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Population Genomics and Phylogeography of a Clonal Bryophyte With Spatially Separated Sexes and Extreme Sex RatiosAlonso-García, MartaCarlos, Villarreal A., JuanMcFarland, KennethGoffinet, Bernard2020DOI: info:10.3389/fpls.2020.00495Frontiers in Plant Sciencev. 111664-462X
Alonso-García, Marta, Carlos, Villarreal A., Juan, McFarland, Kenneth, and Goffinet, Bernard. 2020. "Population Genomics and Phylogeography of a Clonal Bryophyte With Spatially Separated Sexes and Extreme Sex Ratios." Frontiers in Plant Science 11:
ID: 156581
Type: article
Authors: Alonso-García, Marta; Carlos, Villarreal A., Juan; McFarland, Kenneth; Goffinet, Bernard
Keywords: STRI
Abstract: The southern Appalachian (SA) is one of the most biodiversity-rich areas in North America and has been considered a refugium for many disjunct plant species, from the last glacial period to the present. Our study focuses on the SA clonal hornwort, Nothoceros aenigmaticus J. C. Villarreal & K. D. McFarland. This hornwort was described from North Carolina and is widespread in the SA, growing on rocks near or submerged in streams in six and one watersheds of the Tennessee (TR) and Alabama (AR) Rivers, respectively. Males and female populations occur in different watersheds, except in the Little Tennessee (TN) River where an isolated male population exists ca. 48 km upstream from the female populations. The sex ratio of 1:0 seems extreme in each population. In this study, we use nuclear and organellar microsatellites from 250 individuals from six watersheds (seven populations) in the SA region and two populations from Mexico (23 individuals). We, then, selected 86 individuals from seven populations and used genotyping by sequencing to sample over 600 bi-allelic markers. Our results suggest that the SA N. aenigmaticus and Mexican plants are a nested within a clade of sexual tropical populations. In the US populations, we confirm an extreme sex ratio and only contiguous US watersheds share genotypes. The phylogenetic analysis of SNP data resolves four clusters: Mexican populations, male plants (Little Pigeon and Pigeon river watersheds) and two clusters of female plants; one from the Little Tennessee and Hiwassee Rivers (TR) and the other from the Ocoee (TR) and Coosa (AR) Rivers. All clusters are highly differentiated (Fst values over 0.9). In addition, our individual assignment analyses and PCAs reflect the phylogenetic results grouping the SA samples in three clades and recovering males and female plants with high genetic differentiation (Fst values between 0.5 and 0.9 using microsatellites and bi-allelic markers). Our results point to Pleistocene events shaping the biogeographical pattern seen in US populations. The extreme sex ratio reflects isolation and highlights the high vulnerability of the populations in the SA.
Anthoceros genomes illuminate the origin of land plants and the unique biology of hornwortsLi, Fay-WeiNishiyama, TomoakiWaller, ManuelFrangedakis, EftychiosKeller, JeanLi, ZhengFernandez-Pozo, NoeBarker, Michael S.Bennett, TomBlázquez, Miguel A.Cheng, ShifengCuming, Andrew Vries, Jande Vries, SophieDelaux, Pierre-MarcDiop, Issa S.Harrison, C. J.Hauser, DuncanHernández-García, JorgeKirbis, AlexanderMeeks, John C.Monte, IsabelMutte, Sumanth K.Neubauer, AnnaQuandt, DietmarRobison, TannerShimamura, MasakiRensing, Stefan A.Villarreal, Juan CarlosWeijers, DolfWicke, SusannWong, Gane K. -SSakakibara, KeikoSzövényi, Péter2020DOI: info:10.1038/s41477-020-0618-2Nature Plantsv. 6No. 3259272259–2722055-0278
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. J., Hauser, Duncan, Hernández-García, Jorge, Kirbis, Alexander, Meeks, John C., Monte, Isabel, Mutte, Sumanth K., Neubauer, Anna, Quandt, Dietmar et al. 2020. "Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts." Nature Plants 6 (3):259–272.
ID: 155709
Type: article
Authors: 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. J.; 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; Szövényi, Péter
Keywords: STRI
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.
Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolutionBell, DavidLin, QianshiGerelle, Wesley K.Joya, SteveChang, YingTaylor, Z. N.Rothfels, Carl J.Larsson, AndersVillarreal, Juan CarlosLi, Fay-WeiPokorny, LisaSzövényi, PéterCrandall-Stotler, BarbaraDeGironimo, LisaFloyd, Sandra K.Beerling, David J.Deyholos, Michael K.Von Konrat, MattEllis, ShonaShaw, A. J.Chen, TaoWong, Gane K. -SStevenson, Dennis W.Palmer, Jeffrey D.Graham, Sean W.2019DOI: info:10.1002/ajb2.1397American Journal of Botanyv. 107No. 11251–251537-2197
Bell, David, Lin, Qianshi, Gerelle, Wesley K., Joya, Steve, Chang, Ying, Taylor, Z. N., Rothfels, Carl J., Larsson, Anders, Villarreal, Juan Carlos, Li, Fay-Wei, Pokorny, Lisa, Szövényi, Péter, Crandall-Stotler, Barbara, DeGironimo, Lisa, Floyd, Sandra K., Beerling, David J., Deyholos, Michael K., Von Konrat, Matt, Ellis, Shona, Shaw, A. J., Chen, Tao, Wong, Gane K. -S, Stevenson, Dennis W., Palmer, Jeffrey D., and Graham, Sean W. 2019. "Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution." American Journal of Botany 107 (1):1–25.
ID: 153847
Type: article
Authors: Bell, David; Lin, Qianshi; Gerelle, Wesley K.; Joya, Steve; Chang, Ying; Taylor, Z. N.; Rothfels, Carl J.; Larsson, Anders; Villarreal, Juan Carlos; Li, Fay-Wei; Pokorny, Lisa; Szövényi, Péter; Crandall-Stotler, Barbara; DeGironimo, Lisa; Floyd, Sandra K.; Beerling, David J.; Deyholos, Michael K.; Von Konrat, Matt; Ellis, Shona; Shaw, A. J.; Chen, Tao; Wong, Gane K. -S; Stevenson, Dennis W.; Palmer, Jeffrey D.; Graham, Sean W.
Keywords: STRI
Abstract: PREMISE: Phylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene sets, and investigated bryophyte plastome evolution. METHODS: We employed diverse likelihood-based analyses to infer large-scale bryophyte phylogeny for mitochondrial and plastid data sets. We tested for changes in purifying selection in plastid genes of a mycoheterotrophic liverwort (Aneura mirabilis) and a putatively mycoheterotrophic moss (Buxbaumia), and compared 15 bryophyte plastomes for major structural rearrangements. RESULTS: Overall land-plant relationships conflict across analyses, generally weakly. However, an underlying (unrooted) four-taxon tree is consistent across most analyses and published studies. Despite gene coverage patchiness, relationships within mosses, liverworts, and hornworts are largely congruent with previous studies, with plastid results generally better supported. Exclusion of RNA edit sites restores cases of unexpected non-monophyly to monophyly for Takakia and two hornwort genera. Relaxed purifying selection affects multiple plastid genes in mycoheterotrophic Aneura but not Buxbaumia. Plastid genome structure is nearly invariant across bryophytes, but the tufA locus, presumed lost in embryophytes, is unexpectedly retained in several mosses. CONCLUSIONS: A common unrooted tree underlies embryophyte phylogeny, (liverworts, mosses), (hornworts, vascular plants)]; rooting inconsistency across studies likely reflects substantial distance to algal outgroups. Analyses combining genomic and transcriptomic data may be misled locally for heavily RNA-edited taxa. The Buxbaumia plastome lacks hallmarks of relaxed selection found in mycoheterotrophic Aneura. Autotrophic bryophyte plastomes, including Buxbaumia, hardly vary in overall structure.
Chemical Profiling of Volatile Components of the Gametophyte and Sporophyte Stages of the Hornwort Leiosporoceros dussii (Leiosporocerotaceae) From Panama by HS-SPME-GC-MSGarrido, AnetteGudiño Ledezma, JoséDurant-Archibold, ArmandoSalazar Allen, NorisJuan, Villarreal A.Gupta, Mahabir P.2019DOI: info:10.1177/1934578X19868875Natural Product Communicationsv. 14No. 8141–41934-578X
Garrido, Anette, Gudiño Ledezma, José, Durant-Archibold, Armando, Salazar Allen, Noris, Juan, Villarreal A., and Gupta, Mahabir P. 2019. "Chemical Profiling of Volatile Components of the Gametophyte and Sporophyte Stages of the Hornwort Leiosporoceros dussii (Leiosporocerotaceae) From Panama by HS-SPME-GC-MS." Natural Product Communications 14 (8):1–4.
