The genome of the extremophile crucifer Thellungiella parvula

Handle URI:
http://hdl.handle.net/10754/561836
Title:
The genome of the extremophile crucifer Thellungiella parvula
Authors:
Dassanayake, Maheshi; Oh, Dongha; Haas, Jeffrey S.; Hernández, Álvaro Gonzalez; Hong, Hyewon; Ali, Shahjahan; Yun, Daejin; Bressan, Ray Anthony; Zhu, Jian-Kang; Bohnert, Hans Jürgen; Cheeseman, John McP
Abstract:
Thellungiella parvula is related to Arabidopsis thaliana and is endemic to saline, resource-poor habitats, making it a model for the evolution of plant adaptation to extreme environments. Here we present the draft genome for this extremophile species. Exclusively by next generation sequencing, we obtained the de novo assembled genome in 1,496 gap-free contigs, closely approximating the estimated genome size of 140 Mb. We anchored these contigs to seven pseudo chromosomes without the use of maps. We show that short reads can be assembled to a near-complete chromosome level for a eukaryotic species lacking prior genetic information. The sequence identifies a number of tandem duplications that, by the nature of the duplicated genes, suggest a possible basis for T. parvula's extremophile lifestyle. Our results provide essential background for developing genomically influenced testable hypotheses for the evolution of environmental stress tolerance. © 2011 Nature America, Inc. All rights reserved.
KAUST Department:
Biosciences Core Lab; Center for Desert Agriculture; Core Labs; Biological and Environmental Sciences and Engineering (BESE) Division
Publisher:
Springer Nature
Journal:
Nature Genetics
Issue Date:
7-Aug-2011
DOI:
10.1038/ng.889
PubMed ID:
21822265
PubMed Central ID:
PMC3586812
Type:
Article
ISSN:
10614036
Sponsors:
We thank M. P. D'Urzo (Purdue University, West Lafayette, Indiana, USA) for providing plant materials and J.-H. Mun (National Academy of Agricultural Science, Suwon, Korea) for providing the B. rapa chromosome sequence. We also gratefully acknowledge M. Vaughn (University of Texas, Austin, Texas, USA), S. Jackman, M. Krzywinski (Michael Smith Genome Sciences Center, Vancouver, British Columbia, Canada) and SeqAnswers online forum (see URLs) for advice on genome assembly and visualization. Funding has been provided by King Abdullah University of Science and Technology, Thuwal, Saudi Arabia, by the World Class by recording the numbers of genes included or not included in a subcategory for each species and ranking the statistical significance of the differences.
Additional Links:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586812
Appears in Collections:
Articles; Biosciences Core Lab; Center for Desert Agriculture; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorDassanayake, Maheshien
dc.contributor.authorOh, Donghaen
dc.contributor.authorHaas, Jeffrey S.en
dc.contributor.authorHernández, Álvaro Gonzalezen
dc.contributor.authorHong, Hyewonen
dc.contributor.authorAli, Shahjahanen
dc.contributor.authorYun, Daejinen
dc.contributor.authorBressan, Ray Anthonyen
dc.contributor.authorZhu, Jian-Kangen
dc.contributor.authorBohnert, Hans Jürgenen
dc.contributor.authorCheeseman, John McPen
dc.date.accessioned2015-08-03T09:32:04Zen
dc.date.available2015-08-03T09:32:04Zen
dc.date.issued2011-08-07en
dc.identifier.issn10614036en
dc.identifier.pmid21822265en
dc.identifier.doi10.1038/ng.889en
dc.identifier.urihttp://hdl.handle.net/10754/561836en
dc.description.abstractThellungiella parvula is related to Arabidopsis thaliana and is endemic to saline, resource-poor habitats, making it a model for the evolution of plant adaptation to extreme environments. Here we present the draft genome for this extremophile species. Exclusively by next generation sequencing, we obtained the de novo assembled genome in 1,496 gap-free contigs, closely approximating the estimated genome size of 140 Mb. We anchored these contigs to seven pseudo chromosomes without the use of maps. We show that short reads can be assembled to a near-complete chromosome level for a eukaryotic species lacking prior genetic information. The sequence identifies a number of tandem duplications that, by the nature of the duplicated genes, suggest a possible basis for T. parvula's extremophile lifestyle. Our results provide essential background for developing genomically influenced testable hypotheses for the evolution of environmental stress tolerance. © 2011 Nature America, Inc. All rights reserved.en
dc.description.sponsorshipWe thank M. P. D'Urzo (Purdue University, West Lafayette, Indiana, USA) for providing plant materials and J.-H. Mun (National Academy of Agricultural Science, Suwon, Korea) for providing the B. rapa chromosome sequence. We also gratefully acknowledge M. Vaughn (University of Texas, Austin, Texas, USA), S. Jackman, M. Krzywinski (Michael Smith Genome Sciences Center, Vancouver, British Columbia, Canada) and SeqAnswers online forum (see URLs) for advice on genome assembly and visualization. Funding has been provided by King Abdullah University of Science and Technology, Thuwal, Saudi Arabia, by the World Class by recording the numbers of genes included or not included in a subcategory for each species and ranking the statistical significance of the differences.en
dc.publisherSpringer Natureen
dc.relation.urlhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586812en
dc.titleThe genome of the extremophile crucifer Thellungiella parvulaen
dc.typeArticleen
dc.contributor.departmentBiosciences Core Laben
dc.contributor.departmentCenter for Desert Agricultureen
dc.contributor.departmentCore Labsen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalNature Geneticsen
dc.identifier.pmcidPMC3586812en
dc.contributor.institutionDepartment of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United Statesen
dc.contributor.institutionOffice of Networked Information Technology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United Statesen
dc.contributor.institutionCenter for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, IL, United Statesen
dc.contributor.institutionDivision of Applied Life Science, BK21 Program, Gyeongsang National University, Jinju, South Koreaen
dc.contributor.institutionDepartment of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United Statesen
dc.contributor.institutionDepartment of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United Statesen
kaust.authorAli, Shahjahanen
kaust.authorBressan, Ray Anthonyen
kaust.authorZhu, Jian-Kangen
kaust.authorBohnert, Hans Jürgenen

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