Abstract
Oryza coarctata plants, collected from Sundarban delta of West Bengal, India, have been used in the present study to generate draft genome sequences, employing the hybrid genome assembly with Illumina reads and third generation Oxford Nanopore sequencing technology. We report for the first time that more than 85.71 % of the genome coverage and the data have been deposited in NCBI SRA, with BioProject ID PRJNA396417.
Highlights
Soil salinity is a major abiotic stress of rice cultivation globally (Molla et al, 2015), and rice cultivation areas under soil salinity stress are increasing gradually
To determine the genome size, 20 mg of young leaf tissue from Net house grown plants was chopped into small pieces and stained with RNase containing propidium iodide (50 μg/ml) (BD Science, India) as per the protocol of Dolezel et al (2007)
The genome (KKLL) of O. coarctata is tetraploid (2n=4X=48) with a genome size estimated by flow cytometer is found to be approximately 665Mb
Summary
Soil salinity is a major abiotic stress of rice cultivation globally (Molla et al, 2015), and rice cultivation areas under soil salinity stress are increasing gradually. Genetic potential for salt tolerance of rice that exists among the natural population has been largely exploited, and alternative useful alleles may further enhance salinity tolerance. Wild species are a potential source of many useful genes and QTLs that may not be present in the gene pool of the domesticated species. Known as Asian wild rice, grows naturally in the coastal region of South-East Asian countries. It flowers and set seeds under as high as 40 E.Ce dS m-1 saline soil (Bal & Dutt, 1986). It is the only species in the genus Oryza that is halophyte in nature. With the exception of one transcriptomic (Garg et al, 2014) and one miRNA (Mondal et al, 2014) experiment, no large scale generation of any other genomic resource is available for this important species, several pinitol biosynthesis pathway genes have been cloned to study the functional genomics (Sengupta & Majumder, 2009)
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