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Population genomics of a reindeer lichen species from North American lichen woodlandsAlonso-Garcia, MartaGrewe, FelixPayette, SergeVillarreal, Juan Carlos A.DOI: info:10.1002/ajb2.1601v. 108No. 1159–171
Alonso-Garcia, Marta, Grewe, Felix, Payette, Serge, and Villarreal, Juan Carlos A. 2021. "Population genomics of a reindeer lichen species from North American lichen woodlands." American Journal of Botany 108 (1):159– 171. https://doi.org/10.1002/ajb2.1601
ID: 158396
Type: article
Authors: Alonso-Garcia, Marta; Grewe, Felix; Payette, Serge; Villarreal, Juan Carlos A.
Abstract: PREMISE Lichens are one of the main structural components of plant communities in the North American boreal biome. They play a pivotal role in lichen woodlands, a large ecosystem situated north of the closed-crown forest zone, and south of the forest-tundra zone. In Eastern Canada (Quebec), there is a remnant LW found 500 km south of its usual distribution range, in the Parc National des Grands-Jardins, originated mainly because of wildfires. We inferred the origin of the lichen Cladonia stellaris from this LW and assessed its genetic diversity in a postfire succession. METHODS We genotyped 122 individuals collected across a latitudinal gradient in Quebec. Using the software Stacks, we compared four different approaches of locus selection and single-nucleotide polymorphism calling. We identified the best fitting approach to investigate population structure and estimate genetic diversity of C. stellaris. RESULTS Populations in southern Quebec are not genetically different from those of northern LWs. The species consists of at least four phylogenetic lineages with elevated levels of genetic diversity and low co-ancestry. In Parc National des Grands-Jardins, we reported high values of genetic diversity not related with time since fire disturbance and low genetic differentiation among populations with different fire histories. CONCLUSIONS This first population genomic study of C. stellaris is an important step forward to understand the origin and biogeographic patterns of lichen woodlands in North America. Our findings also contribute to the understanding of the effect of postfire succession on the genetic structure of the species.
Stigonema associated with boreal Stereocaulon possesses the alternative vanadium nitrogenaseVillarreal A., Juan CarlosRenaudin, M.Beaulieu-Laliberte, A.Bellenger, J. P.DOI: info:10.1017/S0024282921000062v. 53No. 2215–220
Villarreal A., Juan Carlos, Renaudin, M., Beaulieu-Laliberte, A., and Bellenger, J. P. 2021. "Stigonema associated with boreal Stereocaulon possesses the alternative vanadium nitrogenase." Lichenologist 53 (2):215– 220. https://doi.org/10.1017/S0024282921000062
ID: 159064
Type: article
Authors: Villarreal A., Juan Carlos; Renaudin, M.; Beaulieu-Laliberte, A.; Bellenger, J. P.
Population Genomics and Phylogeography of a Clonal Bryophyte With Spatially Separated Sexes and Extreme Sex RatiosAlonso-García, MartaCarlos, Villarreal A., JuanMcFarland, KennethGoffinet, BernardDOI: info:10.3389/fpls.2020.00495v. 11
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:https://doi.org/10.3389/fpls.2020.00495
ID: 156581
Type: article
Authors: Alonso-García, Marta; Carlos, Villarreal A., Juan; McFarland, Kenneth; Goffinet, Bernard
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.
Specialized bacteriome uncovered in the coralloid roots of the epiphytic gymnosperm, Zamia pseudoparasiticaBell‐Doyon, PhilipLaroche, JérômeSaltonstall, KristinVillareal Aguilar, Juan CarlosDOI: info:10.1002/edn3.66v. 2418–428
Bell‐Doyon, Philip, Laroche, Jérôme, Saltonstall, Kristin, and Villareal Aguilar, Juan Carlos. 2020. "Specialized bacteriome uncovered in the coralloid roots of the epiphytic gymnosperm, Zamia pseudoparasitica." Environmental DNA 2:418– 428. https://doi.org/10.1002/edn3.66
ID: 154061
Type: article
Authors: Bell‐Doyon, Philip; Laroche, Jérôme; Saltonstall, Kristin; Villareal Aguilar, Juan Carlos
Abstract: Epiphytes face several constraints regarding nutrient acquisition: They are disconnected from soil minerals and they have to mainly rely on nutrients leached by precipitation and microbes. The cycad, Zamia pseudoparasitica Yates, is the only known strictly epiphytic gymnosperm, and it is endemic to Panamanian rainforests. Cycads have evolved specialized coralloid roots that host endophytic cyanobacteria specialized in nitrogen fixation. We collected coralloid roots from plants in the Omar Torrijos National Park, Provincia de Coclé. DNA was extracted from fresh inner coralloid roots, and the bacteriome was described using two molecular markers: rbcL-rbcX (targeting cyanobacteria) and 16S (all bacteria). Sixteen samples were sequenced for rbcL-rbcX yielding sequences belonging to a monophyletic group within the order Nostocales. One hundred and sixty-five amplicon sequence variants (ASVs) were found in at least two of our 27 samples amplified for 16S. Nostocales, Rhizobiales, and Acetobacterales were the three most diverse and abundant orders of bacteria found within the coralloid roots, and the candidate phylum WPS-2 was also found in many samples. We performed a de novo assembly from a single culture of the endophytic cyanobacteria. A phylogenomic analysis of the isolate places the cyanobacterium in a sister clade to mostly symbiotic taxa from mosses, liverworts, and lichens. Additionally, the isolate has genes putatively involved in symbiotic signaling, hormogonium differentiation, ammonium transport, nitrogen fixation, heterocyst differentiation, sulfate transport, and secondary metabolites. Although dominated by organisms with the capacity to fix nitrogen, coralloid roots are also inhabited by a diverse community of other taxa which may also play biologically important roles.
