Comparative genomics and transcriptomics of Chrysolophus provide insights into the evolution of complex plumage coloration.
Comparative genomics and transcriptomics of Chrysolophus provide insights into the evolution of complex plumage coloration.
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红腹锦鸡的比较基因组学和转录组学为复杂羽毛颜色的进化提供了见解
DOI：
10.1093/gigascience/giy113
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发表时间：
2018-10-01
期刊：
影响因子：
9.2
通讯作者：
Zuo Y
中科院分区：
文献类型：
--
作者：
Gao G;Xu M;Bai C;Yang Y;Li G;Xu J;Wei Z;Min J;Su G;Zhou X;Guo J;Hao Y;Zhang G;Yang X;Xu X;Widelitz RB;Chuong CM;Zhang C;Yin J;Zuo Y
摘要背景作为鸟类最易识别的特征之一，羽毛颜色对理解颜色的进化和机制有很大的影响。羽毛和皮肤是探索脊椎动物基因组学和颜色模式复杂性的理想组织。锦鸡属的两个物种，锦鸡（Chrysolophus pictus）和阿默斯特夫人的野鸡（Chrysolophus amherstiae），在它们的羽毛中表现出鲜艳的颜色，但具有极端的表型差异，使这两个物种成为研究鸟类羽毛着色机制的伟大模型。结果获得了高覆盖度的锦鸡全基因组序列，共注释了15,552个蛋白质编码基因。阿默斯特夫人的野鸡基因组测序覆盖率低。在羽毛色素鉴定的基础上，通过一系列基因组和转录组的比较，研究了羽毛颜色的复杂特征。通过对锦鸡和锦鸡在不同背景下的谱系特异性序列变异的分析，发现4个黑素合成基因和一些脂类相关基因可能分别是黑色素和类胡萝卜素色素形成的候选基因组因子。此外，一项对47只鸟类的研究显示，在广泛的鸟类中存在一些与类胡萝卜素着色相关的候选基因。转录组数据进一步揭示了这两种着色的重要调控因子，特别是小眼症相关转录因子基因的一个剪接转录本，用于褐黑素合成。结论对锦鸡及其姊妹鸡基因组的分析以及与其他鸟类基因组的比较有助于揭示锦鸡羽色的内在调控规律。本研究为进一步研究鸟类羽毛的进化和多样性提供了重要的基因组信息和见解。
Abstract Background As one of the most recognizable characteristics in birds, plumage color has a high impact on understanding the evolution and mechanisms of coloration. Feather and skin are ideal tissues to explore the genomics and complexity of color patterns in vertebrates. Two species of the genus Chrysolophus, golden pheasant (Chrysolophus pictus) and Lady Amherst's pheasant (Chrysolophus amherstiae), exhibit brilliant colors in their plumage, but with extreme phenotypic differences, making these two species great models to investigate plumage coloration mechanisms in birds. Results We sequenced and assembled a genome of golden pheasant with high coverage and annotated 15,552 protein-coding genes. The genome of Lady Amherst's pheasant is sequenced with low coverage. Based on the feather pigment identification, a series of genomic and transcriptomic comparisons were conducted to investigate the complex features of plumage coloration. By identifying the lineage-specific sequence variations in Chrysolophus and golden pheasant against different backgrounds, we found that four melanogenesis biosynthesis genes and some lipid-related genes might be candidate genomic factors for the evolution of melanin and carotenoid pigmentation, respectively. In addition, a study among 47 birds showed some candidate genes related to carotenoid coloration in a broad range of birds. The transcriptome data further reveal important regulators of the two colorations, particularly one splicing transcript of the microphthalmia-associated transcription factor gene for pheomelanin synthesis. Conclusions Analysis of the golden pheasant and its sister pheasant genomes, as well as comparison with other avian genomes, are helpful to reveal the underlying regulation of their plumage coloration. The present study provides important genomic information and insights for further studies of avian plumage evolution and diversity.
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影响因子：
4.3
作者：
Hida T;Wakamatsu K;Sviderskaya EV;Donkin AJ;Montoliu L;Lynn Lamoreux M;Yu B;Millhauser GL;Ito S;Barsh GS;Jimbow K;Bennett DC
通讯作者：
Bennett DC
影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
黄色皮肤基因的鉴定显示了家鸡的杂种起源。
影响因子：
4.5
作者：
Eriksson, Jonas;Larson, Greger;Gunnarsson, Ulrika;Bed'hom, Bertrand;Tixier-Boichard, Michele;Stromstedt, Lina;Wright, Dominic;Jungerius, Annemieke;Vereijken, Addie;Randi, Ettore;Jensen, Per;Andersson, Leif
通讯作者：
Andersson, Leif
DOI：
10.1126/science.1253451
发表时间：
2014-12-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Jarvis ED;Mirarab S;Aberer AJ;Li B;Houde P;Li C;Ho SY;Faircloth BC;Nabholz B;Howard JT;Suh A;Weber CC;da Fonseca RR;Li J;Zhang F;Li H;Zhou L;Narula N;Liu L;Ganapathy G;Boussau B;Bayzid MS;Zavidovych V;Subramanian S;Gabaldón T;Capella-Gutiérrez S;Huerta-Cepas J;Rekepalli B;Munch K;Schierup M;Lindow B;Warren WC;Ray D;Green RE;Bruford MW;Zhan X;Dixon A;Li S;Li N;Huang Y;Derryberry EP;Bertelsen MF;Sheldon FH;Brumfield RT;Mello CV;Lovell PV;Wirthlin M;Schneider MP;Prosdocimi F;Samaniego JA;Vargas Velazquez AM;Alfaro-Núñez A;Campos PF;Petersen B;Sicheritz-Ponten T;Pas A;Bailey T;Scofield P;Bunce M;Lambert DM;Zhou Q;Perelman P;Driskell AC;Shapiro B;Xiong Z;Zeng Y;Liu S;Li Z;Liu B;Wu K;Xiao J;Yinqi X;Zheng Q;Zhang Y;Yang H;Wang J;Smeds L;Rheindt FE;Braun M;Fjeldsa J;Orlando L;Barker FK;Jønsson KA;Johnson W;Koepfli KP;O'Brien S;Haussler D;Ryder OA;Rahbek C;Willerslev E;Graves GR;Glenn TC;McCormack J;Burt D;Ellegren H;Alström P;Edwards SV;Stamatakis A;Mindell DP;Cracraft J;Braun EL;Warnow T;Jun W;Gilbert MT;Zhang G
通讯作者：
Zhang G
影响因子：
7
作者：
Curwen, V;Eyras, E;Clamp, M
通讯作者：
Clamp, M