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.

Figure 1

The cluster bean genome features. (A) Circular representation of the 7 pseudomolecules; (B) Genome wide distribution of protein coding genes; (C) Genome wide distribution of Retrotransposons; (D) Genome wide distribution of DNA elements; (E) Genome wide distribution of SSRs; (F) Distribution of syntenic regions in cluster bean genome.

Figure 2

The LAI evaluation of the genome assembly of Cluster bean and seven other plant species including four grain legumes (Chickpea, Mungbean, Pigeonpea, and Soybean), two model plants (Arabidopsis, Medicago) along with a gold standard genome assembly of Rice.

Figure 3

Gene family analysis of predicted cluster bean genes in comparison to major crop and model plant genomes and phylogenetic analysis of the same with 51 common Orthologs and the number of gene families experienced gene expansion (Green), Gene loss (Red), and Gene retained (Blue).

Figure 4

(a) Frequency distributions of synonymous substitution rates (Ks) between paralogous genes of Cluster bean (Cyamopsis tetragonoloba), Vigna radiata, Phaseolus vulgaris, Medicago truncatula, Glycine max, Cicer arietinum, Cajanus cajan, and Arabidopsis thaliana. (b) Enrichment analysis of genes retained after the ancient WGD of Cluster bean genome.

Figure 5

Evolution of legume genomes. Reconstructed ancestral genomes (A1-A10) and genomes of selected legumes are represented in a tree lay out and colour of the chromosomal segments are linked to source chromosome in the ancestral genome.

Figure 6

Transcriptome analysis of six cluster bean tissues (Shoot, Leaf, Flower, Pod_25_DAF, Pod_39_DAF, and Pod_50_DAF). (a) Violin plot showing transcript abundance in six cluster bean tissues. (b) Schematic representation of galactomannan biosynthesis pathway. (c) Heat map showing expression pattern of some of the genes involved in galactomannan biosynthesis among six cluster bean tissues.