ID: 152053
Type: article
Authors: Garrido, Anette; Gudiño Ledezma, José; Durant-Archibold, Armando; Salazar Allen, Noris; Juan, Villarreal A.; Gupta, Mahabir P.
Keywords: STRI
Abstract: We report for the first time the chemical profiling of volatile organic compounds (VOCs) of gametophyte and sporophyte life stages of Leiosporoceros dussii, from Panama by using headspace-solid phase microextraction-gas chromatography-mass spectrometry in order to assess distinguishing chemical markers between the male and female gametophytes, and sporophytes of this hornwort. A total of 27 VOCs were identified in L. dussii. Furthermore, the gametophyte and sporophyte showed clear differences in the type and amount of VOCs. The main constituents of L. dussii female thalli were menthacamphor (17.8%), hexanol (12.3%), and menthyl acetate (12.3%), while the major compounds of the male thalli were hexanol (25.3%), β-ionone (21.1%), benzeneacetaldehyde (17.6%), and β-cyclocitral (14.0%). The main VOCs of the sporophytes were hexanal (19.3%), β-cyclocitral (17.6%), 2-nonenal (15.8%), hexanol (12.5%), and β-ionone (10.2%). Unique compounds found in the female thalli were 3-pentanone, 3-octenol, nonanol, estragole, and menthyl acetate, and in the male thalli were methyl heptenone, nonanal, neoisomenthol, and bornyl acetate. Isomenthol, thymol, isomenthol acetate, and β-methylnaphthalene were only found in the sporophyte. The characteristic VOCs identified in L. dussii suggest a difference between the chemical constituents of L. dussii and other hornworts species. The presence of simple VOCs when compared with compounds previously characterized in another hornwort genera may support the distinct genetic nature of this species.
One thousand plant transcriptomes and the phylogenomics of green plantsLeebens-Mack, James H.Barker, Michael S.Carpenter, Eric J.Deyholos, Michael K.Gitzendanner, Matthew A.Graham, Sean W.Grosse, IvoLi, ZhengMelkonian, MichaelMirarab, SiavashPorsch, MartinQuint, MarcelRensing, Stefan A.Soltis, Douglas E.Soltis, Pamela S.Stevenson, Dennis W.Ullrich, Kristian K.Wickett, Norman J.DeGironimo, LisaEdger, Patrick P.Jordon-Thaden, Ingrid E.Joya, SteveLiu, TaoMelkonian, BarbaraMiles, Nicholas W.Pokorny, LisaQuigley, CharlotteThomas, PhilipVillarreal, Juan CarlosAugustin, Megan M.Barrett, Matthew D.Baucom, Regina S.Beerling, David J.Benstein, Ruben MaximilianBiffin, EdBrockington, Samuel F.Burge, Dylan O.Burris, Jason N.Burris, Kellie P.Burtet-Sarramegna, ValerieCaicedo, Ana L.Cannon, Steven B.Cebi, ZehraChang, YingChater, CasparCheeseman, John M.Chen, TaoClarke, Neil D.Clayton, HarmonyCovshoff, SarahCrandall-Stotler, Barbara J.Cross, HughdePamphilis, Claude W.Der, Joshua P.Determann, RonDickson, Rowan C.Di Stilio, Veronica S.Ellis, ShonaFast, EvaFeja, NicoleField, Katie J.Filatov, Dmitry A.Finnegan, Patrick M.Floyd, Sandra K.Fogliani, BrunoGarcia, NicolasGateble, GildasGodden, Grant T.Goh, Falicia (Qi Yun)Greiner, StephanHarkess, AlexHeaney, James MikeHelliwell, Katherine E.Heyduk, KarolinaHibberd, Julian M.Hodel, Richard G. J.Hollingsworth, Peter M.Johnson, Marc T. J.Jost, RicardaJoyce, BlakeKapralov, Maxim V.Kazamia, ElenaKellogg, Elizabeth A.Koch, Marcus A.Von Konrat, MattKonyves, KalmanKutchan, Toni M.Lam, VivienneLarsson, AndersLeitch, Andrew R.Lentz, RoswithaLi, Fay-WeiLowe, Andrew J.Ludwig, MarthaManos, Paul S.Mavrodiev, EvgenyMcCormick, Melissa K.McKain, MichaelMcLellan, TracyMcNeal, Joel R.Miller, Richard E.Nelson, Matthew