1
|
Melton AE, Chen S, Zhao Y, Fu C, Xiang QYJ, Cheng S, Wong GKS, Soltis PS, Soltis DE, Gitzendanner MA. Genetic insights into the evolution of genera with the eastern Asia-eastern North America floristic disjunction: a transcriptomics analysis. Am J Bot 2020; 107:1736-1748. [PMID: 33280088 DOI: 10.1002/ajb2.1579] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/29/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Large disjunctions in species distributions provide excellent opportunities to study processes that shape biogeographic patterns. One such disjunction is the eastern Asia-eastern North America (EA-ENA) floristic disjunction. For many genera with this disjunction, species richness is greater in EA than in ENA; this pattern has been attributed, in part, to higher rates of molecular evolution and speciation in EA. Longer branch lengths have been found in some EA clades, relative to their ENA sister clades, suggesting that the EA lineages have evolved at a higher rate, possibly due to environmental heterogeneity, potentially contributing to the species richness anomaly. METHODS To evaluate whether rates of molecular evolution are elevated in EA relative to ENA, we used transcriptomes from species in 11 genera displaying this disjunction. Rates of molecular evolution were estimated for up to 385 orthologous nuclear loci per genus. RESULTS No statistically significant differences were identified in pairwise comparisons between EA and ENA sister species, suggesting equal rates of molecular evolution for both species; the data also suggest similar selection pressures in both regions. For larger genera, evidence likewise argues against more species-rich clades having higher molecular evolutionary rates, regardless of region. Our results suggest that genes across multiple gene ontology categories are evolving at similar rates under purifying selection in species in both regions. CONCLUSIONS Our data support the hypothesis that greater species richness in EA than ENA is due to factors other than an overall increase in rates of molecular evolution in EA.
Collapse
Affiliation(s)
- Anthony E Melton
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Shichao Chen
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yunpeng Zhao
- Laboratory of Systematic and Evolutionary Botany & Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chengxin Fu
- Laboratory of Systematic and Evolutionary Botany & Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qiu-Yun Jenny Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Shifeng Cheng
- Beijing Genomics Institute, Building NO.7, BGI Park, No.21 Hongan 3rd Street, Yantian District, Shenzhen, China
| | - Gane K-S Wong
- Beijing Genomics Institute, Building NO.7, BGI Park, No.21 Hongan 3rd Street, Yantian District, Shenzhen, China
- Biological Sciences, The University of Alberta, Edmonton, Alberta, T6G 2R3, Canada
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | | |
Collapse
|
2
|
Sineshchekov OA, Govorunova EG, Li H, Wang Y, Melkonian M, Wong GKS, Brown LS, Spudich JL. Conductance Mechanisms of Rapidly Desensitizing Cation Channelrhodopsins from Cryptophyte Algae. mBio 2020; 11:e00657-20. [PMID: 32317325 PMCID: PMC7175095 DOI: 10.1128/mbio.00657-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 03/26/2020] [Indexed: 01/14/2023] Open
Abstract
Channelrhodopsins guide algal phototaxis and are widely used as optogenetic probes for control of membrane potential with light. "Bacteriorhodopsin-like" cation channelrhodopsins (BCCRs) from cryptophytes differ in primary structure from other CCRs, lacking usual residues important for their cation conductance. Instead, the sequences of BCCR match more closely those of rhodopsin proton pumps, containing residues responsible for critical proton transfer reactions. We report 19 new BCCRs which, together with the earlier 6 known members of this family, form three branches (subfamilies) of a phylogenetic tree. Here, we show that the conductance mechanisms in two subfamilies differ with respect to involvement of the homolog of the proton donor in rhodopsin pumps. Two BCCRs from the genus Rhodomonas generate photocurrents that rapidly desensitize under continuous illumination. Using a combination of patch clamp electrophysiology, absorption, Raman spectroscopy, and flash photolysis, we found that the desensitization is due to rapid accumulation of a long-lived nonconducting intermediate of the photocycle with unusually blue-shifted absorption with a maximum at 330 nm. These observations reveal diversity within the BCCR family and contribute to deeper understanding of their independently evolved cation channel function.IMPORTANCE Cation channelrhodopsins, light-gated channels from flagellate green algae, are extensively used as optogenetic photoactivators of neurons in research and recently have progressed to clinical trials for vision restoration. However, the molecular mechanisms of their photoactivation remain poorly understood. We recently identified cryptophyte cation channelrhodopsins, structurally different from those of green algae, which have separately evolved to converge on light-gated cation conductance. This study reveals diversity within this new protein family and describes a subclade with unusually rapid desensitization that results in short transient photocurrents in continuous light. Such transient currents have not been observed in the green algae channelrhodopsins and are potentially useful in optogenetic protocols. Kinetic UV-visible (UV-vis) spectroscopy and photoelectrophysiology reveal that the desensitization is caused by rapid accumulation of a nonconductive photointermediate in the photochemical reaction cycle. The absorption maximum of the intermediate is 330 nm, the shortest wavelength reported in any rhodopsin, indicating a novel chromophore structure.
