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菜豆染色体水平基因组组装为食用胶（半乳甘露聚糖）生物合成家族基因提供了分子见解。

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

机构信息

ICAR-National Institute for Plant Biotechnology, New Delhi, India.

ICAR-Central Arid Zone Research Institute, Jodhpur, India.

出版信息

Sci Rep. 2023 Jun 19;13(1):9941. doi: 10.1038/s41598-023-33762-3.

DOI:10.1038/s41598-023-33762-3
PMID:37336893
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10279686/
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.

摘要

兵豆（Cyamopsis tetragonoloba (L.) Taub 2n = 14，俗称瓜尔豆。除了作为一种蔬菜作物外，它还是一种丰富的天然杂多糖来源，称为瓜尔胶或半乳甘露聚糖。在这里，我们通过整合来自 Illumina、10X Genomics 和 Oxford Nanopore 技术的测序数据，报告了一种流行的兵豆品种 RGC-936 的染色体规模参考基因组组装。最初生成了 1580 个具有 7.12 Mb N50 值的支架的组装，这些支架被锚定到高密度 SNP 连锁图谱上。最后，获得了 550.31 Mb 的基因组组装（估计基因组大小的 94%，通过流式细胞术为 580 Mb），包括 58 个支架，其中 7 个超级支架的 N50 值非常高，为 78.27 Mb。在 12 个被子植物中单拷贝直系同源物的系统发育分析表明，兵豆与其他豆科植物在 80.6 MYA 有共同的祖先。在我们的分析中，没有发现兵豆最近发生全基因组复制事件的证据。进一步的比较转录组学分析表明，半乳甘露聚糖生物合成相关酶编码基因在豆荚中特异性上调。高质量的兵豆染色体规模基因组组装将有助于理解半乳甘露聚糖生物合成的分子基础，并有助于兵豆的基因组辅助改良。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf35/10279686/9ce48de0f863/41598_2023_33762_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf35/10279686/6b3318fed360/41598_2023_33762_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf35/10279686/71eef6e2ac90/41598_2023_33762_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf35/10279686/1c5b2fda27a3/41598_2023_33762_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf35/10279686/91b75f53df6d/41598_2023_33762_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf35/10279686/a7f62938fa1c/41598_2023_33762_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf35/10279686/9ce48de0f863/41598_2023_33762_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf35/10279686/6b3318fed360/41598_2023_33762_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf35/10279686/71eef6e2ac90/41598_2023_33762_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf35/10279686/1c5b2fda27a3/41598_2023_33762_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf35/10279686/91b75f53df6d/41598_2023_33762_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf35/10279686/a7f62938fa1c/41598_2023_33762_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf35/10279686/9ce48de0f863/41598_2023_33762_Fig6_HTML.jpg

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