, nitrate transporter and assimilation enzymes, and cell wall remodeling protein genes encoding enzymes targeting xyloglucan and pectin. We conclude that the transcriptomes of seedlings derived from the dimorphic diaspores, M+ seeds and IND fruits, undergo transcriptional resetting during the post-germination preemergence growth transition phase from germinated diaspores to growing seedlings. [ABSTRACT FROM AUTHOR]

Published
2024
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21. Genomic imprints of unparalleled growth.

Author

Murik, Omer, Geffen, Or, Shotland, Yoram, Fernandez‐Pozo, Noe, Ullrich, Kristian Karsten, Walther, Dirk, Rensing, Stefan Andreas, and Treves, Haim

Subjects
GENOMIC imprinting, CRUST vegetation, SYNTHETIC biology, DESERT soils, BIOTECHNOLOGY, CHLORELLA, GREEN algae
Abstract

Summary: Chlorella ohadii was isolated from desert biological soil crusts, one of the harshest habitats on Earth, and is emerging as an exciting new green model for studying growth, photosynthesis and metabolism under a wide range of conditions.Here, we compared the genome of C. ohadii, the fastest growing alga on record, to that of other green algae, to reveal the genomic imprints empowering its unparalleled growth rate and resistance to various stressors, including extreme illumination. This included the genome of its close relative, but slower growing and photodamage sensitive, C. sorokiniana UTEX 1663.A larger number of ribosome‐encoding genes, high intron abundance, increased codon bias and unique genes potentially involved in metabolic flexibility and resistance to photodamage are all consistent with the faster growth of C. ohadii. Some of these characteristics highlight general trends in Chlorophyta and Chlorella spp. evolution, and others open new broad avenues for mechanistic exploration of their relationship with growth.This work entails a unique case study for the genomic adaptations and costs of exceptionally fast growth and sheds light on the genomic signatures of fast growth in photosynthetic cells. It also provides an important resource for future studies leveraging the unique properties of C. ohadii for photosynthesis and stress response research alongside their utilization for synthetic biology and biotechnology aims. [ABSTRACT FROM AUTHOR]

Published
2024
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24. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

Author

Curtis, Bruce A., Tanifuji, Goro, Burki, Fabien, Gruber, Ansgar, Irimia, Manuuel, Maruyama, Shinichiro, Arias, Maria C., Ball, Steven G., Gile, Gillian H., Hirakawa, Yoshihisa, Hopkins, Julia F., Kuo, Alan, Rensing, Stefan A., Schmutz, Jeremy, Symeonidi, Aikaterini, Elias, Marek, Eveleigh, Robert J. M., Herman, Emily K., Klute, Mary J., Nakayama, Takuro, Obornik, Miroslav, Reyes-Prieto, Adrian, Armbrust, E. Virginia, Aves, Stephen J., Beiko, Robert G., Coutinho, Pedro, Dacks, Joel B., Durnford, Dion G., Fast, Naomi M., Green, Beverley R., Grisdale, Cameron J., Hempel, Franziska, Henrissat, Bernard, Hoppner, Marc P., Ishida, Ken-Ichiro, Kim, Eunsoo, Koreny, Ludek, Kroth, Peter G., Liu, Yuan, Malik, Shehre-Banoo, Maier, Uwe G., McRose, Darcy, Mock, Thomas, Neilson, Jonathan A. D., Onodera, Naoko T., Poole, Anthony M., Pritham, Ellen J., Richards, Thomas A., Rocap, Gabrielle, Roy, Scott W., Sarai, Chihiro, Schaack, Sarah, Shirato, Shu, Slamovits, Claudio H., Spencer, Davie F., Suzuki, Shigekatsu, Worden, Alexandra Z., Zauner, Stefan, Barry, Kerrie, Bell, Callum, Bharti, Arvind K., Crow, John A., Grimwood, Jane, Kramer, Robin, Lindquist, Erika, Lucas, Susan, Salamov, Asaf, McFadden, Geoffrey I., Lane, Christopher E., Keeling, Patrick J., Gray, Michael W., Grigoriev, Igor V., and Archibald, John M.

Subjects
comparative genomics
Abstract

Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have 21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.

