Comprehensive Transcriptome Analysis Reveals Insights into Phylogeny and Positively Selected Genes of <i>Sillago</i> Species
<i>Sillago</i> species lives in the demersal environments and face multiple stressors, such as localized oxygen depletion, sulfide accumulation, and high turbidity. In this study, we performed transcriptome analyses of seven <i>Sillago</i> species to provide insights into the...
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| Format: | Article |
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MDPI AG
2020-04-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/10/4/633 |
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| author | Fangrui Lou Yuan Zhang Na Song Dongping Ji Tianxiang Gao |
| author_facet | Fangrui Lou Yuan Zhang Na Song Dongping Ji Tianxiang Gao |
| author_sort | Fangrui Lou |
| collection | DOAJ |
| description | <i>Sillago</i> species lives in the demersal environments and face multiple stressors, such as localized oxygen depletion, sulfide accumulation, and high turbidity. In this study, we performed transcriptome analyses of seven <i>Sillago</i> species to provide insights into the phylogeny and positively selected genes of this species. After de novo assembly, 82,024, 58,102, 63,807, 85,990, 102,185, 69,748, and 102,903 unigenes were generated from <i>S.</i> <i>japonica</i>, <i>S.</i> <i>aeolus</i>, <i>S.</i> sp.1, <i>S.</i> <i>sihama</i>, <i>S.</i> sp.2, <i>S. parvisquamis</i>, and <i>S.</i> <i>sinica</i>, respectively. Furthermore, 140 shared orthologous exon markers were identified and then applied to reconstruct the phylogenetic relationships of the seven <i>Sillago</i> species. The reconstructed phylogenetic structure was significantly congruent with the prevailing morphological and molecular biological view of <i>Sillago</i> species relationships. In addition, a total of 44 genes were identified to be positively selected, and these genes were potential participants in the stress response, material (carbohydrate, amino acid and lipid) and energy metabolism, growth and differentiation, embryogenesis, visual sense, and other biological processes. We suspected that these genes possibly allowed <i>Sillago</i> species to increase their ecological adaptation to multiple environmental stressors. |
| first_indexed | 2024-03-10T20:37:58Z |
| format | Article |
| id | doaj.art-98107c9210a740c897c404fb673ac7ab |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-10T20:37:58Z |
| publishDate | 2020-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj.art-98107c9210a740c897c404fb673ac7ab2023-11-19T20:51:32ZengMDPI AGAnimals2076-26152020-04-0110463310.3390/ani10040633Comprehensive Transcriptome Analysis Reveals Insights into Phylogeny and Positively Selected Genes of <i>Sillago</i> SpeciesFangrui Lou0Yuan Zhang1Na Song2Dongping Ji3Tianxiang Gao4Fishery College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, ChinaFishery College, Ocean University of China, Qingdao 266003, Shandong, ChinaFishery College, Ocean University of China, Qingdao 266003, Shandong, ChinaAgricultural Machinery Service Center, Fangchenggang 538000, Guangxi, ChinaFishery College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China<i>Sillago</i> species lives in the demersal environments and face multiple stressors, such as localized oxygen depletion, sulfide accumulation, and high turbidity. In this study, we performed transcriptome analyses of seven <i>Sillago</i> species to provide insights into the phylogeny and positively selected genes of this species. After de novo assembly, 82,024, 58,102, 63,807, 85,990, 102,185, 69,748, and 102,903 unigenes were generated from <i>S.</i> <i>japonica</i>, <i>S.</i> <i>aeolus</i>, <i>S.</i> sp.1, <i>S.</i> <i>sihama</i>, <i>S.</i> sp.2, <i>S. parvisquamis</i>, and <i>S.</i> <i>sinica</i>, respectively. Furthermore, 140 shared orthologous exon markers were identified and then applied to reconstruct the phylogenetic relationships of the seven <i>Sillago</i> species. The reconstructed phylogenetic structure was significantly congruent with the prevailing morphological and molecular biological view of <i>Sillago</i> species relationships. In addition, a total of 44 genes were identified to be positively selected, and these genes were potential participants in the stress response, material (carbohydrate, amino acid and lipid) and energy metabolism, growth and differentiation, embryogenesis, visual sense, and other biological processes. We suspected that these genes possibly allowed <i>Sillago</i> species to increase their ecological adaptation to multiple environmental stressors.https://www.mdpi.com/2076-2615/10/4/633Sillaginidaebottom dwellerRNA-seqorthologous exon markerspositive selection |
| spellingShingle | Fangrui Lou Yuan Zhang Na Song Dongping Ji Tianxiang Gao Comprehensive Transcriptome Analysis Reveals Insights into Phylogeny and Positively Selected Genes of <i>Sillago</i> Species Animals Sillaginidae bottom dweller RNA-seq orthologous exon markers positive selection |
| title | Comprehensive Transcriptome Analysis Reveals Insights into Phylogeny and Positively Selected Genes of <i>Sillago</i> Species |
| title_full | Comprehensive Transcriptome Analysis Reveals Insights into Phylogeny and Positively Selected Genes of <i>Sillago</i> Species |
| title_fullStr | Comprehensive Transcriptome Analysis Reveals Insights into Phylogeny and Positively Selected Genes of <i>Sillago</i> Species |
| title_full_unstemmed | Comprehensive Transcriptome Analysis Reveals Insights into Phylogeny and Positively Selected Genes of <i>Sillago</i> Species |
| title_short | Comprehensive Transcriptome Analysis Reveals Insights into Phylogeny and Positively Selected Genes of <i>Sillago</i> Species |
| title_sort | comprehensive transcriptome analysis reveals insights into phylogeny and positively selected genes of i sillago i species |
| topic | Sillaginidae bottom dweller RNA-seq orthologous exon markers positive selection |
| url | https://www.mdpi.com/2076-2615/10/4/633 |
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