Collapse
Affiliation(s)
- Oleg A Sineshchekov
- Center for Membrane Biology, Department of Biochemistry & Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
| | - Elena G Govorunova
- Center for Membrane Biology, Department of Biochemistry & Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
| | - Hai Li
- Center for Membrane Biology, Department of Biochemistry & Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
| | - Yumei Wang
- Center for Membrane Biology, Department of Biochemistry & Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
| | - Michael Melkonian
- Institute for Plant Sciences, Department of Biology, University of Cologne, Cologne, Germany
- Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - John L Spudich
- Center for Membrane Biology, Department of Biochemistry & Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
| |
Collapse
|
3
|
Li FW, Nishiyama T, Waller M, Frangedakis E, Keller J, Li Z, Fernandez-Pozo N, Barker MS, Bennett T, Blázquez MA, Cheng S, Cuming AC, de Vries J, de Vries S, Delaux PM, Diop IS, Harrison CJ, Hauser D, Hernández-García J, Kirbis A, Meeks JC, Monte I, Mutte SK, Neubauer A, Quandt D, Robison T, Shimamura M, Rensing SA, Villarreal JC, Weijers D, Wicke S, Wong GKS, Sakakibara K, Szövényi P. Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts. Nat Plants 2020; 6:259-272. [PMID: 32170292 PMCID: PMC8075897 DOI: 10.1038/s41477-020-0618-2] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/11/2020] [Indexed: 05/12/2023]
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.
Collapse
Affiliation(s)
- Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA.
- Plant Biology Section, Cornell University, Ithaca, NY, USA.
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Ishikawa, Japan
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | | | - Jean Keller
- LRSV, Université de Toulouse, CNRS, UPS Castanet-Tolosan, Toulouse, France
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Tom Bennett
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, Valencia, Spain
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Jan de Vries
- Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Georg-August University Göttingen, Göttingen, Germany
| | - Sophie de Vries
- Institute of Population Genetics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Pierre-Marc Delaux
- LRSV, Université de Toulouse, CNRS, UPS Castanet-Tolosan, Toulouse, France
| | - Issa S Diop
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Jorge Hernández-García
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, Valencia, Spain
| | - Alexander Kirbis
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - John C Meeks
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, USA
| | - Isabel Monte
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Sumanth K Mutte
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Anna Neubauer
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany
| | - Tanner Robison
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Masaki Shimamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Stefan A Rensing
- Faculty of Biology, Philipps University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg, Germany
| | - Juan Carlos Villarreal
- Department of Biology, Laval University, Quebec City, Quebec, Canada
- Smithsonian Tropical Research Institute, Balboa, Panamá
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Münster, Germany
| | - Gane K-S Wong
- Department of Biological Sciences, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
- BGI-Shenzhen, Shenzhen, China
| | | | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland.
- Zurich-Basel Plant Science Center, Zurich, Switzerland.
| |
Collapse
|
4
|
Bell D, Lin Q, Gerelle WK, Joya S, Chang Y, Taylor ZN, Rothfels CJ, Larsson A, Villarreal JC, Li FW, Pokorny L, Szövényi P, Crandall-Stotler B, DeGironimo L, Floyd SK, Beerling DJ, Deyholos MK, von Konrat M, Ellis S, Shaw AJ, Chen T, Wong GKS, Stevenson DW, Palmer JD, Graham SW. Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution. Am J Bot 2020; 107:91-115. [PMID: 31814117 DOI: 10.1002/ajb2.1397] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
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.
