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检疫性根结线虫南方根结线虫的高精度注释三倍体基因组

High-fidelity annotated triploid genome of the quarantine root-knot nematode, Meloidogyne enterolobii.

作者信息

Poullet Marine, Konigopal Hemanth, Rancurel Corinne, Sallaberry Marine, Lopez-Roques Celine, Mota Ana Paula Zotta, Lledo Joanna, Kiewnick Sebastian, Danchin Etienne G J

机构信息

Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France.

Julius Kühn-Institut, Institute for Plant Protection in Field Crops and Grassland, Messeweg 11-12, 38104, Braunschweig, Germany.

出版信息

Sci Data. 2025 Jan 30;12(1):184. doi: 10.1038/s41597-025-04434-w.

DOI:10.1038/s41597-025-04434-w
PMID:39885189
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11782629/
Abstract

Root-knot nematodes (RKN) of the genus Meloidogyne are obligatory plant endoparasites that cause substantial economic losses to agricultural production and impact the global food supply. These plant parasitic nematodes belong to the most widespread and devastating genus worldwide, yet few measures of control are available. The most efficient way to control RKN is deployment of resistance genes in plants. However, current resistance genes that control other Meloidogyne species are mostly inefficient on Meloidogyne enterolobii. Consequently, M. enterolobii was listed as a European Union quarantine pest requiring regulation. To gain insight into the molecular characteristics underlying its parasitic success, exploring the genome of M. enterolobii is essential. Here, we report a high-quality genome assembly of M. enterolobii using the high-fidelity long-read sequencing technology developed by Pacific Biosciences, combined with a gap-aware sequence transformer, DeepConsensus. The resulting triploid genome assembly spans 285.4 Mb with 556 contigs, a GC% of 30 ± 0.042 and an N50 value of 2.11 Mb, constituting a useful platform for comparative, population and functional genomics.

摘要

根结线虫属（Meloidogyne）的根结线虫是专性植物内寄生线虫，会给农业生产造成巨大经济损失，并影响全球粮食供应。这些植物寄生线虫属于全球分布最广、破坏力最强的属，但可用的防治措施却很少。控制根结线虫最有效的方法是在植物中部署抗性基因。然而，目前控制其他根结线虫物种的抗性基因对南方根结线虫大多无效。因此，南方根结线虫被列为需要监管的欧盟检疫性有害生物。为了深入了解其寄生成功的分子特征，探索南方根结线虫的基因组至关重要。在此，我们报告了南方根结线虫的高质量基因组组装，该组装使用了太平洋生物科学公司开发的高保真长读长测序技术，并结合了一个缺口感知序列变换器DeepConsensus。由此产生的三倍体基因组组装跨度为285.4 Mb，有556个重叠群，GC含量为30±0.042，N50值为2.11 Mb，为比较基因组学、群体基因组学和功能基因组学提供了一个有用的平台。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/57ad/11782629/ce6924710e52/41597_2025_4434_Fig7_HTML.jpg
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本文引用的文献

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Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure.有性、异源多倍体根结线虫的分阶段染色体规模基因组组装揭示了复杂的亚基因组结构。
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Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization.
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