N.Peng, YanhuiRalph, PaulaReal, DanielRiggins, Chance W.Ruhsam, MarkusSage, Rowan F.Sakai, Ann K.Scascitella, MoiraSchilling, Edward E.Schlosser, Eva-MarieSederoff, HeikeServick, SteinSessa, Emily B.Shaw, A. JonathanShaw, Shane W.Sigel, Erin M.Skema, CynthiaSmith, Alison G.Smithson, AnnStewart, C. Neal, Jr.Stinchcombe, John R.Szovenyi, PeterTate, Jennifer A.Tiebel, HelgaTrapnell, DorsetVillegente, MatthieuWang, Chun-NengWeller, Stephen G.Wenzel, MichaelWeststrand, StinaWestwood, James H.Whigham, Dennis F.Wu, ShuangxiuWulff, Adrien S.Yang, YuZhu, DanZhuang, CuiliZuidof, JenniferChase, Mark W.Pires, J. ChrisRothfels, Carl J.Yu, JunChen, CuiChen, LiCheng, ShifengLi, JuanjuanLi, RanLi, XiaLu, HaorongOu, YanxiangSun, XiaoTan, XuemeiTang, JingboTian, ZhijianWang, FengWang, JunWei, XiaofengXu, XunYan, ZhixiangYang, FanZhong, XiaoniZhou, FeiyuZhu, YingZhang, YongAyyampalayam, SaravanarajBarkman, Todd J.Nam-Phuong NguyenMatasci, NaimNelson, David R.Sayyari, ErfanWafula, Eric K.Walls, Ramona L.Warnow, TandyAn, HongArrigo, NilsBaniaga, Anthony E.Galuska, SallyJorgensen, Stacy A.Kidder, Thomas I.Kong, HanghuiLu-Irving, PatriciaMarx, Hannah E.Qi, XinshuaiReardon, Chris R.Sutherland, Brittany L.Tiley, George P.Welles, Shana R.Yu, RongpeiZhan, ShingGramzow, LydiaTheissen, GunterWong, Gane Ka-ShuOne Thousand Plant Transcriptomes2019DOI: info:10.1038/s41586-019-1693-2Naturev. 574No. 7780679+679–+0028-0836
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. et al. 2019. "One thousand plant transcriptomes and the phylogenomics of green plants." Nature 574 (7780):679–+.
ID: 153118
Type: article
Authors: 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 G. J.; Hollingsworth, Peter M.; Johnson, Marc T. J.; 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; McNeal, Joel R.; Miller, Richard E.; Nelson, Matthew N.; Peng, Yanhui; Ralph, Paula; Real, Daniel; Riggins, Chance W.; Ruhsam, Markus; Sage, Rowan F.; Sakai, Ann K.; Scascitella, Moira; Schilling, Edward E.; Schlosser, Eva-Marie; Sederoff, Heike; Servick, Stein; Sessa, Emily B.; Shaw, A. Jonathan; Shaw, Shane W.; Sigel, Erin M.; Skema, Cynthia; Smith, Alison G.; Smithson, Ann; Stewart, C. Neal, Jr.; Stinchcombe, John R.; Szovenyi, Peter; Tate, Jennifer A.; Tiebel, Helga; Trapnell, Dorset; Villegente, Matthieu; Wang, Chun-Neng; Weller, Stephen G.; Wenzel, Michael; Weststrand, Stina; Westwood, James H.; Whigham, Dennis F.; Wu, Shuangxiu; Wulff, Adrien S.; Yang, Yu; Zhu, Dan; Zhuang, Cuili; Zuidof, Jennifer; Chase, Mark W.; Pires, J. Chris; Rothfels, Carl J.; Yu, Jun; Chen, Cui; Chen, Li; Cheng, Shifeng; Li, Juanjuan; Li, Ran; Li, Xia; Lu, Haorong; Ou, Yanxiang; Sun, Xiao; Tan, Xuemei; Tang, Jingbo; Tian, Zhijian; Wang, Feng; Wang, Jun; Wei, Xiaofeng; Xu, Xun; Yan, Zhixiang; Yang, Fan; Zhong, Xiaoni; Zhou, Feiyu; Zhu, Ying; Zhang, Yong; Ayyampalayam, Saravanaraj; Barkman, Todd J.; Nam-Phuong Nguyen; Matasci, Naim; Nelson, David R.; Sayyari, Erfan; Wafula, Eric K.; Walls, Ramona L.; Warnow, Tandy; An, Hong; Arrigo, Nils; Baniaga, Anthony E.; Galuska, Sally; Jorgensen, Stacy A.; Kidder, Thomas I.; Kong, Hanghui; Lu-Irving, Patricia; Marx, Hannah E.; Qi, Xinshuai; Reardon, Chris R.; Sutherland, Brittany L.; Tiley, George P.; Welles, Shana R.; Yu, Rongpei; Zhan, Shing; Gramzow, Lydia; Theissen, Gunter; Wong, Gane Ka-Shu; One Thousand Plant Transcriptomes
Keywords: SERC
Abstract: Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) 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.
