Indica rice genome assembly, annotation and mining of blast disease resistance genes

Abstract

BackgroundRice is a major staple food crop in the world. Over 80 % of rice cultivation area is under indica rice. Currently, genomic resources are lacking for indica as compared to japonica rice. In this study, we generated deep-sequencing data (Illumina and Pacific Biosciences sequencing) for one of the indica rice cultivars, HR-12 from India.ResultsWe assembled over 86 % (389 Mb) of rice genome and annotated 56,284 protein-coding genes from HR-12 genome using Illumina and PacBio sequencing. Comprehensive comparative analyses between indica and japonica subspecies genomes revealed a large number of indica specific variants including SSRs, SNPs and InDels. To mine disease resistance genes, we sequenced few indica rice cultivars that are reported to be highly resistant (Tetep and Tadukan) and susceptible (HR-12 and Co-39) against blast fungal isolates in many countries including India. Whole genome sequencing of rice genotypes revealed high rate of mutations in defense related genes (NB-ARC, LRR and PK domains) in resistant cultivars as compared to susceptible. This study has identified R-genes Pi-ta and Pi54 from durable indica resistant cultivars; Tetep and Tadukan, which can be used in marker assisted selection in rice breeding program.ConclusionsThis is the first report of whole genome sequencing approach to characterize Indian rice germplasm. The genomic resources from our work will have a greater impact in understanding global rice diversity, genetics and molecular breeding.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2523-7) contains supplementary material, which is available to authorized users.

Genome and Transcriptome sequence of Finger millet (Eleusine coracana (L.) Gaertn.) provides insights into drought tolerance and nutraceutical properties

“…Blast pathogen attacks the plant at three different plant growth stages viz., seedling, finger and neck [78]. The estimated yield loss due to blast is around 28%, but under favorable condition it may be up to 80–90% [79–81]. So far, no resistance genes (R-genes) have been mapped in finger millet except few recent studies [82, 83].…”

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

“…A complete list of identified TEs, their integrity and copy number can be found in Supplementary Table 3. 13 Li et al 33 Velasco et al 6 Sequenced genome size (Mb) 643. …”

“…Recently, several high-quality genome assemblies have been published using one or both technologies [9][10][11][12][13][14] . The use of long-read sequencing technologies may also tackle potential assembly issues that are related to the presence of highly similar sequences resulting from whole-genome duplication events that frequently occurred in angiosperm genomes 15 .…”

Development of a goosegrass (Eleusine indica) draft genome and application to weed science research

“…Repetitive DNA can affect genetic diversity, gene duplication, and genome stability . A total of 104,378,430 bp (21.9% of the draft genome) of repetitive DNA was identified in the goosegrass genome.…”

“…Repetitive DNA can affect genetic diversity, gene duplication, and genome stability. 35 A total of 104,378,430 bp (21.9% of the draft genome) of repetitive DNA was identified in the goosegrass genome. Retrotransposon elements were the largest mobile elements found in the genome (15.4%), of which most were long terminal repeat-type (LTR) retroelements (13.8%), followed by long interspersed nuclear elements (LINEs) (1.4%) and short interspersed nuclear elements (SINEs) (0.2%).…”