完全来自长序列数据的芒果染色体级基因组。

IF 3.9 2区 生物学 Q1 GENETICS & HEREDITY
Plant Genome Pub Date : 2024-06-01 Epub Date: 2024-03-10 DOI:10.1002/tpg2.20441
Upendra Kumari Wijesundara, Ardashir Kharabian Masouleh, Agnelo Furtado, Natalie L Dillon, Robert J Henry
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引用次数: 0

摘要

长线程测序技术的改进大大加快了植物基因组测序的速度。目前的从头装配通常是通过将长读数序列数据装配成等位基因,然后通过染色质构象捕获将等位基因装配到染色体水平来实现的。我们在此报告的是仅使用 PacBio 高保真(HiFi)长读数的染色体级芒果基因组。高覆盖率(204 倍)的 HiFi 读数组装出了 17 条染色体,每条染色体都是单个等位基因,两端都有端粒。其余三条染色体分别由两条等位基因代表,一端为端粒,另一端为核糖体重复序列。通过分析等位基因末端,可以将它们配对并连接起来,从而生成端粒到端粒但核糖体重复序列长度不确定的其余三条完整染色体。根据 "通用单拷贝同源物基准分析"(Benchmarking Universal Single-Copy Orthologs)的评估,组装的基因组为 365 Mb,完整性为 100%。组装的单倍型显示出广泛的结构差异。这种使用极高基因组覆盖率的方法可能有助于为许多其他植物组装高质量的基因组。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
A chromosome-level genome of mango exclusively from long-read sequence data.

Improvements in long-read sequencing techniques have greatly accelerated plant genome sequencing. Current de novo assemblies are routinely achieved by assembling long-read sequence data into contigs that are assembled to chromosome level by chromatin conformation capture. We report here a chromosome-level mango genome using only PacBio high-fidelity (HiFi) long reads. HiFi reads at high coverage (204x) resulted in the assembly of 17 chromosomes, each as a single contig with telomeres at both ends. The remaining three chromosomes were represented each by two contigs, with telomeres at one end and ribosomal repeats at the other end. Analyzing contig ends allowed them to be paired and linked to generate the remaining three complete chromosomes, telomere-to-telomere but with ribosomal repeats of uncertain length. The assembled genome was 365 Mb with 100% completeness as assessed by Benchmarking Universal Single-Copy Orthologs analysis. The haplotypes assembled demonstrated extensive structural differences. This approach using very high genome coverage may be useful for assembling high-quality genomes for many other plants.

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来源期刊
Plant Genome
Plant Genome PLANT SCIENCES-GENETICS & HEREDITY
CiteScore
6.00
自引率
4.80%
发文量
93
审稿时长
>12 weeks
期刊介绍: The Plant Genome publishes original research investigating all aspects of plant genomics. Technical breakthroughs reporting improvements in the efficiency and speed of acquiring and interpreting plant genomics data are welcome. The editorial board gives preference to novel reports that use innovative genomic applications that advance our understanding of plant biology that may have applications to crop improvement. The journal also publishes invited review articles and perspectives that offer insight and commentary on recent advances in genomics and their potential for agronomic improvement.
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