Complete genomes of symbiotic cyanobacteria clarify the evolution of Vanadium-nitrogenaseNelson, JessicaHauser, DuncanGudiño, José A.Guadalupe, Yessenia A.Meeks, John C.Salazar, Noris AllenVillarreal, Juan CarlosLi, Fay-Wei2019DOI: info:10.1093/gbe/evz137Genome Biology and Evolution1171–171759-6653
Nelson, Jessica, Hauser, Duncan, Gudiño, José A., Guadalupe, Yessenia A., Meeks, John C., Salazar, Noris Allen, Villarreal, Juan Carlos, and Li, Fay-Wei. 2019. "Complete genomes of symbiotic cyanobacteria clarify the evolution of Vanadium-nitrogenase." Genome Biology and Evolution 1–17.
ID: 151739
Type: article
Authors: Nelson, Jessica; Hauser, Duncan; Gudiño, José A.; Guadalupe, Yessenia A.; Meeks, John C.; Salazar, Noris Allen; Villarreal, Juan Carlos; Li, Fay-Wei
Keywords: STRI
Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association StudiesPiot, AnthonyPrunier, JulienIsabel, NathalieKlápště, JaroslavEl-Kassaby, YousryVillarreal Aguilar, Juan CarlosPorth, Ilga2019DOI: info:10.3389/fgene.2019.01384Frontiers in Geneticsv. 10Article 1384Article 13841664-8021
Piot, Anthony, Prunier, Julien, Isabel, Nathalie, Klápště, Jaroslav, El-Kassaby, Yousry, Villarreal Aguilar, Juan Carlos, and Porth, Ilga. 2019. "Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association Studies." Frontiers in Genetics 10:Article 1384.
ID: 154730
Type: article
Authors: Piot, Anthony; Prunier, Julien; Isabel, Nathalie; Klápště, Jaroslav; El-Kassaby, Yousry; Villarreal Aguilar, Juan Carlos; Porth, Ilga
Keywords: STRI
Abstract: Genome-wide association studies are powerful tools to elucidate the genome-to-phenome relationship. In order to explain most of the observed heritability of a phenotypic trait, a sufficient number of individuals and a large set of genetic variants must be examined. The development of high-throughput technologies and cost-efficient resequencing of complete genomes have enabled the genome-wide identification of genetic variation at large scale. As such, almost all existing genetic variation becomes available, and it is now possible to identify rare genetic variants in a population sample. Rare genetic variants that were usually filtered out in most genetic association studies are the most numerous genetic variations across genomes and hold great potential to explain a significant part of the missing heritability observed in association studies. Rare genetic variants must be identified with high confidence, as they can easily be confounded with sequencing errors. In this study, we used a pre-filtered data set of 1,014 pure Populus trichocarpa entire genomes to identify rare and common small genetic variants across individual genomes. We compared variant calls between Platypus and HaplotypeCaller pipelines, and we further applied strict quality filters for improved genetic variant identification. Finally, we only retained genetic variants that were identified by both variant callers increasing calling confidence. Based on these shared variants and after stringent quality filtering, we found high genomic diversity in P. trichocarpa germplasm, with 7.4 million small genetic variants. Importantly, 377k non-synonymous variants (5% of the total) were uncovered. We highlight the importance of genomic diversity and the potential of rare defective genetic variants in explaining a significant portion of P. trichocarpa's phenotypic variability in association genetics. The ultimate goal is to associate both rare and common alleles with poplar's wood quality traits to support selective breeding for an improved bioenergy feedstock.
