Chromosome-scale genome assembly of the autoalloenneaploid Arundo donax

Grassland Research Pub Date : 2024-08-06 DOI:10.1002/glr2.12091

Mengmeng Ren, Fupeng Liu, Xiaohong Han, Daohong Wu, Hai Peng

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Abstract

Background

Arundo donax L. has great potential as an energy crop due to its high biomass yield and broad adaptability, while lack of a reference genome is a hindrance to genetic improvement efforts for this species.

Methods

Genome assembly of A. donax was conducted by utilizing PacBio SMRT sequencing and high-throughput chromosome conformation capture technology, with further analysis exploring the plant's ploidy, whole-genome duplication event, and evolutionary history through comparative genomics.

Results

The genome assembly of A. donax consists of 1.30 Gb with a contig N50 size of 33.15 Mb. A total of 74 403 gene models were identified, with over 90% of genes being functionally annotated. Karyotype and synteny analyses revealed that A. donax is an autoalloenneaploid (3n = 9x = 108) and has experienced significant gene family expansion and two whole-genome duplication events during its evolutionary history. Furthermore, utilizing the genome assembly, a variety of salinity stress-related genes were uncovered through the analysis of public RNA-seq data.

Conclusions

This study presents the initial chromosome-scale genome assembly of A. donax, which will advance genetic comprehension and support the genetic enhancement of this important energy crop.

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自交不育旱金莲的染色体级基因组组装

背景唐蜡（Arundo donax L.）因其生物质产量高、适应性广而具有作为能源作物的巨大潜力，但参考基因组的缺乏阻碍了该物种的遗传改良工作。方法利用 PacBio SMRT 测序和高通量染色体构象捕获技术对唐蜡进行基因组组装，并通过比较基因组学进一步分析探讨该植物的倍性、全基因组重复事件和进化历史。结果唐蜡（A. donax）的基因组组装有 1.30 Gb，等位基因 N50 大小为 33.15 Mb。共鉴定出 74 403 个基因模型，其中 90% 以上的基因有功能注释。核型和合成分析表明，唐蜡是一种自交系单倍体（3n = 9x = 108），在其进化史上经历了显著的基因家族扩张和两次全基因组复制事件。此外，利用基因组组装，通过分析公开的 RNA-seq 数据，发现了多种与盐度胁迫相关的基因。结论本研究提出了唐蜡（A. donax）染色体组规模的初步基因组组装，这将促进对遗传的理解，并支持这一重要能源作物的遗传改良。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Grassland Research

CiteScore

0.70

自引率

0.00%

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