The chromosome-scale genome assembly of cluster bean provides molecular insight into edible gum (galactomannan) biosynthesis family genes

Abstract

Cluster bean (Cyamopsis tetragonoloba (L.) Taub 2n = 14, is commonly known as Guar. Apart from being a vegetable crop, it is an abundant source of a natural hetero-polysaccharide called guar gum or galactomannan. Here, we are reporting a chromosome-scale reference genome assembly of a popular cluster bean cultivar RGC-936, by combining sequencing data from Illumina, 10X Genomics, Oxford Nanopore technologies. An initial assembly of 1580 scaffolds with an N50 value of 7.12 Mb was generated and these scaffolds were anchored to a high density SNP linkage map. Finally, a genome assembly of 550.31 Mb (94% of the estimated genome size of ~ 580 Mb (through flow cytometry) with 58 scaffolds was obtained, including 7 super scaffolds with a very high N50 value of 78.27 Mb. Phylogenetic analysis using single copy orthologs among 12 angiosperms showed that cluster bean shared a common ancestor with other legumes 80.6 MYA. No evidence of recent whole genome duplication event in cluster bean was found in our analysis. Further comparative transcriptomics analyses revealed pod-specific up-regulation of genes encoding enzymes involved in galactomannan biosynthesis. The high-quality chromosome-scale cluster bean genome assembly will facilitate understanding of the molecular basis of galactomannan biosynthesis and aid in genomics-assisted improvement of cluster bean.

PacBio Full-Length Transcriptome of a Tetraploid Sinocyclocheilus multipunctatus Provides Insights into the Evolution of Cavefish

“…The transcriptome sequences of S. multipunctatus were compared with BLASTP (Evalue < 1 × 10 −5 ) to find conserved paralog sequences to detect polypoidization events in the transcriptome of S. multipunctatus. Protein sequences of Ctenopharyngodon idellus, Cyprinus carpio, Carassius auratus, and three Sinocyclocheilus species were also analyzed and used for comparison using the WGDdetector software (https://github.com/yongzhiyang2 012/wgddetector, accessed on 12 January 2023) [37], which has shown high performance in detecting recent and ancient WGD events; for example, it was applied in the study of WGD events of Lautoconus ventricosus [38], Xenopus laevis [37], and Cyamopsis tetragonoloba [39]. The protein and CDS sequences within each gene family were automatically compared using MAFFT [40] and PAL2NAL [29], and assigned the corresponding Ks values to each pair of similar sequences (gap-stripped comparison length > 90 bp) within each gene family based on the Nei-Gojobori algorithm.…”

Genome Assemblies of Two Ormosia Species: Gene Duplication Related to Their Evolutionary Adaptation

“…Transcription factors function as transcriptional regulation of gene expression, which is crucial to the plant's response to various abiotic and biotic stresses [64,65]. In Astragalus sinicus, functional insight of WGD retained genes showed they were also related to plant hormone signal transduction, accompanied by plant-pathogen interaction [66].…”

“…It has been found that hormones are crucial in the process of nodulation [66]. Therefore, WGD shared by legume species could contribute to the hormonal regulation of nodulation.…”

Predictive Role of Cluster Bean (Cyamopsis tetragonoloba) Derived miRNAs in Human and Cattle Health

“…It is grown in India for vegetable, green manure and seed production. It is also recognized as a medicinal plant and possesses a high quantity of phytochemicals [19,20]. It is commonly used to cure various diseases like ulcer, secretion, hyperglycemia, and cathartic [21].…”