斑胸草雀参考基因组组装。

A Reference Genome Assembly for the Spotted Flycatcher (Muscicapa striata).

机构信息

Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR7205, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.

Plateforme Génomique (GeT-PlaGe), Genotoul, US1426, INRAE, Castanet-Tolosan, France.

出版信息

Genome Biol Evol. 2023 Aug 1;15(8). doi: 10.1093/gbe/evad140.

DOI:10.1093/gbe/evad140

PMID:37506263

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10402868/

Abstract

The spotted flycatcher (Muscicapa striata) forms with the Mediterranean flycatcher (Muscicapa tyrrhenica) a newly recognized species pair of trans-Saharan migratory passerines. These flycatchers present a nested peripatric distribution, a pattern especially unusual among high dispersal species that questions the eco-evolutionary factors involved during the speciation process. Here, we present a genome assembly for M. striata assembled using a combination of Nanopore and Illumina sequences. The final assembly is 1.08 Gb long and consists of 4,779 contigs with an N50 of 3.2 Mb. The completeness of our M. striata genome assembly is supported by the number of BUSCO (95%) and ultraconserved element (UCE) (4889/5041; 97.0%) loci retrieved. This assembly showed high synteny with the Ficedula albicollis reference genome, the closest species for which a chromosome-scale reference genome is available. Several inversions were identified and will need to be investigated at the family level.

摘要

斑姬鹟（Muscicapa striata）与地中海姬鹟（Muscicapa tyrrhenica）形成了一个新的跨撒哈拉迁徙雀形目物种对。这些食虫鸟呈现出嵌套的边缘分布模式，这种模式在高扩散物种中特别罕见，这使得我们对物种形成过程中涉及的生态进化因素产生了质疑。在这里，我们提供了一个使用纳米孔和 Illumina 序列组合组装的斑姬鹟基因组组装。最终的组装长度为 1.08Gb，由 4779 个 contigs 组成，N50 为 3.2Mb。我们的斑姬鹟基因组组装的完整性得到了 BUSCO（95%）和超保守元件（UCE）（4889/5041；97.0%）数量的支持。该组装与白眉姬鹟（Ficedula albicollis）参考基因组高度同线性，白眉姬鹟是目前最接近的具有染色体级参考基因组的物种。鉴定出了几个倒位，需要在科水平上进行研究。