School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia.
Deakin Genomics Centre, Deakin University, Geelong, VIC 3220, Australia.
Gigascience. 2022 Mar 29;11. doi: 10.1093/gigascience/giac025.
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.
盔花蜜鸟（Lichenostomus melanops cassidix）是一种极度濒危的鸟类，仅分布于澳大利亚维多利亚州。为了协助其保护工作，对该物种的种群进行了遗传拯救。为了了解、监测和调节遗传拯救对盔花蜜鸟基因组的影响，需要获得该物种的染色体长度基因组和高密度连锁图谱。
我们结合使用 Illumina、Oxford Nanopore 和 Hi-C 测序技术，组装出盔花蜜鸟的染色体长度基因组，包含 906 个 scaffolds，总长为 1.1Gb，scaffold N50 为 63.8Mb。注释得到 57181 个基因模型。利用一个包含 257 只鸟和 53111 个单核苷酸多态性的家系，我们获得了 25 条常染色体和 Z 染色体的高密度连锁和重组图谱。总的雌雄平均连锁图谱长度为 1347cM，其中雄性图谱比雌性图谱长 6.7%。重组图谱揭示了雌雄两性之间存在可育重组率的性二型（总体上雄性更高），平均重组率为 1.8cM/Mb。比较分析表明，盔花蜜鸟基因组与 3 种雀形目物种（例如，32 个 Hi-C scaffolds 映射到 30 个斑胸草雀常染色体和 Z 染色体）具有高度的同线性。基因组组装和连锁图谱表明，盔花蜜鸟的 1A 染色体相对于斑马雀发生了分裂，形成了 2 条染色体。PSMC 分析显示，从中更新世到晚更新世期间，有效种群大小下降了约 15 倍，降至约 6 万。
注释的染色体长度基因组和高密度连锁图谱为进化研究提供了丰富的资源，对于指导盔花蜜鸟的保护工作将是至关重要的。
