The wild allotetraploid sesame genome provides novel insights into evolution and lignan biosynthesis

Analysing a Group of Homologous BAHD Enzymes Provides Insights into the Evolutionary Transition of Rosmarinic Acid Synthases from Hydroxycinnamoyl-CoA:Shikimate/Quinate Hydroxycinnamoyl Transferases

The interplay of various enzymes and compounds gives rise to the intricate secondary metabolic networks observed today. However, the current understanding of their formation and expansion remains limited. BAHD acyltransferases play important roles in the biosynthesis of numerous significant secondary metabolites. In plants, they are widely distributed and exhibit a diverse range of activities. Among them, rosmarinic acid synthase (RAS) and hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyl transferase (HCT) have gained significant recognition and have been extensively investigated as prominent members of the BAHD acyltransferase family. Here, we conducted a comprehensive study on a unique group of RAS homologous enzymes in Mentha longifolia that display both catalytic activities and molecular features similar to HCT and Lamiaceae RAS. Subsequent phylogenetic and comparative genome analyses revealed their derivation from expansion events within the HCT gene family, indicating their potential as collateral branches along the evolutionary trajectory, leading to Lamiaceae RAS while still retaining certain ancestral vestiges. This discovery provides more detailed insights into the evolution from HCT to RAS. Our collective findings indicate that gene duplication is the driving force behind the observed evolutionary pattern in plant-specialized enzymes, which probably originated from ancestral enzyme promiscuity and were subsequently shaped by principles of biological adaptation.

Genomic evolution and insights into agronomic trait innovations of Sesamum species

Sesame is an ancient oilseed crop with high oil content and quality. However, the evolutionary history and genetic mechanisms of its valuable agronomic traits remain unclear. Here, we report chromosome-scale genomes of cultivated sesame (Sesamum indicum L.) and six wild Sesamum species, representing all three karyotypes within this genus. Karyotyping and genome-based phylogenic analysis revealed the evolutionary route of Sesamum species from n = 13 to n = 16 and revealed that allotetraploidization occurred in the wild species Sesamum radiatum. Early divergence of the Sesamum genus (48.5-19.7 million years ago) during the Tertiary period and its ancient phylogenic position within eudicots were observed. Pan-genome analysis revealed 9164 core gene families in the 7 Sesamum species. These families are significantly enriched in various metabolic pathways, including fatty acid (FA) metabolism and FA biosynthesis. Structural variations in SiPT1 and SiDT1 within the phosphatidyl ethanolamine-binding protein gene family lead to the genomic evolution of plant-architecture and inflorescence-development phenotypes in Sesamum. A genome-wide association study (GWAS) of an interspecific population and genome comparisons revealed a long terminal repeat insertion and a sequence deletion in DIR genes of wild Sesamum angustifolium and cultivated sesame, respectively; both variations independently cause high susceptibility to Fusarium wilt disease. A GWAS of 560 sesame accessions combined with an overexpression study confirmed that the NAC1 and PPO genes play an important role in upregulating oil content of sesame. Our study provides high-quality genomic resources for cultivated and wild Sesamum species and insights that can improve molecular breeding strategies for sesame and other oilseed crops.

A two-sequence motif-based method for the inventory of gene families in fragmented and poorly annotated genome sequences

Databases of genome sequences are growing exponentially, but, in some cases, assembly is incomplete and genes are poorly annotated. For evolutionary studies, it is important to identify all members of a given gene family in a genome. We developed a method for identifying most, if not all, members of a gene family from raw genomes in which assembly is of low quality, using the P-type ATPase superfamily as an example. The method is based on the translation of an entire genome in all six reading frames and the co-occurrence of two family-specific sequence motifs that are in close proximity to each other. To test the method's usability, we first used it to identify P-type ATPase members in the high-quality annotated genome of barley (Hordeum vulgare). Subsequently, after successfully identifying plasma membrane H+-ATPase family members (P3A ATPases) in various plant genomes of varying quality, we tested the hypothesis that the number of P3A ATPases correlates with the ability of the plant to tolerate saline conditions. In 19 genomes of glycophytes and halophytes, the total number of P3A ATPase genes was found to vary from 7 to 22, but no significant difference was found between the two groups. The method successfully identified P-type ATPase family members in raw genomes that are poorly assembled.