Morphology supports ­the setaphyte hypothesis: mosses plus liverworts form a natural groupRenzaglia, Karen S.Villarreal Aguilar, Juan CarlosGarbary, David J.2018DOI: info:10.11646/bde.40.2.1Bryophyte Diversity and Evolutionv. 40No. 2111711–172381-9685
Renzaglia, Karen S., Villarreal Aguilar, Juan Carlos, and Garbary, David J. 2018. "Morphology supports ­the setaphyte hypothesis: mosses plus liverworts form a natural group." Bryophyte Diversity and Evolution 40 (2):11–17.
ID: 150134
Type: article
Authors: Renzaglia, Karen S.; Villarreal Aguilar, Juan Carlos; Garbary, David J.
Keywords: STRI
Abstract: The origin and early diversification of land plants is one of the major unresolved problems in evolutionary biology. Occurring nearly half a billion years ago, the transmigration of green organisms to land changed the landscape and provided the food source for terrestrial life to invade a vast uninhabited space, adapt and radiate. Although bryophytes (mosses, liverworts and hornworts) are often regarded as the earliest terrestrial organisms, the order of their divergence remains contentious even as molecular analyses become more conclusive with expanded taxon sampling, massive genetic data and more sophisticated methods of analysis (Cox et al. 2018; Morris et al. 2018). Indeed, virtually every combination of relationships among bryophytes has been proposed based on molecules (Qiu et al. 2006; Wickett et al. 2014; Cox et al. 2018). Fortunately, in 2018 it appears that we are approaching a consensus based on molecules, and that is that although bryophytes may or may not be monophyletic, mosses plus liverworts form a natural group (Puttick et al. 2018). In this essay, we point out that this inference is neither new nor surprising as it has been the fundamental conclusion of morphological analyses for over 25 years starting with an exhaustive cladistic analysis of characters associated with motile cell development in green plants (Garbary et al. 1993).
Genome-wide organellar analyses from the hornwort Leiosporoceros dussii show low frequency of RNA editingVillarreal A., Juan CarlosTurmel, MoniqueBourgouin-Couture, J.Salazar Allen, NorisLi, Fay-WeiCheng, ShifengRenzaglia, KarenLemieux, Claude2018DOI: info:10.1371/journal.pone.0200491PLOS ONEv. 13No. 81181–181932-6203
Villarreal A., Juan Carlos, Turmel, Monique, Bourgouin-Couture, J., Salazar Allen, Noris, Li, Fay-Wei, Cheng, Shifeng, Renzaglia, Karen, and Lemieux, Claude. 2018. "Genome-wide organellar analyses from the hornwort Leiosporoceros dussii show low frequency of RNA editing." PLOS ONE 13 (8):1–18.
ID: 148559
Type: article
Authors: Villarreal A., Juan Carlos; Turmel, Monique; Bourgouin-Couture, J.; Salazar Allen, Noris; Li, Fay-Wei; Cheng, Shifeng; Renzaglia, Karen; Lemieux, Claude
Keywords: STRI
Abstract: Because hornworts occupy a pivotal position in early land colonization as sister to other bryophytes, sister to tracheophytes, or sister to all other land plants, a renewed interest has arisen in their phylogenetic diversity, morphology, and genomes. To date, only five organellar genome sequences are available for hornworts. We sequenced the plastome (155,956 bp) and mitogenome (212,153 bp) of the hornwort Leiosporoceros dussii, the sister taxon to all hornworts. The Leiosporoceros organellar genomes show conserved gene structure and order with respect to the other hornworts and other bryophytes. Additionally, using RNA-seq data we quantified the frequency of RNA-editing events (the canonical C-to-U and the reverse editing U-to-C) in both organellar genomes. In total, 109 sites were found in the plastome and 108 in the mitogenome, respectively. The proportion of edited sites corresponds to 0.06% of the plastome and 0.05% of the mitogenome (in reference to the total genome size), in contrast to 0.58% of edited sites in the plastome of Anthoceros angustus (161,162 bp). All edited sites in the plastome and 88 of 108 sites in the mitogenome are C-to-U conversions. Twenty reverse edited sites (U-to-C conversions) were found in the mitogenome (17.8%) and none in the plastome. The low frequency of RNA editing in Leiosporoceros, which is nearly 88% less than in the plastome of Anthoceros and the mitogenome of Nothoceros, indicates that the frequency of RNA editing has fluctuated during hornwort diversification. Hornworts are a pivotal land plant group to unravel the genomic implications of RNA editing and its maintenance despite the evident evolutionary disadvantages.
