Comparative Genomics of Synechococcus elongatus Explains the Phenotypic Diversity of the Strains.
Comparative Genomics of Synechococcus elongatus Explains the Phenotypic Diversity of the Strains.
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作者：
大约60年前，长聚球藻首次被分离出来，PCC7942是光合作用、昼夜生物学和生物技术研究的典范。最近分离到的UTEX 3055以及随后在生物膜和趋光性表型上的发现表明，实验室菌株长链霉菌是高度驯化的。我们对长链球菌现有的基因组进行了全面的基因组比较，并对另外两个实验室菌株进行了测序，以追踪标准实验室菌株中本土表型的丢失，并确定有用表型的遗传基础。基因组比对分析提供了长链球菌的基因组描述，并纠正了模式菌株PCC6301公布的序列中的大量错误。菌株之间的基因集和单核苷酸多态(SNPs)的比较澄清了菌株的分离历史，并与大规模的基因组差异一起支持了实验室驯化的假说。实验室菌株中的前噬菌体基因，而不是UTEX 3055，影响色素沉着，而UTEX 3055中独特的基因是趋光性所必需的。这项研究中发现的基因组差异包括以前报道的实际上是测序错误的SNPs，以及具有表型后果的SNPs和基因组差异。昼夜节律反应调节因子RpaA中的一个SNP引起了混乱，在这里被澄清为属于PCC7942的一个异常克隆，用于已发表的基因组序列，这混淆了对昼夜节律适应性研究的解释。
Strains of the freshwater cyanobacterium Synechococcus elongatus were first isolated approximately 60 years ago, and PCC 7942 is well established as a model for photosynthesis, circadian biology, and biotechnology research. The recent isolation of UTEX 3055 and subsequent discoveries in biofilm and phototaxis phenotypes suggest that lab strains of S. elongatus are highly domesticated. We performed a comprehensive genome comparison among the available genomes of S. elongatus and sequenced two additional laboratory strains to trace the loss of native phenotypes from the standard lab strains and determine the genetic basis of useful phenotypes. The genome comparison analysis provides a pangenome description of S. elongatus, as well as correction of extensive errors in the published sequence for the type strain PCC 6301. The comparison of gene sets and single nucleotide polymorphisms (SNPs) among strains clarifies strain isolation histories and, together with large-scale genome differences, supports a hypothesis of laboratory domestication. Prophage genes in laboratory strains, but not UTEX 3055, affect pigmentation, while unique genes in UTEX 3055 are necessary for phototaxis. The genomic differences identified in this study include previously reported SNPs that are, in reality, sequencing errors, as well as SNPs and genome differences that have phenotypic consequences. One SNP in the circadian response regulator rpaA that has caused confusion is clarified here as belonging to an aberrant clone of PCC 7942, used for the published genome sequence, that has confounded the interpretation of circadian fitness research.
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影响因子：
2.7
作者：
Garrison NL;Rodriguez J;Agnarsson I;Coddington JA;Griswold CE;Hamilton CA;Hedin M;Kocot KM;Ledford JM;Bond JE
通讯作者：
Bond JE
DOI：
10.1126/science.abd4453
发表时间：
2021-10-08
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Chavan AG;Swan JA;Heisler J;Sancar C;Ernst DC;Fang M;Palacios JG;Spangler RK;Bagshaw CR;Tripathi S;Crosby P;Golden SS;Partch CL;LiWang A
通讯作者：
LiWang A
影响因子：
2.6
作者：
Chen, You;Holtman, C. Kay;Golden, Susan S.
通讯作者：
Golden, Susan S.
影响因子：
11
作者：
Chenard, C.;Chan, A. M.;Suttle, C. A.
通讯作者：
Suttle, C. A.
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T