Published
2012

27. Developmental Control and Plasticity of Fruit and Seed Dimorphism in Aethionema arabicum

Author

Lenser, Teresa, Graeber, Kai, Cevik, Özge Selin, Adigüzel, Nezaket, Dönmez, Ali A., Grosche, Christopher, Kettermann, Marcel, Mayland-Quellhorst, Sara, Mérai, Zsuzsanna, Mohammadin, Setareh, Nguyen, Thu-Phuong, Rümpler, Florian, Schulze, Christina, Sperber, Katja, Steinbrecher, Tina, Wiegand, Nils, Strnad, Miroslav, Scheid, Ortrun Mittelsten, Rensing, Stefan A., Schranz, Michael Eric, Theißen, Günter, Mummenhoff, Klaus, and Leubner-Metzger, Gerhard

Published
2016

28. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants

Author

Rensing, Stefan A., Lang, Daniel, Zimmer, Andreas D., Terry, Astrid, Salamov, Asaf, Shapiro, Harris, Nishiyama, Tomaoki, Perroud, Pierre-Francois, Lindquist, Erika A., Kamisugi, Yasuko, Tanahashi, Takako, Sakakibara, Keiko, Fujita, Tomomichi, Oishi, Kazuko, Shin, Tadasu, Kuroki, Yoko, Toyoda, Atsushi, Suzuki, Yutaka, Hashimoto, Shin-ichi, Yamaguchi, Kazuo, Sugano, Sumio, Kohara, Yuji, Fujiyama, Asao, Anterola, Aldwin, Aoki, Setsuyuki, Ashton, Neil, Barbazuk, W. Brad, Barker, Elizabeth, Bennetzen, Jeffrey L., Blankenship, Robert, Cho, Sung Hyun, Dutcher, Susan K., Estelle, Mark, Fawcett, Jeffrey A., Gundlach, Heidrum, Hanada, Kousuke, Melkozernov, Alexander, Murata, Takashi, Nelson, David R., Pils, Birgit, Prigge, Michael, Reiss, Bernd, Renner, Tanya, Rombauts, Stephane, Rushton, Paul J., Sanderfoot, Anton, Schween, Gabriele, Shiu, Shin-Han, Stueber, Kurt, Theodoulou, Frederica L., Tu, Hank, Peer, Yves Van de, Verrier, Paul J., Waters, Elizabeth, Wood, Andrew, Yang, Lixing, Cove, David, Cuming, Andrew C., Hasebe, Mitsayasu, Lucas, Susan, Mishler, Brent D., Reski, Ralf, Grigoriev, Igor V., Quatrano, Rakph S., and Boore, Jeffrey L.

Abstract

We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.

Published
2007

36. Forschungsinformationsmanagement

Author

Adam, Sascha, Bode, Frank, Christ, Claudia, Hanke, Vanessa, Marchetti, Christian, Marschall, Nicolas, Möller, Jan-Christian, Nagel, Michael, Preuß, Stefanie, Quester-Brüning, Beate, Rensing, Stefan, Rieger, Klaus-Peter, Suchodoletz, Dirk von, Tobias, Regine, Vogt, Sebastian, Wallenstein, Sebastian, and Weinreich, Sigrud

Abstract

Die Bedeutung von Forschungsberichterstattung für Universitäten nimmt kontinuierlich zu. So müssen Universitäten Berichtspflichten gegenüber Geldgebern und Ministerien erfüllen, Informationen zur internen Entscheidungsfindung und Steuerung bereithalten sowie Rechenschaft über ihre Geldgeber gegenüber der Öffentlichkeit ablegen. Forschungsberichterstattung ist somit von hoher strategischer Bedeutung für die Steuerungs- und Wettbewerbsfähigkeit der Universitäten sowie für die Sichtbarkeit und Transparenz ihrer Forschungsleistungen nach außen. Gleichzeitig stellen die steigenden Anforderungen an die Forschungsberichterstattung die Universitäten in Baden-Württemberg vor schwierige Aufgaben, da die benötigten Daten zu Forschungsaktivitäten oft nur verteilt und in uneinheitlicher Form in den Institutionen vorliegen. Dies führt zu einem hohen administrativen Aufwand in der Forschungsberichterstattung. Aus diesem Grund empfiehlt auch der Wissenschaftsrat den Hochschulen, ihre Forschungsberichterstattung zu professionalisieren. Dieses Papier des Think Tank Forschungsinformationsmanagement schlägt daher vor, dass sich die baden-württembergischen Universitäten zu einem Verbund zum Thema Forschungsinformationssysteme („BW.CRIS“) zusammenschließen. Ziel des Verbundes ist, Kompetenzen in diesem Bereich zu bündeln, gemeinsame Lösungen für gemeinsame Herausforderungen zu erarbeiten und im gegenseitigen Austausch von den Erfahrungen der anderen Universitäten zu lernen. Im Verbund erhalten die Landesuniversitäten zudem eine starke Stimme und können so die Landesinteressen gegenüber Softwareanbietern, der KFiD oder weiteren Akteuren auf Bundesebene erfolgreich vertreten. Ein zentraler Erfolgsfaktor für den Anschub und die nachhaltige Arbeit eines solchen Verbundes wäre seine gezielte Unterstützung auf Landesebene. Eine solche baden-württembergische Landesinitiative zum Thema Forschungsinformationssysteme würde die baden-württembergischen Universitäten in der Digitalisierung ihrer Forschungsberichterstattung erheblich voranbringen und so die strategische Steuerungsfähigkeit der Hochschulleitungen maßgeblich erhöhen.

