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

Dong Ha Oh, Maheshi Dassanayake, Jeffrey S. Haas, Anna Kropornika, Chris Wright, Matilde Paino d'Urzo, Hyewon Hong, Shahjahan Ali, Alvaro Hernandez, Georgina M. Lambert, Gunsu Inan, David W Galbraith, Ray A. Bressan, Dae Jin Yun, Jian Kang Zhu, John M. Cheeseman, Hans J. Bohnert

Research output: Contribution to journalArticle

66 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1040-1052
Number of pages13
JournalPlant Physiology
Volume154
Issue number3
DOIs
StatePublished - Nov 2010

Fingerprint

Halophila
Arabidopsis
Genome
Gene Expression
gene expression
genome
salts
Salts
Salt-Tolerant Plants
halophytes
bacterial artificial chromosomes
Synteny
pyrimidines
Plant Structures
Bacterial Artificial Chromosomes
5' untranslated regions
Sodium-Hydrogen Antiporter
5' Untranslated Regions
Salinity
stress tolerance

ASJC Scopus subject areas

  • Plant Science
  • Genetics
  • Physiology

Cite this

Genome structures and halophyte-specific gene expression of the extremophile thellungiella parvula in comparison with Thellungiella salsuginea (Thellungiella halophila) and arabidopsis. / Oh, Dong Ha; Dassanayake, Maheshi; Haas, Jeffrey S.; Kropornika, Anna; Wright, Chris; d'Urzo, Matilde Paino; Hong, Hyewon; Ali, Shahjahan; Hernandez, Alvaro; Lambert, Georgina M.; Inan, Gunsu; Galbraith, David W; Bressan, Ray A.; Yun, Dae Jin; Zhu, Jian Kang; Cheeseman, John M.; Bohnert, Hans J.

In: Plant Physiology, Vol. 154, No. 3, 11.2010, p. 1040-1052.

Research output: Contribution to journalArticle

Oh, DH, Dassanayake, M, Haas, JS, Kropornika, A, Wright, C, d'Urzo, MP, Hong, H, Ali, S, Hernandez, A, Lambert, GM, Inan, G, Galbraith, DW, Bressan, RA, Yun, DJ, Zhu, JK, Cheeseman, JM & Bohnert, HJ 2010, 'Genome structures and halophyte-specific gene expression of the extremophile thellungiella parvula in comparison with Thellungiella salsuginea (Thellungiella halophila) and arabidopsis', Plant Physiology, vol. 154, no. 3, pp. 1040-1052. https://doi.org/10.1104/pp.110.163923
Oh, Dong Ha ; Dassanayake, Maheshi ; Haas, Jeffrey S. ; Kropornika, Anna ; Wright, Chris ; d'Urzo, Matilde Paino ; Hong, Hyewon ; Ali, Shahjahan ; Hernandez, Alvaro ; Lambert, Georgina M. ; Inan, Gunsu ; Galbraith, David W ; Bressan, Ray A. ; Yun, Dae Jin ; Zhu, Jian Kang ; Cheeseman, John M. ; Bohnert, Hans J. / Genome structures and halophyte-specific gene expression of the extremophile thellungiella parvula in comparison with Thellungiella salsuginea (Thellungiella halophila) and arabidopsis. In: Plant Physiology. 2010 ; Vol. 154, No. 3. pp. 1040-1052.
@article{b5c2050f3a1344cba7fdfadadc742488,
title = "Genome structures and halophyte-specific gene expression of the extremophile thellungiella parvula in comparison with Thellungiella salsuginea (Thellungiella halophila) and arabidopsis",
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.",
author = "Oh, {Dong Ha} and Maheshi Dassanayake and Haas, {Jeffrey S.} and Anna Kropornika and Chris Wright and d'Urzo, {Matilde Paino} and Hyewon Hong and Shahjahan Ali and Alvaro Hernandez and Lambert, {Georgina M.} and Gunsu Inan and Galbraith, {David W} and Bressan, {Ray A.} and Yun, {Dae Jin} and Zhu, {Jian Kang} and Cheeseman, {John M.} and Bohnert, {Hans J.}",
year = "2010",
month = "11",
doi = "10.1104/pp.110.163923",
language = "English (US)",
volume = "154",
pages = "1040--1052",
journal = "Plant Physiology",
issn = "0032-0889",
publisher = "American Society of Plant Biologists",
number = "3",

}

TY - JOUR

T1 - Genome structures and halophyte-specific gene expression of the extremophile thellungiella parvula in comparison with Thellungiella salsuginea (Thellungiella halophila) and arabidopsis

AU - Oh, Dong Ha

AU - Dassanayake, Maheshi

AU - Haas, Jeffrey S.

AU - Kropornika, Anna

AU - Wright, Chris

AU - d'Urzo, Matilde Paino

AU - Hong, Hyewon

AU - Ali, Shahjahan

AU - Hernandez, Alvaro

AU - Lambert, Georgina M.

AU - Inan, Gunsu

AU - Galbraith, David W

AU - Bressan, Ray A.

AU - Yun, Dae Jin

AU - Zhu, Jian Kang

AU - Cheeseman, John M.

AU - Bohnert, Hans J.

PY - 2010/11

Y1 - 2010/11

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=78249231997&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=78249231997&partnerID=8YFLogxK

U2 - 10.1104/pp.110.163923

DO - 10.1104/pp.110.163923

M3 - Article

C2 - 20833729

AN - SCOPUS:78249231997

VL - 154

SP - 1040

EP - 1052

JO - Plant Physiology

JF - Plant Physiology

SN - 0032-0889

IS - 3

ER -