Collapse
Affiliation(s)
- David Bell
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
- UBC Botanical Garden and Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, British Columbia, V6T 1Z4, Canada
- Royal Botanic Garden, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Qianshi Lin
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
- UBC Botanical Garden and Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Wesley K Gerelle
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
- UBC Botanical Garden and Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Steve Joya
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Ying Chang
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Z Nathan Taylor
- Department of Biology, Indiana University, Bloomington, Indiana, 47405, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California Berkeley, Berkeley, California, 94702, USA
| | - Anders Larsson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Juan Carlos Villarreal
- Department of Biology, Université Laval, Québec, G1V 0A6, Canada
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Plant Biology Section, Cornell University, Ithaca, New York, 14853, USA
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, TW9 3DS, Surrey, UK
- Centre for Plant Biotechnology and Genomics (CBGP, UPM-INIA), 28223, Pozuelo de Alarcón (Madrid), Spain
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | | | - Lisa DeGironimo
- Department of Biology, College of Arts and Science, New York University, New York, New York, 10003, USA
| | - Sandra K Floyd
- School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia
| | - David J Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Michael K Deyholos
- Department of Biology, University of British Columbia, Kelowna, British Columbia, V1V 1V7, Canada
| | - Matt von Konrat
- Field Museum of Natural History, Chicago, Illinois, 60605, USA
| | - Shona Ellis
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Tao Chen
- Shenzhen Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, China
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | | | - Jeffrey D Palmer
- Department of Biology, Indiana University, Bloomington, Indiana, 47405, USA
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
- UBC Botanical Garden and Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, British Columbia, V6T 1Z4, Canada
| |
Collapse
|
5
|
Visger CJ, Wong GKS, Zhang Y, Soltis PS, Soltis DE. Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass. Am J Bot 2019; 106:280-291. [PMID: 30779448 DOI: 10.1002/ajb2.1239] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/03/2018] [Indexed: 05/28/2023]
Abstract
PREMISE OF THE STUDY Studies of gene expression and polyploidy are typically restricted to characterizing differences in transcript concentration. Using diploid and autotetraploid Tolmiea, we present an integrated approach for cross-ploidy comparisons that account for differences in transcriptome size and cell density and make multiple comparisons of transcript abundance. METHODS We use RNA spike-in standards in concert with cell size and density to identify and correct for differences in transcriptome size and compare levels of gene expression across multiple scales: per transcriptome, per cell, and per biomass. KEY RESULTS In total, ~17% of all loci were identified as differentially expressed (DEGs) between the diploid and autopolyploid species. The per-transcriptome normalization, the method researchers typically use, captured the fewest DEGs (58% of total DEGs) and failed to detect any DEGs not found by the alternative normalizations. When transcript abundance was normalized per biomass and per cell, ~66% and ~82% of the total DEGs were recovered, respectively. The discrepancy between per-transcriptome and per-cell recovery of DEGs occurs because per-transcriptome normalizations are concentration-based and therefore blind to differences in transcriptome size. CONCLUSIONS While each normalization enables valid comparisons at biologically relevant scales, a holistic comparison of multiple normalizations provides additional explanatory power not available from any single approach. Notably, autotetraploid loci tend to conserve diploid-like transcript abundance per biomass through increased gene expression per cell, and these loci are enriched for photosynthesis-related functions.
Collapse
Affiliation(s)
- Clayton J Visger
- Department of Biological Sciences, California State University Sacramento, Sacramento, CA, 95819, USA
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Beijing Genomics Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Yong Zhang
- Beijing Genomics Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
- Shenzhen Hua Han Gene Co. Ltd., 7F Jian An Shan Hai Building, No. 8000, Shennan Road, Futian District, Shenzhen, 518040, China
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| |
Collapse
|
6
|
Li FW, Brouwer P, Carretero-Paulet L, Cheng S, de Vries J, Delaux PM, Eily A, Koppers N, Kuo LY, Li Z, Simenc M, Small I, Wafula E, Angarita S, Barker MS, Bräutigam A, dePamphilis C, Gould S, Hosmani PS, Huang YM, Huettel B, Kato Y, Liu X, Maere S, McDowell R, Mueller LA, Nierop KGJ, Rensing SA, Robison T, Rothfels CJ, Sigel EM, Song Y, Timilsena PR, Van de Peer Y, Wang H, Wilhelmsson PKI, Wolf PG, Xu X, Der JP, Schluepmann H, Wong GKS, Pryer KM. Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nat Plants 2018; 4:460-472. [PMID: 29967517 PMCID: PMC6786969 DOI: 10.1038/s41477-018-0188-8] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/24/2018] [Indexed: 05/18/2023]
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.
Collapse
Affiliation(s)
- Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA.