Published
2022
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37. Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis

Author

Tisserant, Emilie, Malbreil, Mathilde, Kuo, Alan, Kohler, Annegret, Symeonidi, Aikaterini, Balestrini, Raffaella, Charron, Philippe, Duensing, Nina, Frey, Nicolas Frei dit, Gianinazzi-Pearson, Vivienne, Gilbert, Luz B., Handa, Yoshihiro, Herr, Joshua R., Hijri, Mohamed, Koul, Raman, Kawaguchi, Masayoshi, Krajinski, Franziska, Lammers, Peter J., Masclaux, Frederic G., Murat, Claude, Morin, Emmanuelle, Ndikumana, Steve, Pagni, Marco, Petitpierre, Denis, Requena, Natalia, Rosikiewicz, Pawel, Riley, Rohan, Saito, Katsuharu, Clemente, Hélène San, Shapiro, Harris, van Tuinen, Diederik, Bécard, Guillaume, Bonfante, Paola, Paszkowski, Uta, Shachar-Hill, Yair Y., Tuskan, Gerald A., Young, Peter W., Sanders, Ian R., Henrissat, Bernard, Rensing, Stefan A., Grigoriev, Igor V., Corradi, Nicolas, Roux, Christophe, and Martin, Francis

Published
2013

38. Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida

Author

Collén, Jonas, Porcel, Betina, Carré, Wilfrid, Ball, Steven G., Chaparro, Cristian, Tonon, Thierry, Barbeyron, Tristan, Michel, Gurvan, Noel, Benjamin, Valentin, Klaus, Elias, Marek, Artiguenave, François, Arun, Alok, Aury, Jean-Marc, Barbosa-Neto, José F., Bothwell, John H., Bouget, François-Yves, Brillet, Loraine, Cabello-Hurtado, Francisco, Capella-Gutiérrez, Salvador, Charrier, Bénédicte, Cladière, Lionel, Cock, J. Mark, Coelho, Susana M., Colleoni, Christophe, Czjzek, Mirjam, Da Silva, Corinne, Delage, Ludovic, Denoeud, France, Deschamps, Philippe, Dittami, Simon M., Gabaldón, Toni, Gachon, Claire M. M., Groisillier, Agnès, Hervé, Cécile, Jabbari, Kamel, Katinka, Michael, Kloareg, Bernard, Kowalczyk, Nathalie, Labadie, Karine, Leblanc, Catherine, Lopez, Pascal J., McLachlan, Deirdre H., Meslet-Cladiere, Laurence, Moustafa, Ahmed, Nehr, Zofia, Collén, Pi Nyvall, Panaud, Olivier, Partensky, Frédéric, Poulain, Julie, Rensing, Stefan A., Rousvoal, Sylvie, Samson, Gaelle, Symeonidi, Aikaterini, Weissenbach, Jean, Zambounis, Antonios, Wincker, Patrick, and Boyen, Catherine

Published
2013

39. Additional file 6 of Comparative transcriptomics identifies candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae)

Author

Gramzow, Lydia, Klupsch, Katharina, Fernández-Pozo, Noé, Hölzer, Martin, Marz, Manja, Rensing, Stefan A., and Theißen, Günter

Abstract

Additional file 6: Supplementary Table 1. Genes that were excluded from the ortholog transcriptome and which are annotated as “DNA-binding transcription factor activity” (GO:0003700).

Published
2022
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42. Additional file 1 of Comparative transcriptomics identifies candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae)

Author

Gramzow, Lydia, Klupsch, Katharina, Fernández-Pozo, Noé, Hölzer, Martin, Marz, Manja, Rensing, Stefan A., and Theißen, Günter

Subjects
education, natural sciences, behavioral disciplines and activities
Abstract

Additional file 1: Supplementary Data 1. Perl script for the detection of chimeric transcripts in the trinity assembly of the Lepidium transcriptomes.

