Genome structures and halophyte-specific gene expression of the extremophile thellungiella parvula in comparison with Thellungiella salsuginea (Thellungiella halophila) and arabidopsis

Handle URI:
http://hdl.handle.net/10754/561564
Title:
Genome structures and halophyte-specific gene expression of the extremophile thellungiella parvula in comparison with Thellungiella salsuginea (Thellungiella halophila) and arabidopsis
Authors:
Oh, Dongha; Dassanayake, Maheshi; Haas, Jeffrey S.; Kropornika, Anna; Wright, Chris L.; D'Urzo, Matilde Paino; Hong, Hyewon; Ali, Shahjahan; Hernández, Álvaro Gonzalez; Lambert, Georgina M.; Inan, Günsu; Galbraith, David; Bressan, Ray Anthony; Yun, Daejin; Zhu, Jian-Kang; Cheeseman, John McP; Bohnert, Hans Jürgen
Abstract:
The genome of Thellungiella parvula, a halophytic relative of Arabidopsis (Arabidopsis thaliana), is being assembled using Roche-454 sequencing. Analyses of a 10-Mb scaffold revealed synteny with Arabidopsis, with recombination and inversion and an uneven distribution of repeat sequences. T. parvula genome structure and DNA sequences were compared with orthologous regions from Arabidopsis and publicly available bacterial artificial chromosome sequences from Thellungiella salsuginea (previously Thellungiella halophila). The three-way comparison of sequences, from one abiotic stress-sensitive species and two tolerant species, revealed extensive sequence conservation and microcolinearity, but grouping Thellungiella species separately from Arabidopsis. However, the T. parvula segments are distinguished from their T. salsuginea counterparts by a pronounced paucity of repeat sequences, resulting in a 30% shorter DNA segment with essentially the same gene content in T. parvula. Among the genes is SALT OVERLY SENSITIVE1 (SOS1), a sodium/proton antiporter, which represents an essential component of plant salinity stress tolerance. Although the SOS1 coding region is highly conserved among all three species, the promoter regions show conservation only between the two Thellungiella species. Comparative transcript analyses revealed higher levels of basal as well as salt-induced SOS1 expression in both Thellungiella species as compared with Arabidopsis. The Thellungiella species and other halophytes share conserved pyrimidine-rich 5' untranslated region proximal regions of SOS1 that are missing in Arabidopsis. Completion of the genome structure of T. parvula is expected to highlight distinctive genetic elements underlying the extremophile lifestyle of this species. © American Society of Plant Biologists.
KAUST Department:
Center for Desert Agriculture; Core Labs; Biological and Environmental Sciences and Engineering (BESE) Division
Publisher:
American Society of Plant Biologists (ASPB)
Journal:
PLANT PHYSIOLOGY
Issue Date:
10-Sep-2010
DOI:
10.1104/pp.110.163923
PubMed ID:
20833729
PubMed Central ID:
PMC2971586
Type:
Article
ISSN:
00320889
Sponsors:
This work was supported by King Abdullah University for Science and Technology of Saudi Arabia, by the World Class University Program, Korea (grant no. R32-10148), by the Biogreen 21 Project of the Rural Development Administration, Korea (grant no. 20070301034030), and by University of Illinois at Urbana-Champaign institutional support.
