Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus
Synechococcus is among the most important contributors to global primary productivity. The genomes of several strains of this taxon have been previously sequenced in an effort to understand the physiology and ecology of these highly diverse microorganisms. Here we present a comparative study of Syne...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2016-01-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/1522.pdf |
| _version_ | 1797420036654104576 |
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| author | Felipe Coutinho Diogo Antonio Tschoeke Fabiano Thompson Cristiane Thompson |
| author_facet | Felipe Coutinho Diogo Antonio Tschoeke Fabiano Thompson Cristiane Thompson |
| author_sort | Felipe Coutinho |
| collection | DOAJ |
| description | Synechococcus is among the most important contributors to global primary productivity. The genomes of several strains of this taxon have been previously sequenced in an effort to understand the physiology and ecology of these highly diverse microorganisms. Here we present a comparative study of Synechococcus genomes. For that end, we developed GenTaxo, a program written in Perl to perform genomic taxonomy based on average nucleotide identity, average amino acid identity and dinucleotide signatures, which revealed that the analyzed strains are drastically distinct regarding their genomic content. Phylogenomic reconstruction indicated a division of Synechococcus in two clades (i.e. Synechococcus and the new genus Parasynechococcus), corroborating evidences that this is in fact a polyphyletic group. By clustering protein encoding genes into homologue groups we were able to trace the Pangenome and core genome of both marine and freshwater Synechococcus and determine the genotypic traits that differentiate these lineages. |
| first_indexed | 2024-03-09T06:56:46Z |
| format | Article |
| id | doaj.art-1e94b4503c6841b3bccf7b5bb7535004 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:56:46Z |
| publishDate | 2016-01-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
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| spelling | doaj.art-1e94b4503c6841b3bccf7b5bb75350042023-12-03T10:02:45ZengPeerJ Inc.PeerJ2167-83592016-01-014e152210.7717/peerj.1522Comparative genomics of Synechococcus and proposal of the new genus ParasynechococcusFelipe Coutinho0Diogo Antonio Tschoeke1Fabiano Thompson2Cristiane Thompson3Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, BrazilInstituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, BrazilInstituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, BrazilInstituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, BrazilSynechococcus is among the most important contributors to global primary productivity. The genomes of several strains of this taxon have been previously sequenced in an effort to understand the physiology and ecology of these highly diverse microorganisms. Here we present a comparative study of Synechococcus genomes. For that end, we developed GenTaxo, a program written in Perl to perform genomic taxonomy based on average nucleotide identity, average amino acid identity and dinucleotide signatures, which revealed that the analyzed strains are drastically distinct regarding their genomic content. Phylogenomic reconstruction indicated a division of Synechococcus in two clades (i.e. Synechococcus and the new genus Parasynechococcus), corroborating evidences that this is in fact a polyphyletic group. By clustering protein encoding genes into homologue groups we were able to trace the Pangenome and core genome of both marine and freshwater Synechococcus and determine the genotypic traits that differentiate these lineages.https://peerj.com/articles/1522.pdfSynechococcusPhylogenomicsGenomicsCyanobacteriaGenomic taxonomy |
| spellingShingle | Felipe Coutinho Diogo Antonio Tschoeke Fabiano Thompson Cristiane Thompson Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus PeerJ Synechococcus Phylogenomics Genomics Cyanobacteria Genomic taxonomy |
| title | Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus |
| title_full | Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus |
| title_fullStr | Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus |
| title_full_unstemmed | Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus |
| title_short | Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus |
| title_sort | comparative genomics of synechococcus and proposal of the new genus parasynechococcus |
| topic | Synechococcus Phylogenomics Genomics Cyanobacteria Genomic taxonomy |
| url | https://peerj.com/articles/1522.pdf |
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