Published
2022
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44. Additional file 1 of Delayed differentiation of epidermal cells walls can underlie pedomorphosis in plants: the case of pedomorphic petals in the hummingbird-pollinated Caiophora hibiscifolia (Loasaceae, subfam. Loasoideae) species

Author

Strelin, Marina M., Zattara, Eduardo E., Ullrich, Kristian, Schallenberg-R��dinger, Mareike, and Rensing, Stefan

Abstract

Additional file 1. Phylogeny of Loasoideae including reconstructions of the ancestral pollinator and the ancestral flower morphology.

Published
2022
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49. The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants

Author

Banks, Jo Ann, Nishiyama, Tomoaki, Hasebe, Mitsuyasu, Bowman, John L., Gribskov, Michael, dePamphilis, Claude, Albert, Victor A., Aono, Naoki, Aoyama, Tsuyoshi, Ambrose, Barbara A., Ashton, Neil W., Axtell, Michael J., Barker, Elizabeth, Barker, Michael S., Bennetzen, Jeffrey L., Bonawitz, Nicholas D., Chapple, Clint, Cheng, Chaoyang, Correa, Luiz Gustavo Guedes, Dacre, Michael, DeBarry, Jeremy, Dreyer, Ingo, Elias, Marek, Engstrom, Eric M., Estelle, Mark, Feng, Liang, Finet, Cédric, Floyd, Sandra K., Frommer, Wolf B., Fujita, Tomomichi, Gramzow, Lydia, Gutensohn, Michael, Harholt, Jesper, Hattori, Mitsuru, Heyl, Alexander, Hirai, Tadayoshi, Hiwatashi, Yuji, Ishikawa, Masaki, Iwata, Mineko, Karol, Kenneth G., Koehler, Barbara, Kolukisaoglu, Uener, Kubo, Minoru, Kurata, Tetsuya, Lalonde, Sylvie, Li, Kejie, Li, Ying, Litt, Amy, Lyons, Eric, Manning, Gerard, Maruyama, Takeshi, Michael, Todd P., Mikami, Koji, Miyazaki, Saori, Morinaga, Shin-ichi, Murata, Takashi, Mueller-Roeber, Bernd, Nelson, David R., Obara, Mari, Oguri, Yasuko, Olmstead, Richard G., Onodera, Naoko, Petersen, Bent Larsen, Pils, Birgit, Prigge, Michael, Rensing, Stefan A., Riaño-Pachón, Diego Mauricio, Roberts, Alison W., Sato, Yoshikatsu, Scheller, Henrik Vibe, Schulz, Burkhard, Schulz, Christian, Shakirov, Eugene V., Shibagaki, Nakako, Shinohara, Naoki, Shippen, Dorothy E., Sørensen, Iben, Sotooka, Ryo, Sugimoto, Nagisa, Sugita, Mamoru, Sumikawa, Naomi, Tanurdzic, Milos, Theißen, Günter, Ulvskov, Peter, Wakazuki, Sachiko, Weng, Jing-Ke, Willats, William W.G.T., Wipf, Daniel, Wolf, Paul G., Yang, Lixing, Zimmer, Andreas D., Zhu, Qihui, Mitros, Therese, Hellsten, Uffe, Loqué, Dominique, Otillar, Robert, Salamov, Asaf, Schmutz, Jeremy, Shapiro, Harris, Lindquist, Erika, Lucas, Susan, Rokhsar, Daniel, and Grigoriev, Igor V.

Published
2011
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50. Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri

Author

Prochnik, Simon E., Umen, James, Nedelcu, Aurora M., Hallmann, Armin, Miller, Stephen M., Nishii, Ichiro, Ferris, Patrick, Kuo, Alan, Mitros, Therese, Fritz-Laylin, Lillian K., Hellsten, Uffe, Chapman, Jarrod, Simakov, Oleg, Rensing, Stefan A., Terry, Astrid, Pangilinan, Jasmyn, Kapitonov, Vladimir, Jurka, Jerzy, Salamov, Asaf, Shapiro, Harris, Schmutz, Jeremy, Grimwood, Jane, Lindquist, Erika, Lucas, Susan, Grigoriev, Igor V., Schmitt, Rüdiger, Kirk, David, and Rokhsar, Daniel S.

Published
2010

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