Repeat_annotation

Manakins represent a family of small suboscine passerine birds characterized by their elaborate courtship displays, non-monogamous mating system, and sexual dimorphism. This family thus serves as a good model for the study of sexual selection. Here we present the genome assemblies of four manakin species (<em>Cryptopipo holochlora, Dixiphia pipra, Machaeropterus deliciosus</em> and <em>Masius chrysopterus</em>) generated by Single-tube Long Fragment Read (stLFR) technology. The assembled genome sizes ranged from 1.10 Gb to 1.19 Gb, with average scaffold N50 of 28 Mb and contig N50 of 169 Kb. On average, 9.82% genome region was annotated as repetitive elements, and 12,059 protein-coding genes were annotated in the genomes. We further identified about 75 Mb Z-linked sequences in manakins, containing 585 to 751 genes and an ~600 Kb pseudoautosomal region (PAR). One interesting finding of these Z-linked sequences is that a possible Z-to-autosome/PAR reversal could happen in <em>Masius chrysopterus</em>. These manakin genomes will contribute to a deeper understanding of evolutionary history and sexual selection in these species.

娇鹟科（Manakins）是一类小型雀形目亚鸣禽，以其复杂精妙的求偶炫耀行为、非单配制交配体系以及显著的性二态性为典型特征，因此该科成为研究性选择的理想模型类群。本研究报道了4种娇鹟的基因组组装序列，分别为*Cryptopipo holochlora*、*Dixiphia pipra*、*Machaeropterus deliciosus*以及*Masius chrysopterus*，均通过单管长片段读取（Single-tube Long Fragment Read, stLFR）技术组装获得。组装完成的基因组大小跨度为1.10 Gb至1.19 Gb，平均支架N50为28 Mb，平均重叠群N50为169 Kb。平均而言，基因组中9.82%的区域被注释为重复序列元件，所有基因组中共注释得到12059个蛋白质编码基因。本研究进一步在娇鹟基因组中鉴定出约75 Mb的Z连锁序列，这些序列包含585至751个蛋白质编码基因，同时带有一个长度约600 Kb的假常染色体区域（pseudoautosomal region, PAR）。针对上述Z连锁序列的一项有趣发现为，*Masius chrysopterus*中可能存在Z染色体-常染色体/假常染色体区域的反转现象。上述娇鹟基因组资源将有助于深入理解该类群的进化历史与性选择机制。