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利用PacBio和Hi-C技术对膜荚黄芪进行染色体水平的基因组组装。

Chromosome-scale genome assembly of Astragalus membranaceus using PacBio and Hi-C technologies.

作者信息

Fan Huijie, Chai Zhi, Yang Xukui, Liu Ake, Sun Haifeng, Wu Zhangyan, Li Qingshan, Ma Cungen, Zhou Ran

机构信息

College of Basic Medical Sciences, Shanxi University of Chinese Medicine, Jinzhong, 030619, China.

BGI Genomics, Shenzhen, 518083, China.

出版信息

Sci Data. 2024 Oct 2;11(1):1071. doi: 10.1038/s41597-024-03852-6.

DOI:10.1038/s41597-024-03852-6
PMID:39358417
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11446949/
Abstract

Astragalus membranaceus (Fisch.) Bge (AM) is a medicinal herb plant belonging to the Leguminosae family. In this study, we present a chromosome-scale genome assembly of AM, aiming to enhance the molecular biology and functional studies of Astragali Radix. The genome size of AM is about 1.43 Gb, with a contig N50 value of 1.67 Mb. A total of 98.16% of the assembly anchored to 9 pseudochromosomes using Hi-C technology. The assembly completeness was estimated to be 97.27% using BUSCO with the long terminal repeat assembly index (LAI) of 16.22 and quality value (QV) of 48.58. Additionally, the genome contained 67.98% repetitive sequences. Genome annotation predicted 29,914 protein-coding genes, including 73 genes involved in the flavonoid biosynthetic pathway and 2,048 transcription factors. The high-quality genome assembly and gene annotation resources will greatly facilitate future functional genomic studies in Leguminosae species.

摘要

膜荚黄芪（Astragalus membranaceus (Fisch.) Bge，AM）是一种豆科药用草本植物。在本研究中，我们展示了膜荚黄芪的染色体水平基因组组装，旨在加强黄芪的分子生物学和功能研究。膜荚黄芪的基因组大小约为1.43 Gb，重叠群N50值为1.67 Mb。使用Hi-C技术，共有98.16%的组装序列锚定到9条假染色体上。使用BUSCO估计组装完整性为97.27%，长末端重复序列组装指数（LAI）为16.22，质量值（QV）为48.58。此外，基因组包含67.98%的重复序列。基因组注释预测有29,914个蛋白质编码基因，包括73个参与黄酮类生物合成途径的基因和2,048个转录因子。高质量的基因组组装和基因注释资源将极大地促进未来豆科物种的功能基因组学研究。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6ff/11446949/8cc0025191c0/41597_2024_3852_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6ff/11446949/d4b72694290b/41597_2024_3852_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6ff/11446949/3a268e59ad0d/41597_2024_3852_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6ff/11446949/3385e65bab16/41597_2024_3852_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6ff/11446949/47936f1e3477/41597_2024_3852_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6ff/11446949/0d5ff1ca5594/41597_2024_3852_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6ff/11446949/fd2d0b9f90ad/41597_2024_3852_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6ff/11446949/ea124e5a9c20/41597_2024_3852_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6ff/11446949/8cc0025191c0/41597_2024_3852_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6ff/11446949/d4b72694290b/41597_2024_3852_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6ff/11446949/3a268e59ad0d/41597_2024_3852_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6ff/11446949/3385e65bab16/41597_2024_3852_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6ff/11446949/47936f1e3477/41597_2024_3852_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6ff/11446949/0d5ff1ca5594/41597_2024_3852_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6ff/11446949/fd2d0b9f90ad/41597_2024_3852_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6ff/11446949/ea124e5a9c20/41597_2024_3852_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6ff/11446949/8cc0025191c0/41597_2024_3852_Fig8_HTML.jpg

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