Extremely low genetic diversity in the European clade of the model bryophyte Anthoceros agrestisDawes, Thomas N.Villareal Aguilar, Juan CarlosSzovenyi, PeterBisang, IreneLi, Fay-WeiHauser, DuncanQuandt, DietmarCargill, D. C.Forrest, Laura L.DOI: info:10.1007/s00606-020-01676-6v. 3061–10
Dawes, Thomas N., Villareal Aguilar, Juan Carlos, Szovenyi, Peter, Bisang, Irene, Li, Fay-Wei, Hauser, Duncan, Quandt, Dietmar, Cargill, D. C., and Forrest, Laura L. 2020. "Extremely low genetic diversity in the European clade of the model bryophyte Anthoceros agrestis." Plant Systematics and Evolution 306:1– 10. https://doi.org/10.1007/s00606-020-01676-6
ID: 155224
Type: article
Authors: Dawes, Thomas N.; Villareal Aguilar, Juan Carlos; Szovenyi, Peter; Bisang, Irene; Li, Fay-Wei; Hauser, Duncan; Quandt, Dietmar; Cargill, D. C.; Forrest, Laura L.
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 C.de 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, PéterDOI: info:10.1038/s41477-020-0618-2v. 6No. 3259–272
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. https://doi.org/10.1038/s41477-020-0618-2
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
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.DOI: info:10.1002/ajb2.1397v. 107No. 11–25
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. https://doi.org/10.1002/ajb2.1397
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.
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.DOI: info:10.1177/1934578X19868875v. 14No. 81–4
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. https://doi.org/10.1177/1934578X19868875
ID: 152053
Type: article
Authors: Garrido, Anette; Gudiño Ledezma, José; Durant-Archibold, Armando; Salazar Allen, Noris; Juan, Villarreal A.; Gupta, Mahabir P.
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 TranscriptomesDOI: info:10.1038/s41586-019-1693-2v. 574No. 7780679–+
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– +. https://doi.org/10.1038/s41586-019-1693-2
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
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-WeiDOI: info:10.1093/gbe/evz1371–17
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. https://doi.org/10.1093/gbe/evz137
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
Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association StudiesPiot, AnthonyPrunier, JulienIsabel, NathalieKlápště, JaroslavEl-Kassaby, YousryVillarreal Aguilar, Juan CarlosPorth, IlgaDOI: info:10.3389/fgene.2019.01384v. 10Article 1384
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. https://doi.org/10.3389/fgene.2019.01384
ID: 154730
Type: article
Authors: Piot, Anthony; Prunier, Julien; Isabel, Nathalie; Klápště, Jaroslav; El-Kassaby, Yousry; Villarreal Aguilar, Juan Carlos; Porth, Ilga
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.DOI: info:10.11646/bde.40.2.1v. 40No. 211–17
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. https://doi.org/10.11646/bde.40.2.1
ID: 150134
Type: article
Authors: Renzaglia, Karen S.; Villarreal Aguilar, Juan Carlos; Garbary, David J.
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, ClaudeDOI: info:10.1371/journal.pone.0200491v. 13No. 81–18
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. https://doi.org/10.1371/journal.pone.0200491
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
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.DOI: info:10.1139/AS-2016-0043v. 3No. 3475–497
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. https://doi.org/10.1139/AS-2016-0043
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.
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, AmeliaDOI: info:10.1104/pp.17.00156v. 174No. 2788–797
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. https://doi.org/10.1104/pp.17.00156
ID: 143430
Type: article
Authors: Renzaglia, Karen S.; Villarreal, Juan Carlos; Piatkowski, Bryan T.; Lucas, Jessica R.; Merced, Amelia
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.DOI: info:10.1111/nph.13716v. 209No. 41734–1746
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. https://doi.org/10.1111/nph.13716
ID: 137657
Type: article
Authors: Villarreal, Juan Carlos; Crandall-Stotler, Barbara; Hart, Michelle L.; Long, David G.; Forrest, Laura L.
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.University 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. University of North Texas Press; Ediciones Universidad de Magallanes.
Nothoceros superbus (Dendrocerotaceae), a new hornwort from Costa RicaVillarreal, Juan CarlosHassel de Menendez, GabrielaSalazar Allen, NorisDOI: info:10.1639/0007-2745(2007)110[279:NSDANH]2.0.COv. 110No. 2279–285
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. https://doi.org/10.1639/0007-2745(2007)110[279:NSDANH]2.0.CO
ID: 73127
Type: article
Authors: Villarreal, Juan Carlos; Hassel de Menendez, Gabriela; Salazar Allen, Noris
Nuevos registros de hepáticas y anthocerotófitas para PanamáDauphin, GregorioPocs, T.Villarreal A., Juan CarlosSalazar Allen, Norisv. 27No. 173–85
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
Anatomical and Ultrastructural Innovations in Leiosporocero's Dussii (Steph.) HasselVillarreal A., Juan CarlosDuff, R. J.Renzaglia, K. S.451
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.