Origin, evolution, and diversification of the wall-associated kinase gene family in plants

KEY MESSAGE

The study of the origin, evolution, and diversification of the wall-associated kinase gene family in plants facilitates their functional investigations in the future. Wall-associated kinases (WAKs) make up one subfamily of receptor-like kinases (RLKs), and function directly in plant cell elongation and responses to biotic and abiotic stresses. The biological functions of WAKs have been extensively characterized in angiosperms; however, the origin and evolutionary history of the WAK family in green plants remain unclear. Here, we performed a comprehensive analysis of the WAK family to reveal its origin, evolution, and diversification in green plants. In total, 1061 WAK genes were identified in 37 species from unicellular algae to multicellular plants, and the results showed that WAK genes probably originated before bryophyte differentiation and were widely distributed in land plants, especially angiosperms. The phylogeny indicated that the land plant WAKs gave rise to five clades and underwent lineage-specific expansion after species differentiation. Cis-acting elements and expression patterns analyses of WAK genes in Arabidopsis and rice demonstrated the functional diversity of WAK genes in these two species. Many gene gains and losses have occurred in angiosperms, leading to an increase in the number of gene copies. The evolutionary trajectory of the WAK family during polyploidization was uncovered using Gossypium species. Our results provide insights into the evolution of WAK genes in green plants, facilitating their functional investigations in the future.

QTL analysis of traits related to seed size and shape in sesame (Sesamum indicum L.)

Seed size and shape are important traits that determine seed yield in sesame. Understanding the genetic basis of seed size and shape is essential for improving the yield of sesame. In this study, F2 and BC1 populations were developed by crossing the Yuzhi 4 and Bengal small-seed (BS) lines for detecting the quantitative trait loci (QTLs) of traits related to seed size and shape. A total of 52 QTLs, including 13 in F2 and 39 in BC1 populations, for seed length (SL), seed width (SW), and length to width ratio (L/W) were identified, explaining phenotypic variations from 3.68 to 21.64%. Of these QTLs, nine stable major QTLs were identified in the two populations. Notably, three major QTLs qSL-LG3-2, qSW-LG3-2, and qSW-LG3-F2 that accounted for 4.94-16.34% of the phenotypic variations were co-localized in a 2.08 Mb interval on chromosome 1 (chr1) with 279 candidate genes. Three stable major QTLs qSL-LG6-2, qLW-LG6, and qLW-LG6-F2 that explained 8.14-33.74% of the phenotypic variations were co-localized in a 3.27 Mb region on chr9 with 398 candidate genes. In addition, the stable major QTL qSL-LG5 was co-localized with minor QTLs qLW-LG5-3 and qSW-LG5 to a 1.82 Mb region on chr3 with 195 candidate genes. Gene annotation, orthologous gene analysis, and sequence analysis indicated that three genes are likely involved in sesame seed development. These results obtained herein provide valuable in-formation for functional gene cloning and improving the seed yield of sesame.

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

Sesame is one of the important traditional oil crops in the world, and has high economic and nutritional value. Recently, due to the novel high throughput sequencing techniques and bioinformatical methods, the study of the genomics, methylomics, transcriptomics, proteomics and metabonomics of sesame has developed rapidly. Thus far, the genomes of five sesame accessions have been released, including white and black seed sesame. The genome studies reveal the function and structure of the sesame genome, and facilitate the exploitation of molecular markers, the construction of genetic maps and the study of pan-genomes. Methylomics focus on the study of the molecular level changes under different environmental conditions. Transcriptomics provide a powerful tool to study abiotic/biotic stress, organ development, and noncoding RNAs, and proteomics and metabonomics also provide some support in studying abiotic stress and important traits. In addition, the opportunities and challenges of multi-omics in sesame genetics breeding were also described. This review summarizes the current research status of sesame from the perspectives of multi-omics and hopes to provide help for further in-depth research on sesame.

Resequencing of 410 Sesame Accessions Identifies SINST1 as the Major Underlying Gene for Lignans Variation

Sesame is a promising oilseed crop that produces specific lignans of clinical importance. Hence, a molecular description of the regulatory mechanisms of lignan biosynthesis is essential for crop improvement. Here, we resequence 410 sesame accessions and identify 5.38 and 1.16 million SNPs (single nucleotide polymorphisms) and InDels, respectively. Population genomic analyses reveal that sesame has evolved a geographic pattern categorized into northern (NC), middle (MC), and southern (SC) groups, with potential origin in the southern region and subsequent introduction to the other regions. Selective sweeps analysis uncovers 120 and 75 significant selected genomic regions in MC and NC groups, respectively. By screening these genomic regions, we unveiled 184 common genes positively selected in these subpopulations for exploitation in sesame improvement. Genome-wide association study identifies 17 and 72 SNP loci for sesamin and sesamolin variation, respectively, and 11 candidate causative genes. The major pleiotropic SNP^C/A locus for lignans variation is located in the exon of the gene SiNST1. Further analyses revealed that this locus was positively selected in higher lignan content sesame accessions, and the "C" allele is favorable for a higher accumulation of lignans. Overexpression of SiNST1^C in sesame hairy roots significantly up-regulated the expression of SiMYB58, SiMYB209, SiMYB134, SiMYB276, and most of the monolignol biosynthetic genes. Consequently, the lignans content was significantly increased, and the lignin content was slightly increased. Our findings provide insights into lignans and lignin regulation in sesame and will facilitate molecular breeding of elite varieties and marker-traits association studies.