De novo genome assembly of the deepwater rice (Oryza sativa) cultivar Pin Gaew 56
TL;DR
A de novo whole-genome assembly of the deepwater rice cultivar PG56 was generated to support genomic studies of the submergence escape response and provides a useful genomic resource for investigating the genetic mechanisms underlying internode elongation and flooding adaptation in deepwater rice.
Abstract
We present the de novo whole-genome assembly of a deepwater rice variety (Oryza sativa cv. Pin Gaew 56). Although the submergence escape response is a vital survival strategy in deepwater rice, current reference genomes lack sufficient genetic information to fully understand the molecular mechanisms behind this complex physiological process. Pin Gaew 56 (PG56) is a well-studied genetic resource with extensively documented physiological and molecular traits related to internode elongation under partial submergence. This study provides a cultivar-specific genomic resource for PG56 that can support further investigation of the genetic basis of the submergence escape response. A de novo whole-genome assembly of the deepwater rice cultivar PG56 was generated to support genomic studies of the submergence escape response. The final assembly has a total length of 407.7 Mb, comprising 138 scaffolds with an N50 of 32.5 Mb. Genome completeness assessed by BUSCO showed 94.5% complete BUSCOs, and continuity in LTR-rich regions was supported by an LTR Assembly Index of 28.2. Assembly quality was further supported by k-mer-based quality assessment and whole-genome synteny alignment against the MH63 reference genome. Together, these data provide a useful genomic resource for investigating the genetic mechanisms underlying internode elongation and flooding adaptation in deepwater rice.