- Plant Biology Section, Cornell University, Ithaca, NY, USA.
| | - Paul Brouwer
- Molecular Plant Physiology Department, Utrecht University, Utrecht, the Netherlands
| | - Lorenzo Carretero-Paulet
- Bioinformatics Institute Ghent and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Shifeng Cheng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet Tolosan, France
| | - Ariana Eily
- Department of Biology, Duke University, Durham, NC, USA
| | - Nils Koppers
- Department of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Dusseldorf, Germany
| | | | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Mathew Simenc
- Department of Biological Science, California State University, Fullerton, CA, USA
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Eric Wafula
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Stephany Angarita
- Department of Biological Science, California State University, Fullerton, CA, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | - Claude dePamphilis
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Sven Gould
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Dusseldorf, Germany
| | | | | | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding, Cologne, Germany
| | - Yoichiro Kato
- Institute for Sustainable Agro-ecosystem Services, University of Tokyo, Tokyo, Japan
| | - Xin Liu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Steven Maere
- Bioinformatics Institute Ghent and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Rose McDowell
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | | | - Klaas G J Nierop
- Geolab, Faculty of Geosciences, Utrecht University, Utrecht, the Netherlands
| | | | - Tanner Robison
- Department of Biology, Utah State University, Logan, UT, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Erin M Sigel
- Department of Biology, University of Louisiana, Lafayette, LA, USA
| | - Yue Song
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Prakash R Timilsena
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Yves Van de Peer
- Bioinformatics Institute Ghent and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Hongli Wang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | | | - Paul G Wolf
- Department of Biology, Utah State University, Logan, UT, USA
| | - Xun Xu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Joshua P Der
- Department of Biological Science, California State University, Fullerton, CA, USA
| | | | - Gane K-S Wong
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Department of Biological Sciences, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | | |
Collapse
|
7
|
Gitzendanner MA, Soltis PS, Wong GKS, Ruhfel BR, Soltis DE. Plastid phylogenomic analysis of green plants: A billion years of evolutionary history. Am J Bot 2018; 105:291-301. [PMID: 29603143 DOI: 10.1002/ajb2.1048] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/13/2017] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY For the past one billion years, green plants (Viridiplantae) have dominated global ecosystems, yet many key branches in their evolutionary history remain poorly resolved. Using the largest analysis of Viridiplantae based on plastid genome sequences to date, we examined the phylogeny and implications for morphological evolution at key nodes. METHODS We analyzed amino acid sequences from protein-coding genes from complete (or nearly complete) plastomes for 1879 taxa, including representatives across all major clades of Viridiplantae. Much of the data used was derived from transcriptomes from the One Thousand Plants Project (1KP); other data were taken from GenBank. KEY RESULTS Our results largely agree with previous plastid-based analyses. Noteworthy results include (1) the position of Zygnematophyceae as sister to land plants (Embryophyta), (2) a bryophyte clade (hornworts, mosses + liverworts), (3) Equisetum + Psilotaceae as sister to Marattiales + leptosporangiate ferns, (4) cycads + Ginkgo as sister to the remaining extant gymnosperms, within which Gnetophyta are placed within conifers as sister to non-Pinaceae (Gne-Cup hypothesis), and (5) Amborella, followed by water lilies (Nymphaeales), as successive sisters to all other extant angiosperms. Within angiosperms, there is support for Mesangiospermae, a clade that comprises magnoliids, Chloranthales, monocots, Ceratophyllum, and eudicots. The placements of Ceratophyllum and Dilleniaceae remain problematic. Within Pentapetalae, two major clades (superasterids and superrosids) are recovered. CONCLUSIONS This plastid data set provides an important resource for elucidating morphological evolution, dating divergence times in Viridiplantae, comparisons with emerging nuclear phylogenies, and analyses of molecular evolutionary patterns and dynamics of the plastid genome.
Collapse
Affiliation(s)
- Matthew A Gitzendanner
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton AB, T6G 2E1, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Brad R Ruhfel
- Department of Biological Sciences, Eastern Kentucky University, Richmond, KY, 40475, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| |
Collapse
|
8
|
Govorunova EG, Sineshchekov OA, Rodarte EM, Janz R, Morelle O, Melkonian M, Wong GKS, Spudich JL. The Expanding Family of Natural Anion Channelrhodopsins Reveals Large Variations in Kinetics, Conductance, and Spectral Sensitivity. Sci Rep 2017; 7:43358. [PMID: 28256618 PMCID: PMC5335703 DOI: 10.1038/srep43358] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/23/2017] [Indexed: 11/09/2022] Open
Abstract
Natural anion channelrhodopsins (ACRs) discovered in the cryptophyte alga Guillardia theta generate large hyperpolarizing currents at membrane potentials above the Nernst equilibrium potential for Cl- and thus can be used as efficient inhibitory tools for optogenetics. We have identified and characterized new ACR homologs in different cryptophyte species, showing that all of them are anion-selective, and thus expanded this protein family to 20 functionally confirmed members. Sequence comparison of natural ACRs and engineered Cl--conducting mutants of cation channelrhodopsins (CCRs) showed radical differences in their anion selectivity filters. In particular, the Glu90 residue in channelrhodopsin 2, which needed to be mutated to a neutral or alkaline residue to confer anion selectivity to CCRs, is nevertheless conserved in all of the ACRs identified. The new ACRs showed a large variation of the amplitude, kinetics, and spectral sensitivity of their photocurrents. A notable variant, designated "ZipACR", is particularly promising for inhibitory optogenetics because of its combination of larger current amplitudes than those of previously reported ACRs and an unprecedentedly fast conductance cycle (current half-decay time 2-4 ms depending on voltage). ZipACR expressed in cultured mouse hippocampal neurons enabled precise photoinhibition of individual spikes in trains of up to 50 Hz frequency.
