无间隙基因组组装和表观遗传图谱揭示了莴苣全基因组三重复制的基因调控。

IF 11.8 2区 生物学 Q1 MULTIDISCIPLINARY SCIENCES
Shuai Cao, Nunchanoke Sawettalake, Lisha Shen
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引用次数: 0

摘要

背景:莴苣是菊科植物的重要成员,是一种全球栽培的经济蔬菜作物。莴苣基因组高度复杂(2.5 Gb;2n = 18),重复序列丰富,目前的莴苣参考基因组存在数千个缺口,阻碍了对莴苣基因组的全面了解:在这里,我们利用长线程 PacBio HiFi 和 Nanopore 测序数据,为具有高转化率的切莴苣提供了一个近乎完整的无间隙参考基因组。与茎用莴苣基因组相比,我们发现了127,681个结构变异(SV,存在于0.41 Gb的序列中),反映了叶用莴苣和茎用莴苣的差异。有趣的是,这些 SV 与转座子和 DNA 甲基化状态有关。此外,我们还发现了 4,612 个全基因组三复制基因,这些基因的高表达水平与低 DNA 甲基化水平和高 N6-甲基腺苷 RNA 修饰有关。DNA甲基化变化还与参与胼胝体形成的基因激活有关:我们的无间隙莴苣基因组组装是菊科植物中前所未有的成就,为功能基因组学、表观基因组学和作物育种奠定了坚实的基础,并为理解基因组进化过程中与 DNA 和 RNA 表观遗传学动态相关的基因调控的复杂性提供了新的思路。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce.

Background: Lettuce, an important member of the Asteraceae family, is a globally cultivated cash vegetable crop. With a highly complex genome (∼2.5 Gb; 2n = 18) rich in repeat sequences, current lettuce reference genomes exhibit thousands of gaps, impeding a comprehensive understanding of the lettuce genome.

Findings: Here, we present a near-complete gapless reference genome for cutting lettuce with high transformability, using long-read PacBio HiFi and Nanopore sequencing data. In comparison to stem lettuce genome, we identify 127,681 structural variations (SVs, present in 0.41 Gb of sequence), reflecting the divergence of leafy and stem lettuce. Interestingly, these SVs are related to transposons and DNA methylation states. Furthermore, we identify 4,612 whole-genome triplication genes exhibiting high expression levels associated with low DNA methylation levels and high N6-methyladenosine RNA modifications. DNA methylation changes are also associated with activation of genes involved in callus formation.

Conclusions: Our gapless lettuce genome assembly, an unprecedented achievement in the Asteraceae family, establishes a solid foundation for functional genomics, epigenomics, and crop breeding and sheds new light on understanding the complexity of gene regulation associated with the dynamics of DNA and RNA epigenetics in genome evolution.

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来源期刊
GigaScience
GigaScience MULTIDISCIPLINARY SCIENCES-
CiteScore
15.50
自引率
1.10%
发文量
119
审稿时长
1 weeks
期刊介绍: GigaScience seeks to transform data dissemination and utilization in the life and biomedical sciences. As an online open-access open-data journal, it specializes in publishing "big-data" studies encompassing various fields. Its scope includes not only "omic" type data and the fields of high-throughput biology currently serviced by large public repositories, but also the growing range of more difficult-to-access data, such as imaging, neuroscience, ecology, cohort data, systems biology and other new types of large-scale shareable data.
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