Future directions and priorities for Arctic bryophyte researchLewis, Lily RobertaIckert-Bond, SteffiBiersma, Elisabeth M.Convey, PeterGoffinet, BernardHassel, KristianKruijer, Hans (J D. ).La Farge, CatherineMetzgar, JordanStech, MichaelVillarreal, Juan CarlosMcDaniel, Stuart F.2017DOI: info:10.1139/AS-2016-0043Arctic Sciencev. 3No. 3475497475–4972368-7460
Lewis, Lily Roberta, Ickert-Bond, Steffi, Biersma, Elisabeth M., Convey, Peter, Goffinet, Bernard, Hassel, Kristian, Kruijer, Hans (J D. )., La Farge, Catherine, Metzgar, Jordan, Stech, Michael, Villarreal, Juan Carlos, and McDaniel, Stuart F. 2017. "Future directions and priorities for Arctic bryophyte research." Arctic Science 3 (3):475–497.
ID: 142727
Type: article
Authors: Lewis, Lily Roberta; Ickert-Bond, Steffi; Biersma, Elisabeth M.; Convey, Peter; Goffinet, Bernard; Hassel, Kristian; Kruijer, Hans (J D. ).; La Farge, Catherine; Metzgar, Jordan; Stech, Michael; Villarreal, Juan Carlos; McDaniel, Stuart F.
Keywords: fellow; STRI
Hornwort Stomata: Architecture and Fate Shared with 400-Million-Year-Old Fossil Plants without LeavesRenzaglia, Karen S.Villarreal, Juan CarlosPiatkowski, Bryan T.Lucas, Jessica R.Merced, Amelia2017DOI: info:10.1104/pp.17.00156Plant Physiologyv. 174No. 2788797788–7970032-0889
Renzaglia, Karen S., Villarreal, Juan Carlos, Piatkowski, Bryan T., Lucas, Jessica R., and Merced, Amelia. 2017. "Hornwort Stomata: Architecture and Fate Shared with 400-Million-Year-Old Fossil Plants without Leaves." Plant Physiology 174 (2):788–797.
ID: 143430
Type: article
Authors: Renzaglia, Karen S.; Villarreal, Juan Carlos; Piatkowski, Bryan T.; Lucas, Jessica R.; Merced, Amelia
Keywords: STRI
Abstract: As one of the earliest plant groups to evolve stomata, hornworts are key to understanding the origin and function of stomata. Hornwort stomata are large and scattered on sporangia that grow from their bases and release spores at their tips. We present data from development and immunocytochemistry that identify a role for hornwort stomata that is correlated with sporangial and spore maturation. We measured guard cells across the genera with stomata to assess developmental changes in size and to analyze any correlation with genome size. Stomata form at the base of the sporophyte in the green region, where they develop differential wall thickenings, form a pore, and die. Guard cells collapse inwardly, increase in surface area, and remain perched over a substomatal cavity and network of intercellular spaces that is initially fluid filled. Following pore formation, the sporophyte dries from the outside inwardly and continues to do so after guard cells die and collapse. Spore tetrads develop in spore mother cell walls within a mucilaginous matrix, both of which progressively dry before sporophyte dehiscence. A lack of correlation between guard cell size and DNA content, lack of arabinans in cell walls, and perpetually open pores are consistent with the inactivity of hornwort stomata. Stomata are expendable in hornworts, as they have been lost twice in derived taxa. Guard cells and epidermal cells of hornworts show striking similarities with the earliest plant fossils. Our findings identify an architecture and fate of stomata in hornworts that is ancient and common to plants without sporophytic leaves.
Divergence times and the evolution of morphological complexity in an early land plant lineage (Marchantiopsida) with a slow molecular rateVillarreal, Juan CarlosCrandall-Stotler, BarbaraHart, Michelle L.Long, David G.Forrest, Laura L.2015DOI: info:10.1111/nph.13716New Phytologistv. 209No. 4173417461734–17460028-646X
Villarreal, Juan Carlos, Crandall-Stotler, Barbara, Hart, Michelle L., Long, David G., and Forrest, Laura L. 2015. "Divergence times and the evolution of morphological complexity in an early land plant lineage (Marchantiopsida) with a slow molecular rate." New Phytologist 209 (4):1734–1746.
ID: 137657
Type: article
Authors: Villarreal, Juan Carlos; Crandall-Stotler, Barbara; Hart, Michelle L.; Long, David G.; Forrest, Laura L.