Collapse
Affiliation(s)
- Elena G Govorunova
- Center for Membrane Biology, Department of Biochemistry &Molecular Biology, The University of Texas Health Science Center at Houston, McGovern Medical School, Houston, Texas, USA
| | - Oleg A Sineshchekov
- Center for Membrane Biology, Department of Biochemistry &Molecular Biology, The University of Texas Health Science Center at Houston, McGovern Medical School, Houston, Texas, USA
| | - Elsa M Rodarte
- Department of Neurobiology &Anatomy, The University of Texas Health Science Center at Houston, McGovern Medical School, Houston, Texas, USA
| | - Roger Janz
- Department of Neurobiology &Anatomy, The University of Texas Health Science Center at Houston, McGovern Medical School, Houston, Texas, USA
| | - Olivier Morelle
- Institute of Botany, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Michael Melkonian
- Institute of Botany, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Gane K-S Wong
- Departments of Biological Sciences and of Medicine, University of Alberta, Edmonton, Alberta, Canada.,BGI-Shenzhen, Shenzhen, China
| | - John L Spudich
- Center for Membrane Biology, Department of Biochemistry &Molecular Biology, The University of Texas Health Science Center at Houston, McGovern Medical School, Houston, Texas, USA
| |
Collapse
|
9
|
Bourque S, Jeandroz S, Grandperret V, Lehotai N, Aimé S, Soltis DE, Miles NW, Melkonian M, Deyholos MK, Leebens-Mack JH, Chase MW, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Yan Z, Xie Y, Carpenter EJ, Wong GKS, Wendehenne D, Nicolas-Francès V. The Evolution of HD2 Proteins in Green Plants. Trends Plant Sci 2016; 21:1008-1016. [PMID: 27789157 DOI: 10.1016/j.tplants.2016.10.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/28/2016] [Accepted: 10/04/2016] [Indexed: 05/18/2023]
Abstract
In eukaryotes, protein deacetylation is carried out by two well-conserved histone deacetylase (HDAC) families: RPD3/HDA1 and SIR2. Intriguingly, model plants such as Arabidopsis express an additional plant-specific HDAC family, termed type-2 HDACs (HD2s). Transcriptomic analyses from more than 1300 green plants generated by the 1000 plants (1KP) consortium showed that HD2s appeared early in green plant evolution, the first members being detected in several streptophyte green alga. The HD2 family has expanded via several rounds of successive duplication; members are expressed in all major green plant clades. Interestingly, angiosperm species express new HD2 genes devoid of a zinc-finger domain, one of the main structural features of HD2s. These variants may have been associated with the origin and/or the biology of the ovule/seed.
Collapse
Affiliation(s)
- S Bourque
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France.
| | - S Jeandroz
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - V Grandperret
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - N Lehotai
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - S Aimé
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - D E Soltis
- Department of Biology, Florida Museum of Natural History, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - N W Miles
- Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX 76201, USA
| | - M Melkonian
- Botanical Institute, Cologne Biocenter, University of Cologne, 50674 Cologne, Germany
| | - M K Deyholos
- Department of Biology, University of British Columbia, Kelowna, BC V1V 1V7, Canada
| | - J H Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - M W Chase
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, UK; Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Western Australia
| | - C J Rothfels
- University Herbarium and Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - D W Stevenson
- New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - S W Graham
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - X Wang
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, CAS, 1-104 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - S Wu
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, CAS, 1-104 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - J C Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - P P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48823, USA
| | - Z Yan
- Beijing Genomics Institute (BGI)-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Y Xie
- Beijing Genomics Institute (BGI)-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - E J Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - G K S Wong
- Beijing Genomics Institute (BGI)-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - D Wendehenne
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - V Nicolas-Francès
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
| |
Collapse
|
10
|
Stevenson SR, Kamisugi Y, Trinh CH, Schmutz J, Jenkins JW, Grimwood J, Muchero W, Tuskan GA, Rensing SA, Lang D, Reski R, Melkonian M, Rothfels CJ, Li FW, Larsson A, Wong GKS, Edwards TA, Cuming AC. 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. Plant Cell 2016; 28:1310-27. [PMID: 27194706 PMCID: PMC4944411 DOI: 10.1105/tpc.16.00091] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/18/2016] [Accepted: 05/13/2016] [Indexed: 05/19/2023]
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.
