Improved assembly and annotation of the sesame genome

Abstract

Sesame (Sesamum indicum L.) is an important oilseed crop that produces abundant seed oil and has a pleasant flavor and high nutritional value. To date, several Illumina-based genome assemblies corresponding to different sesame genotypes have been published and widely used in genetic and genomic studies of sesame. However, these assemblies consistently showed low continuity with numerous gaps. Here, we reported a high-quality, reference-level sesame genome assembly by integrating PacBio high-fidelity sequencing and Hi-C technology. Our updated sesame assembly was 309.35 Mb in size with a high chromosome anchoring rate (97.54%) and contig N50 size (13.48 Mb), which were better than previously published genomes. We identified 163.38 Mb repetitive elements and 24,345 high-confidence protein-coding genes in the updated sesame assembly. Comparative genomic analysis showed that sesame shared an ancient whole-genome duplication event with two Lamiales species. A total of 2,782 genes were tandemly duplicated. We also identified several genes that were likely involved in fatty acid and triacylglycerol biosynthesis. Our improved sesame assembly and annotation will facilitate future genetic studies and genomics-assisted breeding of sesame.

Chromosome-Level Genome Assembly of Herpetospermum pedunculosum (Cucurbitaceae)

“…Four ncRNAs, including tRNAs, miRNAs, rRNAs, and snRNAs, were annotated as previously outlined by Wang et al (2022) . The tRNAs were predicted using tRNAscan-SE v1.4, while snRNAs and miRNAs were predicted using the cmsearch program in Infernal v1.1.3 ( Nawrocki and Eddy 2013 ) based on the Rfam database.…”

Current Progress, Applications and Challenges of Multi-Omics Approaches in Sesame Genetic Improvement

“…Baizhima and Mishuozhima [ 6 ], whose assembled genomes were 267 Mb and 254 Mb, respectively. There were two other sesames, Baizhima and Xiaozihei, assembled in this year, and the genomes were 309 and 305 Mb, respectively [ 7 , 8 ]. The above sequenced genomes could help one to deeply understand the genetic basis of sesame diversity, and also provide a large number of genes and variation profiles related to important traits and environmental adaptation, and promote the progress of sesame at a molecular level.…”

Applications of Molecular Markers for Developing Abiotic-Stress-Resilient Oilseed Crops

“…More recent advances involving expressed sequence tags (ESTs) also aided genome annotation and could further boost the molecular breeding program. Decent attempts that have been made in the genome sequencing of major oilseeds, such as sesame [ 158 , 159 ], safflower [ 160 , 161 ], rapeseed [ 162 ], mustard [ 163 ], sunflower [ 164 , 165 ], castor [ 166 , 167 ], flax seed [ 168 ], and peanut [ 169 ], have revolutionized the development of advanced co-dominant markers, such as SSR and SNPs, for the molecular mapping of abiotic resilience in oilseed crops. Soybean was sequenced through advanced high throughput technology in 2010 [ 170 ], and much progress has been made in this oilseed crop relevant to molecular breeding program for the achievement of abiotic stress tolerance and has been fairly covered in a review by Arya et al [ 45 ].…”