The genome of the extremophile crucifer Thellungiella parvula

• Published in: Nature genetics Vol. 43; no. 9; pp. 913 - 918
• Main Authors: Dassanayake, Maheshi, Oh, Dong-Ha, Haas, Jeffrey S, Hernandez, Alvaro, Hong, Hyewon, Ali, Shahjahan, Yun, Dae-Jin, Bressan, Ray A, Zhu, Jian-Kang, Bohnert, Hans J, Cheeseman, John M
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.09.2011; Nature Publishing Group
• Subjects: 631/181/2474; 631/208/212/748; 631/449/2661; Agriculture; Animal Genetics and Genomics; Arabidopsis thaliana; Bacteria; Base Sequence; Biological and medical sciences; Biomedical and Life Sciences; Biomedicine; Brassicaceae - genetics; Cancer Research; Chromosomes; Chromosomes, Plant - genetics; Colleges & universities; Environmental stress; Evolution; Fundamental and applied biological sciences. Psychology; Gene Function; Genetics; Genetics of eukaryotes. Biological and molecular evolution; Genome, Plant; Genomes; Genomics; Human Genetics; letter; Molecular Sequence Data; Physiological aspects; Plants; Rural development; Salinity; Stress, Physiological - genetics; Tandem Repeat Sequences; Thellungiella; United States; Genome
• ISSN: 1061-4036; 1546-1718; 1546-1718
• DOI: 10.1038/ng.889

Dong-Ha Oh and colleagues report the draft genome of the extremophile crucifer plant Thellungiella parvula . This species is endemic to highly saline environments subject to extreme temperatures. The genome was primarily assembled using next-generation sequencing data. Thellungiella parvula 1 is related to Arabidopsis thaliana and is endemic to saline, resource-poor habitats 2 , 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.