Collapse
Affiliation(s)
- Sean R Stevenson
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598 HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Jerry W Jenkins
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598 HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Jane Grimwood
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598 HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Stefan A Rensing
- University of Marburg, Plant Cell Biology, D-35043 Marburg, Germany BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Daniel Lang
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Ralf Reski
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | | | - Carl J Rothfels
- Department of Integrative Biology, University of California, Berkeley California 94720-3140
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Anders Larsson
- Uppsala University, Systematic Biology, 752 36 Uppsala, Sweden
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E1, Canada BGI-Shenzhen, Shenzhen 518083, China
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| |
Collapse
|
11
|
Rothfels CJ, Li FW, Sigel EM, Huiet L, Larsson A, Burge DO, Ruhsam M, Deyholos M, Soltis DE, Stewart CN, Shaw SW, Pokorny L, Chen T, dePamphilis C, DeGironimo L, Chen L, Wei X, Sun X, Korall P, Stevenson DW, Graham SW, Wong GKS, Pryer KM. The evolutionary history of ferns inferred from 25 low-copy nuclear genes. Am J Bot 2015. [PMID: 26199366 DOI: 10.3732/ajb.1500089] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data.• METHODS Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection.• KEY RESULTS Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data.• CONCLUSIONS Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.
Collapse
Affiliation(s)
- Carl J Rothfels
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Erin M Sigel
- Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, P.O. Box 37012 Washington, District of Columbia 20013-7012 USA
| | - Layne Huiet
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Anders Larsson
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden
| | - Dylan O Burge
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California 94118 USA
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK
| | - Michael Deyholos
- Department of Biology, University of British Columbia, Okanagan Campus, 1177 Research Road, Kelowna, British Columbia V1V 1V7, Canada
| | - Douglas E Soltis
- Florida Museum of Natural History, Department of Biology, and the Genetics Institute. University of Florida. Gainesville, Florida 32611 USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA
| | | | - Lisa Pokorny
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico-Consejo Superior de Investigaciones Científicas, 28014 Madrid, Spain
| | - Tao Chen
- Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Claude dePamphilis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 USA
| | - Lisa DeGironimo
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA
| | - Li Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xiaofeng Wei
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xiao Sun
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Petra Korall
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden
| | - Dennis W Stevenson
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA
| | - Sean W Graham
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| |
Collapse
|
12
|
Becker B, Doan JM, Wustman B, Carpenter EJ, Chen L, Zhang Y, Wong GKS, Melkonian M. The Origin and Evolution of the Plant Cell Surface: Algal Integrin-Associated Proteins and a New Family of Integrin-Like Cytoskeleton-ECM Linker Proteins. Genome Biol Evol 2015; 7:1580-9. [PMID: 25977459 PMCID: PMC4494055 DOI: 10.1093/gbe/evv089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The extracellular matrix of scaly green flagellates consists of small organic scales consisting of polysaccharides and scale-associated proteins (SAPs). Molecular phylogenies have shown that these organisms represent the ancestral stock of flagellates from which all green plants (Viridiplantae) evolved. The molecular characterization of four different SAPs is presented. Three SAPs are type-2 membrane proteins with an arginine/alanine-rich short cytoplasmic tail and an extracellular domain that is most likely of bacterial origin. The fourth protein is a filamin-like protein. In addition, we report the presence of proteins similar to the integrin-associated proteins α-actinin (in transcriptomes of glaucophytes and some viridiplants), LIM-domain proteins, and integrin-associated kinase in transcriptomes of viridiplants, glaucophytes, and rhodophytes. We propose that the membrane proteins identified are the predicted linkers between scales and the cytoskeleton. These proteins are present in many green algae but are apparently absent from embryophytes. These proteins represent a new protein family we have termed gralins for green algal integrins. Gralins are absent from embryophytes. A model for the evolution of the cell surface proteins in Plantae is discussed.
