Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum.
Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum.
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DOI：
10.1016/j.cell.2018.10.023
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发表时间：
2018-11-29
期刊：
影响因子：
64.5
通讯作者：
Rokas A
中科院分区：
文献类型：
--
作者：
Shen XX;Opulente DA;Kominek J;Zhou X;Steenwyk JL;Buh KV;Haase MAB;Wisecaver JH;Wang M;Doering DT;Boudouris JT;Schneider RM;Langdon QK;Ohkuma M;Endoh R;Takashima M;Manabe RI;Čadež N;Libkind D;Rosa CA;DeVirgilio J;Hulfachor AB;Groenewald M;Kurtzman CP;Hittinger CT;Rokas A
Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as genetically diverse as plants or animals. To understand budding yeast evolution, we analyzed the genomes of 332 yeast species, including 220 newly sequenced ones, which represent nearly a third of all known budding yeast diversity. Here we establish a robust genus-level phylogeny comprised of 12 major clades, infer the timescale of diversification from the Devonian Period to the present, quantify horizontal gene transfer (HGT), and reconstruct the evolution of 45 metabolic traits and the metabolic toolkit of the Budding Yeast Common Ancestor (BYCA). We infer that BYCA was metabolically complex and chronicle the tempo and mode of genomic and phenotypic evolution across the subphylum, which is characterized by very low HGT levels and widespread losses of traits and the genes that control them. More generally, our results argue that reductive evolution is a major mode of evolutionary diversification. An integrated phylogeny of over 300 budding yeast species encompasses the natural diversity and history of diversification of Saccharomycotina with insights into a metabolically-complex common ancestor and common reductive evolution leading to metabolic specialization.
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影响因子：
14.9
作者：
Grigoriev IV;Nikitin R;Haridas S;Kuo A;Ohm R;Otillar R;Riley R;Salamov A;Zhao X;Korzeniewski F;Smirnova T;Nordberg H;Dubchak I;Shabalov I
通讯作者：
Shabalov I
影响因子：
7.7
作者：
Gonçalves C;Wisecaver JH;Kominek J;Oom MS;Leandro MJ;Shen XX;Opulente DA;Zhou X;Peris D;Kurtzman CP;Hittinger CT;Rokas A;Gonçalves P
通讯作者：
Gonçalves P
影响因子：
10.7
作者：
Minh BQ;Nguyen MA;von Haeseler A
通讯作者：
von Haeseler A
影响因子：
14.9
作者：
Huerta-Cepas J;Capella-Gutiérrez S;Pryszcz LP;Marcet-Houben M;Gabaldón T
通讯作者：
Gabaldón T
影响因子：
64.8
作者：
Dujon, B;Sherman, D;Souciet, JL
通讯作者：
Souciet, JL