Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan.
Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan.
Genome Biol Evol. 2022 May 31;14(6). doi: 10.1093/gbe/evac083.
The mandarin duck, Aix galericulata, is popular in East Asian cultures and displays exaggerated sexual dimorphism, especially in feather traits during breeding seasons. We generated and annotated the first mandarin duck de novo assembly, which was 1.08 Gb in size and encoded 16,615 proteins. Using a phylogenomic approach calibrated with fossils and molecular divergences, we inferred that the last common ancestor of ducks occurred 13.3-26.7 Ma. The majority of the mandarin duck genome repetitive sequences belonged to the chicken repeat 1 (CR1) retroposon CR1-J2_Pass, which underwent a duck lineage-specific burst. Synteny analyses among ducks revealed infrequent chromosomal rearrangements in which breaks were enriched in LINE retrotransposons and DNA transposons. The calculation of the dN/dS ratio revealed that the majority of duck genes were under strong purifying selection. The expanded gene families in the mandarin duck are primarily involved in olfactory perception as well as the development and morphogenesis of feather and branching structures. This new reference genome will improve our understanding of the morphological and physiological characteristics of ducks and provide a valuable resource for functional genomics studies to investigate the feather traits of the mandarin duck.
鸳鸯，Aix galericulata，在东亚文化中很受欢迎，表现出明显的性二态性，特别是在繁殖季节的羽毛特征上。我们生成并注释了第一个鸳鸯从头组装基因组，大小为 1.08Gb，编码了 16615 个蛋白质。利用与化石和分子分歧校准的系统基因组学方法，我们推断出鸭类的最后共同祖先出现在 13.3-26.7Ma。鸳鸯基因组的大部分重复序列属于鸡重复 1（CR1）反转录转座子 CR1-J2_Pass，该转座子在鸭类中发生了特异性爆发。鸭类之间的同线性分析显示，染色体断裂在 LINE 反转座子和 DNA 转座子中富集。dN/dS 比值的计算表明，大多数鸭类基因受到强烈的纯化选择。鸳鸯中扩展的基因家族主要参与嗅觉感知，以及羽毛和分支结构的发育和形态发生。这个新的参考基因组将提高我们对鸭类形态和生理特征的理解，并为功能基因组学研究提供有价值的资源，以研究鸳鸯的羽毛特征。