Collapse
Affiliation(s)
- Burkhard Becker
- Biozentrum Köln, Botanical Institute, Universität zu Köln, Germany
| | - Jean Michel Doan
- Biozentrum Köln, Botanical Institute, Universität zu Köln, Germany
| | - Brandon Wustman
- Biozentrum Köln, Botanical Institute, Universität zu Köln, Germany
| | - Eric J Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Li Chen
- BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China
| | - Yong Zhang
- BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | | |
Collapse
|
13
|
|
14
|
Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, Yang L, Hawkins S, Neutelings G, Datla R, Lambert G, Galbraith DW, Grassa CJ, Geraldes A, Cronk QC, Cullis C, Dash PK, Kumar PA, Cloutier S, Sharpe AG, Wong GKS, Wang J, Deyholos MK. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J 2012; 72:461-73. [PMID: 22757964 DOI: 10.1111/j.1365-313x.2012.05093.x] [Citation(s) in RCA: 252] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N(50) =694 kb, including contigs with N(50)=20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K(s) ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species.
Collapse
Affiliation(s)
- Zhiwen Wang
- BGI-Shenzen, Bei Shan Industrial Zone, Yantian District, Shenzhen 518083, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Zhang HM, Bacon LD, Heidari M, Muir WM, Groenen MAM, Zhang Y, Wong GKS, Fulton JE, O'Sullivan NP, Albers GAA, Vereijken ALJ, Rattink AP, Okimoto R, McKay JC, McLeod S, Cheng HH. Genetic variation at the tumour virus B locus in commercial and laboratory chicken populations assessed by a medium-throughput or a high-throughput assay. Avian Pathol 2007; 36:283-91. [PMID: 17620174 DOI: 10.1080/03079450701449248] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The tumour virus B (TVB) locus encodes cellular receptors mediating infection by three subgroups of avian leukosis virus (B, D, and E). Three major alleles, TVB*S1, TVB*S3, and TVB*R, have been described. TVB*S1 encodes a cellular receptor mediating infection of subgroups B, D, and E. TVB*S3 encodes the receptor for two subgroups, B and D, and TVB*R encodes a dysfunctional receptor that does not permit infection by any of the subgroups, B, D, or E. Genetic diversity at the TVB locus of chickens was investigated in both layer and broiler commercial pure lines and laboratory lines. Genotyping assays were developed for both medium-throughput and high-throughput analysis. Of the 36 broiler lines sampled, 14 were fixed for the susceptible allele TVB*S1. Across all broiler lines, 83% of chickens were typed as TVB*S1/*S1, 3% as TVB*R/*R, and 14% as TVB*S1/*R. In the egg-layer lines, five of the 16 tested were fixed for TVB*S1/*S1. About 44% of egg-layers were typed as TVB*S1/*S1, 15% as TVB*R/*R, with the rest segregating for two or three of the alleles. In the laboratory chickens, 60% were fixed for TVB*S1/*S1, 6% for TVB*S3/*S3, 14% for TVB*R/*R, and the rest were heterozygotes (TVB*S1/*S3 or TVB*S1/*R). All commercial pure lines examined in this study carry the TVB*S1 allele that sustains the susceptibility to avian leukosis viruses B, D, and E. More importantly, the TVB*R allele was identified in multiple populations, thus upholding the opportunities for genetic improvement through selection.
Collapse
Affiliation(s)
- H M Zhang
- USDA, ARS, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Muzny DM, Scherer SE, Kaul R, Wang J, Yu J, Sudbrak R, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZM, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song XZ, Steffen D, Wei S, Wheeler DA, Wright MW, Worley KC, Yuan Y, Zhang Z, Adams CQ, Ansari-Lari MA, Ayele M, Brown MJ, Chen G, Chen Z, Clendenning J, Clerc-Blankenburg KP, Chen R, Chen Z, Davis C, Delgado O, Dinh HH, Dong W, Draper H, Ernst S, Fu G, Gonzalez-Garay ML, Garcia DK, Gillett W, Gu J, Hao B, Haugen E, Havlak P, He X, Hennig S, Hu S, Huang W, Jackson LR, Jacob LS, Kelly SH, Kube M, Levy R, Li Z, Liu B, Liu J, Liu W, Lu J, Maheshwari M, Nguyen BV, Okwuonu GO, Palmeiri A, Pasternak S, Perez LM, Phelps KA, Plopper FJH, Qiang B, Raymond C, Rodriguez R, Saenphimmachak C, Santibanez J, Shen H, Shen Y, Subramanian S, Tabor PE, Verduzco D, Waldron L, Wang J, Wang J, Wang Q, Williams GA, Wong GKS, Yao Z, Zhang J, Zhang X, Zhao G, Zhou J, Zhou Y, Nelson D, Lehrach H, Reinhardt R, Naylor SL, Yang H, Olson M, Weinstock G, Gibbs RA. The DNA sequence, annotation and analysis of human chromosome 3. Nature 2006; 440:1194-8. [PMID: 16641997 DOI: 10.1038/nature04728] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Accepted: 03/17/2006] [Indexed: 11/09/2022]
Abstract
After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.
