Knowledge Resource Center for Ecological Environment in Arid Area
| DOI | 10.1186/s12864-020-06829-y |
| Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation | |
| Vazquez-Rosas-Landa, Mirna1,2; Ponce-Soto, Gabriel Yaxal1; Aguirre-Liguori, Jonas1; Thakur, Shalabh3; Scheinvar, Enrique1; Barrera-Redondo, Josue1; Ibarra-Laclette, Enrique2; Guttman, David S.3,4; Eguiarte, Luis E.1; Souza, Valeria1 | |
| 通讯作者 | Souza, Valeria |
| 来源期刊 | BMC GENOMICS
 |
| ISSN | 1471-2164 |
| 出版年 | 2020 |
| 卷号 | 21期号:1 |
| 英文摘要 | BackgroundIn bacteria, pan-genomes are the result of an evolutionary tug of war between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size (N-e), resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT and mutation, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses, elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Cienegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes.ResultsWe obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high N-e estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low N-e, suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.005 to 2.725, which are similar to oceanic Vibrionaceae estimations. However, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation, purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes associated with these SNPs were related to sodium transport.ConclusionsDifferent lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported for the first time. Most Vibrionaceae lineages of CCB are adapted to their micro-habitats rather than to the sampled environments. This pattern of adaptation is concordant with the association of closed pan-genomes and local adaptation. |
| 英文关键词 | Pan-genome Population genomics Vibrionaceae Recombination Selection Effective population size |
| 类型 | Article |
| 语种 | 英语 |
| 国家 | Mexico ; Canada |
| 开放获取类型 | Green Published, Green Submitted, gold |
| 收录类别 | SCI-E |
| WOS记录号 | WOS:000543547600005 |
| WOS关键词 | 2 MICROBIAL MATS ; ESCHERICHIA-COLI ; COMPARATIVE METAGENOMICS ; LINKAGE DISEQUILIBRIUM ; GENE-TRANSFER ; EVOLUTION ; BASIN ; SIZE ; DIFFERENTIATION ; PERFORMANCE |
| WOS类目 | Biotechnology & Applied Microbiology ; Genetics & Heredity |
| WOS研究方向 | Biotechnology & Applied Microbiology ; Genetics & Heredity |
| 来源机构 | Universidad Nacional Autónoma de México |
| 资源类型 | 期刊论文 |
| 条目标识符 | http://119.78.100.177/qdio/handle/2XILL650/319443 |
| 作者单位 | 1.Univ Nacl Autonoma Mexico, Inst Ecol, Dept Ecol Evolut, Ciudad Univ, Ciudad De Mexico 04510, Mexico; 2.Inst Ecol AC INECOL, Red Estudios Mol Avanzados, Cluster Cient & Tecnol BioMimic, Carretera Antigua Coatepec 351, Xalapa 91070, Veracruz, Mexico; 3.Univ Toronto, Dept Cell & Syst Biol, Toronto, ON, Canada; 4.Univ Toronto, Ctr Anal Genome Evolut & Funct, Toronto, ON, Canada |
| 推荐引用方式 GB/T 7714 | Vazquez-Rosas-Landa, Mirna,Ponce-Soto, Gabriel Yaxal,Aguirre-Liguori, Jonas,et al. Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation[J]. Universidad Nacional Autónoma de México,2020,21(1). |
| APA | Vazquez-Rosas-Landa, Mirna.,Ponce-Soto, Gabriel Yaxal.,Aguirre-Liguori, Jonas.,Thakur, Shalabh.,Scheinvar, Enrique.,...&Souza, Valeria.(2020).Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation.BMC GENOMICS,21(1). |
| MLA | Vazquez-Rosas-Landa, Mirna,et al."Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation".BMC GENOMICS 21.1(2020). |
| 条目包含的文件 | 条目无相关文件。 | |||||
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