Additional Links:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2971586
Appears in Collections:
Articles; Center for Desert Agriculture; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorOh, Donghaen
dc.contributor.authorDassanayake, Maheshien
dc.contributor.authorHaas, Jeffrey S.en
dc.contributor.authorKropornika, Annaen
dc.contributor.authorWright, Chris L.en
dc.contributor.authorD'Urzo, Matilde Painoen
dc.contributor.authorHong, Hyewonen
dc.contributor.authorAli, Shahjahanen
dc.contributor.authorHernández, Álvaro Gonzalezen
dc.contributor.authorLambert, Georgina M.en
dc.contributor.authorInan, Günsuen
dc.contributor.authorGalbraith, Daviden
dc.contributor.authorBressan, Ray Anthonyen
dc.contributor.authorYun, Daejinen
dc.contributor.authorZhu, Jian-Kangen
dc.contributor.authorCheeseman, John McPen
dc.contributor.authorBohnert, Hans Jürgenen
dc.date.accessioned2015-08-02T09:14:19Zen
dc.date.available2015-08-02T09:14:19Zen
dc.date.issued2010-09-10en
dc.identifier.issn00320889en
dc.identifier.pmid20833729en
dc.identifier.doi10.1104/pp.110.163923en
dc.identifier.urihttp://hdl.handle.net/10754/561564en
dc.description.abstractThe genome of Thellungiella parvula, a halophytic relative of Arabidopsis (Arabidopsis thaliana), is being assembled using Roche-454 sequencing. Analyses of a 10-Mb scaffold revealed synteny with Arabidopsis, with recombination and inversion and an uneven distribution of repeat sequences. T. parvula genome structure and DNA sequences were compared with orthologous regions from Arabidopsis and publicly available bacterial artificial chromosome sequences from Thellungiella salsuginea (previously Thellungiella halophila). The three-way comparison of sequences, from one abiotic stress-sensitive species and two tolerant species, revealed extensive sequence conservation and microcolinearity, but grouping Thellungiella species separately from Arabidopsis. However, the T. parvula segments are distinguished from their T. salsuginea counterparts by a pronounced paucity of repeat sequences, resulting in a 30% shorter DNA segment with essentially the same gene content in T. parvula. Among the genes is SALT OVERLY SENSITIVE1 (SOS1), a sodium/proton antiporter, which represents an essential component of plant salinity stress tolerance. Although the SOS1 coding region is highly conserved among all three species, the promoter regions show conservation only between the two Thellungiella species. Comparative transcript analyses revealed higher levels of basal as well as salt-induced SOS1 expression in both Thellungiella species as compared with Arabidopsis. The Thellungiella species and other halophytes share conserved pyrimidine-rich 5' untranslated region proximal regions of SOS1 that are missing in Arabidopsis. Completion of the genome structure of T. parvula is expected to highlight distinctive genetic elements underlying the extremophile lifestyle of this species. © American Society of Plant Biologists.en
dc.description.sponsorshipThis work was supported by King Abdullah University for Science and Technology of Saudi Arabia, by the World Class University Program, Korea (grant no. R32-10148), by the Biogreen 21 Project of the Rural Development Administration, Korea (grant no. 20070301034030), and by University of Illinois at Urbana-Champaign institutional support.en
dc.publisherAmerican Society of Plant Biologists (ASPB)en
dc.relation.urlhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC2971586en
dc.titleGenome structures and halophyte-specific gene expression of the extremophile thellungiella parvula in comparison with Thellungiella salsuginea (Thellungiella halophila) and arabidopsisen
dc.typeArticleen
dc.contributor.departmentCenter for Desert Agricultureen
dc.contributor.departmentCore Labsen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalPLANT PHYSIOLOGYen
dc.identifier.pmcidPMC2971586en
dc.contributor.institutionDepartment of Plant Biology, University of Illinois, Urbana, IL 61801, United Statesen
dc.contributor.institutionOffice of Networked Information Technology, School of Integrative Biology, University of Illinois, Urbana, IL 61801, United Statesen
dc.contributor.institutionCenter for Comparative and Functional Genomics, University of Illinois, Urbana, IL 61801, United Statesen
dc.contributor.institutionDepartment of Crop Sciences, University of Illinois, Urbana, IL 61801, United Statesen
dc.contributor.institutionDivision of Applied Life Science, Gyeongsang National University, Jinju 660-701, South Koreaen
dc.contributor.institutionDepartment of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, United Statesen
dc.contributor.institutionDepartment of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, AZ 85721, United Statesen
dc.contributor.institutionDepartment of Botany and Plant Sciences, University of California, Riverside, CA 92521, United Statesen
kaust.authorAli, Shahjahanen
kaust.authorBressan, Ray Anthonyen
kaust.authorZhu, Jian-Kangen
kaust.authorBohnert, Hans Jürgenen

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