Collapse
Affiliation(s)
- Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Qin E, Zhu Q, Yu M, Fan B, Chang G, Si B, Yang B, Peng W, Jiang T, Liu B, Deng Y, Liu H, Zhang Y, Wang C, Li Y, Gan Y, Li X, Lü F, Tan G, Cao W, Yang R, Wang J, Li W, Xu Z, Li Y, Wu Q, Lin W, Chen W, Tang L, Deng Y, Han Y, Li C, Lei M, Li G, Li W, Lü H, Shi J, Tong Z, Zhang F, Li S, Liu B, Liu S, Dong W, Wang J, Wong GKS, Yu J, Yang H. A complete sequence and comparative analysis of a SARS-associated virus (Isolate BJ01). Chin Sci Bull 2003; 48:941-948. [PMID: 32214698 PMCID: PMC7088533 DOI: 10.1007/bf03184203] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2003] [Indexed: 11/01/2022]
Abstract
The genome sequence of the Severe Acute Respiratory Syndrome (SARS)-associated virus provides essential information for the identification of pathogen(s), exploration of etiology and evolution, interpretation of transmission and pathogenesis, development of diagnostics, prevention by future vaccination, and treatment by developing new drugs. We report the complete genome sequence and comparative analysis of an isolate (BJ01) of the coronavirus that has been recognized as a pathogen for SARS. The genome is 29725 nt in size and has 11 ORFs (Open Reading Frames). It is composed of a stable region encoding an RNA-dependent RNA polymerase (composed of 2 ORFs) and a variable region representing 4 CDSs (coding sequences) for viral structural genes (the S, E, M, N proteins) and 5 PUPs (putative uncharacterized proteins). Its gene order is identical to that of other known coronaviruses. The sequence alignment with all known RNA viruses places this virus as a member in the family of Coronaviridae. Thirty putative substitutions have been identified by comparative analysis of the 5 SARS-associated virus genome sequences in GenBank. Fifteen of them lead to possible amino acid changes (non-synonymous mutations) in the proteins. Three amino acid changes, with predicted alteration of physical and chemical features, have been detected in the S protein that is postulated to be involved in the immunoreactions between the virus and its host. Two amino acid changes have been detected in the M protein, which could be related to viral envelope formation. Phylogenetic analysis suggests the possibility of non-human origin of the SARS-associated viruses but provides no evidence that they are man-made. Further efforts should focus on identifying the etiology of the SARS-associated virus and ruling out conclusively the existence of other possible SARS-related pathogen(s).
Collapse
Affiliation(s)
- E’de Qin
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Qingyu Zhu
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Man Yu
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Baochang Fan
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Guohui Chang
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Bingyin Si
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Bao’an Yang
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Wenming Peng
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Tao Jiang
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Bohua Liu
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Yongqiang Deng
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Hong Liu
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Yu Zhang
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Cui’e Wang
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Yuquan Li
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Yonghua Gan
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Xiaoyu Li
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Fushuang Lü
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Gang Tan
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Wuchun Cao
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Ruifu Yang
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, 100071 Beijing, China
| | - Jian Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Wei Li
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Zuyuan Xu
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Yan Li
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Qingfa Wu
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Wei Lin
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Weijun Chen
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Lin Tang
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Yajun Deng
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Yujun Han
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Changfeng Li
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Meng Lei
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Guoqing Li
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Wenjie Li
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Hong Lü
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Jianping Shi
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Zongzhong Tong
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Feng Zhang
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Songgang Li
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Bin Liu
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Siqi Liu
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Wei Dong
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Jun Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Gane K-S Wong
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Jun Yu
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| | - Huanming Yang
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing
- National Center for Genome Information, 101300 Beijing, China
| |
Collapse
|
18
|
Guillaudeux T, Janer M, Bubb K, Wong GKS, Olson MV, Spies T, Geraphty DE. The centromeric end of HLA class I: MCD maps of yac derived cosmids and sequence analysis of 250 KB of genomic DNA. Hum Immunol 1996. [DOI: 10.1016/0198-8859(96)85037-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|