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重要香料植物角胡卢巴（Trigonella corniculata (L.)L.，即长柄胡卢巴/小茴香）的染色体水平基因组组装

Chromosome-scale genome assembly of Trigonella corniculata (L.)L. (Nagauri pan /Kasuri methi), an important spice.

作者信息

Gaikwad Ambika Baldev, Yadav Sheel, Kumari Ratna, Maurya Wanchha, Rangan Parimalan, Singh Rakesh, Singh Gyanendra Pratap

机构信息

ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.

出版信息

Sci Data. 2025 Mar 26;12(1):509. doi: 10.1038/s41597-025-04858-4.

DOI:10.1038/s41597-025-04858-4
PMID:40140648
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11947087/
Abstract

Trigonella corniculata (L) L. or Nagauri pan /Kasuri methi, is an important spice crop with high nutraceutical potential. We report the de novo chromosome-scale assembly of T. corniculata genome using high coverage PacBio, Illumina and Hi-C reads. The assembly spans 798 Mb (Megabases) in 282 scaffolds with a scaffold N50 of 99.6 Mb. More than 98% of the sequence length is captured in eight different pseudomolecules with an average length of 98 Mb. A BUSCO score of over 97% is suggestive of the high degree of completeness and contiguity of the genome. A total of 64,801 protein-coding genes are predicted. Genome-wide Simple Sequence Repeats (99,149) have been identified and wet lab validated at forty-eight loci. The chromosome-scale genome assembly of T. corniculata and the SSR markers identified in this study will provide a strong foundation for future structural and functional genomics studies in T. corniculata and other fenugreek species.

摘要

葫芦巴（Trigonella corniculata (L) L.）或纳高里潘/卡苏里小茴香，是一种具有高营养保健潜力的重要香料作物。我们报告了利用高覆盖度的PacBio、Illumina和Hi-C测序 reads对葫芦巴基因组进行的从头染色体水平组装。该组装体跨越798兆碱基（Mb），分布在282个支架中，支架N50为99.6兆碱基。超过98%的序列长度被捕获在8个不同的假分子中，平均长度为98兆碱基。BUSCO评分超过97%表明基因组具有高度的完整性和连续性。总共预测了64,801个蛋白质编码基因。全基因组简单序列重复（99,149个）已被鉴定，并在48个位点进行了湿实验室验证。葫芦巴的染色体水平基因组组装以及本研究中鉴定的SSR标记将为葫芦巴和其他胡芦巴属物种未来的结构和功能基因组学研究提供坚实的基础。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcb0/11947087/c224c2a8865f/41597_2025_4858_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcb0/11947087/46c3e00f7377/41597_2025_4858_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcb0/11947087/3ba984cf1ee7/41597_2025_4858_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcb0/11947087/936eab4edac8/41597_2025_4858_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcb0/11947087/0a55197b0d57/41597_2025_4858_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcb0/11947087/a56514b72ede/41597_2025_4858_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcb0/11947087/c224c2a8865f/41597_2025_4858_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcb0/11947087/46c3e00f7377/41597_2025_4858_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcb0/11947087/3ba984cf1ee7/41597_2025_4858_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcb0/11947087/936eab4edac8/41597_2025_4858_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcb0/11947087/0a55197b0d57/41597_2025_4858_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcb0/11947087/a56514b72ede/41597_2025_4858_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcb0/11947087/c224c2a8865f/41597_2025_4858_Fig6_HTML.jpg

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本文引用的文献

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2
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Front Plant Sci. 2023 May 10;14:1161499. doi: 10.3389/fpls.2023.1161499. eCollection 2023.
3
A large-scale assessment of the quality of plant genome assemblies using the LTR assembly index.
使用LTR组装指数对植物基因组组装质量进行的大规模评估。
AoB Plants. 2023 Apr 4;15(3):plad015. doi: 10.1093/aobpla/plad015. eCollection 2023 Jun.
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