Keywords: STRI; fellow
The enigmatic hornworts of the Cape Horn miniature forests/ Los enigmáticos antocerotes de los bosques en miniature del Cabo de HornosVillarreal, Juan CarlosSalazar Allen, NorisGoffinet, B.Rozzi, R.Lewis, L.Buck, W.Massardo, F.2012119125Punta Arenas, ChileUniversity of North Texas Press; Ediciones Universidad de Magallanes119–125
Villarreal, Juan Carlos and Salazar Allen, Noris. 2012. "The enigmatic hornworts of the Cape Horn miniature forests/ Los enigmáticos antocerotes de los bosques en miniature del Cabo de Hornos." in Miniature Forests of Cape Horn/Los Bosques en Miniatura del Cabo de Hornos: Ecotourism with Hand Lens-Ecoturismo con Lupa, edited by Goffinet, B., Rozzi, R., Lewis, L., Buck, W., and Massardo, F., 119–125. Punta Arenas, Chile: University of North Texas Press; Ediciones Universidad de Magallanes.
ID: 118949
Type: chapter
Authors: Villarreal, Juan Carlos; Salazar Allen, Noris
Keywords: STRI
Nothoceros superbus (Dendrocerotaceae), a new hornwort from Costa RicaVillarreal, Juan CarlosHassel de Menendez, GabrielaSalazar Allen, Noris2007DOI: info:10.1639/0007-2745(2007)110[279:NSDANH]2.0.COBryologistv. 110No. 2279285279–2850007-2745
Villarreal, Juan Carlos, Hassel de Menendez, Gabriela, and Salazar Allen, Noris. 2007. "Nothoceros superbus (Dendrocerotaceae), a new hornwort from Costa Rica." Bryologist 110 (2):279–285.[279:NSDANH]2.0.CO
ID: 73127
Type: article
Authors: Villarreal, Juan Carlos; Hassel de Menendez, Gabriela; Salazar Allen, Noris
Keywords: NH-EOL; stri
Nuevos registros de hepáticas y anthocerotófitas para PanamáDauphin, GregorioPocs, T.Villarreal A., Juan CarlosSalazar Allen, Noris2006Tropical Bryologyv. 27No. 1738573–850935-5626
Dauphin, Gregorio, Pocs, T., Villarreal A., Juan Carlos, and Salazar Allen, Noris. 2006. "Nuevos registros de hepáticas y anthocerotófitas para Panamá." Tropical Bryology 27 (1):73–85.
ID: 110817
Type: article
Authors: Dauphin, Gregorio; Pocs, T.; Villarreal A., Juan Carlos; Salazar Allen, Noris
Keywords: STRI
Anatomical and Ultrastructural Innovations in Leiosporocero's Dussii (Steph.) HasselVillarreal A., Juan CarlosDuff, R. J.Renzaglia, K. S.2005451451
Villarreal A., Juan Carlos, Duff, R. J., and Renzaglia, K. S. 2005. "Anatomical and Ultrastructural Innovations in Leiosporocero's Dussii (Steph.) Hassel." in XVII International Botanical Congress - Abstracts, 451.
ID: 51931
Type: chapter
Authors: Villarreal A., Juan Carlos; Duff, R. J.; Renzaglia, K. S.
Keywords: stri
Impacto Ecologico Del Magle Rojo (Rhizophora Mangle) Sucesivo Al Derrame De Petroleo Del Caribe De PanamáVillarreal, Carlos A.2005169
Villarreal, Carlos A. 2005. "Impacto Ecologico Del Magle Rojo (Rhizophora Mangle) Sucesivo Al Derrame De Petroleo Del Caribe De Panamá."
ID: 51930
Type: thesis
Authors: Villarreal, Carlos A.
Keywords: stri
Estudio De La Morfología, Distribución Geográfica y Altitudinal De Megaceros Vincentianus (Lehm. & Lindb.) Campbell (Dendrocerotaceae: Anthocerotophyta) En La República De PanamáVillarreal A., Juan Carlos200260
Villarreal A., Juan Carlos. 2002. "Estudio De La Morfología, Distribución Geográfica y Altitudinal De Megaceros Vincentianus (Lehm. & Lindb.) Campbell (Dendrocerotaceae: Anthocerotophyta) En La República De Panamá."
ID: 50920
Type: thesis
Authors: Villarreal A., Juan Carlos
Keywords: stri