Improved 93-11 Genome and Time-Course Transcriptome Expand Resources for Rice Genomics

Abstract

In 2002, the first crop genome was published using the rice cultivar 93-11, which is the progenitor of the first super-hybrid rice. The genome sequence has served as a reference genome for the indica cultivars, but the assembly has not been updated. In this study, we update the 93-11 genome assembly to a gap-less sequence using ultra-depth single molecule real-time (SMRT) reads, Hi-C sequencing, reference-guided, and gap-closing approach. The differences in the genome collinearity and gene content between the 93-11 and the Nipponbare reference genomes confirmed to map the indica cultivar sequencing data to the 93-11 genome, instead of the reference. Furthermore, time-course transcriptome data showed that the expression pattern was consistently correlated with the stages of seed development. Alternative splicing of starch synthesis-related genes and genomic variations of waxy make it a novel resource for targeted breeding. Collectively, the updated high quality 93-11 genome assembly can improve the understanding of the genome structures and functions of Oryza groups in molecular breeding programs.

Development of genomic and genetic resources facilitating molecular genetic studies on untapped Myanmar rice germplasms

“…In addition, our IMY genome assembly scored a Merqury quality value (QV) of 31.42 and a Merqury k-mer completeness of 96.89. Since a recent publication reported that an improved genome assembly of the indica variety 93-11, which is a well-known high-quality genome assembly, scored a QV of 31.55 (Wang et al 2022), our assembly was of sufficient quality as a high-quality genome assembly.…”

High-quality reference transcriptome construction improves RNA-seq quantification in Oryza sativa indica

“…The quality of the transcriptome annotation could help with fast and accurate estimation of transcript expression and AS events using the RNA-seq data with the help of the 3DRNA-seq tool ( Chaudhary and Kalkal, 2021 ; Guo et al, 2021 ; Vitoriano et al, 2021 ; Escudero-Martinez et al, 2022 ). Despite rice being an important crop plant and several attempts being made in the past to improve its transcriptome annotation and AS diversity, IndicaRTD contains a significantly higher number of transcript isoforms ( Lu et al, 2010 ; Zhang et al, 2010 ; Zhang H. et al, 2019 ; Schaarschmidt et al, 2020 ; Wang S. et al, 2022 ; Hasan et al, 2022 ; He et al, 2022 ). Several single gene studies have identified the role of AS transcript isoforms in the eukaryotic system including the plant system specifically in rice ( Ganie and Reddy, 2021 ; Singh and Ahi, 2022 ; Wright et al, 2022 ).…”

“…Recently, alternative splicing (AS) emerged as one of the key regulatory mechanisms in the eukaryotic system ( Wang S. et al, 2022 ; Wright et al, 2022 ). AS plays a significant role in the development and response to biotic and abiotic stressors in plants and therefore provides key revenue to exploit and increase rice production ( Calixto et al, 2018 ; Filichkin et al, 2018 ; James et al, 2018 ; Laloum et al, 2018 ; Zhang G. et al, 2019 ; Dantas et al, 2019 ; Qin et al, 2020 ).…”

Genetic Diversity and Breeding Signatures for Regional Indica Rice Improvement in Guangdong of Southern China

“…National indica rice sequencing data from RiceVarMap database (Zhao et al 2015 ), variations of 3024 3KRG accession from SNP-seek database (Locedie et al 2017 ) and variations of 998 wild rice lines from our recently research (Zhang et al 2022 ) that used to conduct population structure and phylogenetic analysis in this study were subjected to the same data processing pipeline. A recently released and refined indica 9311 reference genome was also used to check the results of population structure analysis (Wang et al 2022 ).…”