A Chromosome-Scale and Annotated Reference Genome Assembly of Plecia longiforceps Duda, 1934 (Diptera: Bibionidae).

IF 3.2 2区生物学 Q2 EVOLUTIONARY BIOLOGY

Genome Biology and Evolution Pub Date : 2024-10-09 DOI:10.1093/gbe/evae205

Jonghwan Choi, Taemin Kang, Sun-Jae Park, Seunggwan Shin

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Abstract

Urbanization is a leading factor effecting global biodiversity, driving rapid evolutionary processes in the local biota. Species that adapt and proliferate in city environments can become pests, with human activities facilitating their dispersal and excessive outbreaks. Here we present the first genome data of Plecia longiforceps, a lovebug pest in Eastern Asia with intensive aggregations recently occurring in the Seoul Metropolitan Area of Korea. PacBio HiFi and ONT Pore-C sequencing data were used to construct a highly continuous assembly with a total size of 707 Mb and 8 major pseudochromosomes, its integrity supported by the N50 length of 98.1 Mb and 96.8% BUSCO completeness. Structural and functional annotation using transcriptome data and ab initio predictions revealed a high proportion (69.3%) of repeat sequences, and synteny analysis with Bibio marci showed high levels of genomic collinearity. The genome will serve as an essential resource for both population genomics and molecular research on lovebug dispersal and outbreaks, and also implement studies on the eco-evolutionary processes of insects in urbanizing habitats.

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Plecia longiforceps Duda, 1934 (Diptera: Bibionidae) 的染色体尺度和注释参考基因组组装。

城市化是影响全球生物多样性的一个主要因素，它推动了当地生物群的快速进化过程。在城市环境中适应和繁殖的物种可能会成为害虫，人类活动会促进它们的传播和过度爆发。在这里，我们首次展示了Plecia longiforceps的基因组数据，它是东亚的一种爱虫害虫，最近在韩国首尔大都会区出现了密集聚集。我们利用 PacBio HiFi 和 ONT Pore-C 测序数据构建了一个总大小为 707Mb 和 8 个主要假染色体的高度连续的基因组，其完整性得到了 98.1Mb 的 N50 长度和 96.8% 的 BUSCO 完整性的支持。利用转录组数据和 ab initio 预测进行的结构和功能注释显示，重复序列的比例很高（69.3%），利用 Bibio marci 进行的同源分析显示，基因组的共线性很高。该基因组将成为研究lovebug传播和爆发的种群基因组学和分子研究的重要资源，同时也是研究城市化生境中昆虫生态进化过程的重要依据。

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

Genome Biology and Evolution EVOLUTIONARY BIOLOGY-GENETICS & HEREDITY

CiteScore

5.80

自引率

6.10%

发文量

169

审稿时长

1 months

期刊介绍： About the journal Genome Biology and Evolution (GBE) publishes leading original research at the interface between evolutionary biology and genomics. Papers considered for publication report novel evolutionary findings that concern natural genome diversity, population genomics, the structure, function, organisation and expression of genomes, comparative genomics, proteomics, and environmental genomic interactions. Major evolutionary insights from the fields of computational biology, structural biology, developmental biology, and cell biology are also considered, as are theoretical advances in the field of genome evolution. GBE’s scope embraces genome-wide evolutionary investigations at all taxonomic levels and for all forms of life — within populations or across domains. Its aims are to further the understanding of genomes in their evolutionary context and further the understanding of evolution from a genome-wide perspective.