Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater.
Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater.
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一种极度濒危的澳大利亚鸟类：盔蜜水的染色体长度基因组组装和连锁图谱。
DOI：
10.1093/gigascience/giac025
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发表时间：
2022-03-29
期刊：
影响因子：
9.2
通讯作者：
Pavlova A
中科院分区：
文献类型：
--
作者：
Robledo-Ruiz DA;Gan HM;Kaur P;Dudchenko O;Weisz D;Khan R;Lieberman Aiden E;Osipova E;Hiller M;Morales HE;Magrath MJL;Clarke RH;Sunnucks P;Pavlova A
盔吸蜜鸟（Lichenostomus melanops）是澳大利亚维多利亚特有的一种濒危鸟类。为了帮助其保护，人口是遗传拯救的主题。为了了解，监测和调节基因拯救对盔吸蜜鸟基因组的影响，需要一个染色体长度的基因组和一个高密度的连锁图谱。我们使用Illumina，Oxford Nanopore和Hi-C测序技术的组合来组装头盔吸蜜鸟的染色体长度基因组，包括906个支架，长度为1.1 Gb，支架N50为63.8 Mb。注释包括57，181个基因模型。利用257只鸡的系谱和53，111个单核苷酸多态性，我们获得了25个常染色体和Z染色体的高密度连锁和重组图谱。总的性别平均连锁图谱长度为1，347 cM，其中雄性图谱比雌性图谱长6.7%。杂交图谱显示性二态重组率（男性总体较高），平均重组率为1.8 cM/Mb。比较分析显示，盔吸蜜鸟基因组与3种雀形目物种（例如，32个Hi-C支架映射到30个斑胸草雀常染色体和Z染色体）。基因组组装和连锁图谱显示，盔吸蜜鸟与斑胸草雀相比，1A染色体分裂为2条染色体。PSMC分析显示，从更新世中期到晚期，有效种群规模下降了2.15倍，降至2.60，000。注释的染色体长度的基因组和高密度的连锁图谱提供了丰富的资源，进化研究，并将在指导保护工作的盔吸蜜鸟。
The helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population is the subject of genetic rescue. To understand, monitor, and modulate the effects of genetic rescue on the helmeted honeyeater genome, a chromosome-length genome and a high-density linkage map are required. We used a combination of Illumina, Oxford Nanopore, and Hi-C sequencing technologies to assemble a chromosome-length genome of the helmeted honeyeater, comprising 906 scaffolds, with length of 1.1 Gb and scaffold N50 of 63.8 Mb. Annotation comprised 57,181 gene models. Using a pedigree of 257 birds and 53,111 single-nucleotide polymorphisms, we obtained high-density linkage and recombination maps for 25 autosomes and Z chromosome. The total sex-averaged linkage map was 1,347 cM long, with the male map being 6.7% longer than the female map. Recombination maps revealed sexually dimorphic recombination rates (overall higher in males), with average recombination rate of 1.8 cM/Mb. Comparative analyses revealed high synteny of the helmeted honeyeater genome with that of 3 passerine species (e.g., 32 Hi-C scaffolds mapped to 30 zebra finch autosomes and Z chromosome). The genome assembly and linkage map suggest that the helmeted honeyeater exhibits a fission of chromosome 1A into 2 chromosomes relative to zebra finch. PSMC analysis showed a ∼15-fold decline in effective population size to ∼60,000 from mid- to late Pleistocene. The annotated chromosome-length genome and high-density linkage map provide rich resources for evolutionary studies and will be fundamental in guiding conservation efforts for the helmeted honeyeater.
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影响因子：
4.9
作者：
Kawakami T;Smeds L;Backström N;Husby A;Qvarnström A;Mugal CF;Olason P;Ellegren H
通讯作者：
Ellegren H
影响因子：
7
作者：
Backstrom, Niclas;Forstmeier, Wolfgang;Ellegren, Hans
通讯作者：
Ellegren, Hans
影响因子：
4.9
作者：
Frankham, Richard
通讯作者：
Frankham, Richard
影响因子：
9.3
作者：
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通讯作者：
Aiden EL
影响因子：
3.4
作者：
Gan HM;Schultz MB;Austin CM
通讯作者：
Austin CM