The Chloroplast Genome of the Lichen Photobiont <i>Trebouxiophyceae</i> sp. DW1 and Its Phylogenetic Implications
Lichens are symbiotic associations of algae and fungi. The genetic mechanism of the symbiosis of lichens and the influence of symbiosis on the size and composition of the genomes of symbiotic algae have always been intriguing scientific questions explored by lichenologists. However, there were limit...
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MDPI AG
2022-10-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/10/1840 |
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| author | Lidan Wang Shenglu Zhang Jinjin Fang Xinjie Jin Reyim Mamut Pan Li |
| author_facet | Lidan Wang Shenglu Zhang Jinjin Fang Xinjie Jin Reyim Mamut Pan Li |
| author_sort | Lidan Wang |
| collection | DOAJ |
| description | Lichens are symbiotic associations of algae and fungi. The genetic mechanism of the symbiosis of lichens and the influence of symbiosis on the size and composition of the genomes of symbiotic algae have always been intriguing scientific questions explored by lichenologists. However, there were limited data on lichen genomes. Therefore, we isolated and purified a lichen symbiotic alga to obtain a single strain (<i>Trebouxiophyceae</i> sp. DW1), and then obtained its chloroplast genome information by next-generation sequencing (NGS). The chloroplast genome is 129,447 bp in length, and the GC content is 35.2%. Repetitive sequences with the length of 30–35 bp account for 1.27% of the total chloroplast genome. The simple sequence repeats are all mononucleotide repeats. Codon usage analysis showed that the genome tended to use codon ending in A/U. By comparing the length of different regions of Trebouxiophyceae genomes, we found that the changes in the length of exons, introns, and intergenic sequences affect the size of genomes. Trebouxiophyceae had an unstable chloroplast genome structure, with IRs repeatedly losing during evolution. Phylogenetic analysis showed that Trebouxiophyceae is paraphyletic, and <i>Trebouxiophyceae</i> sp. DW1 is sister to the clade of <i>Koliella longiseta</i> and <i>Pabia signiensis</i>. |
| first_indexed | 2024-03-09T03:38:46Z |
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| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T03:38:46Z |
| publishDate | 2022-10-01 |
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| series | Genes |
| spelling | doaj.art-c10d0e09217b4ca2b73d8de98c16d9222023-12-03T14:45:26ZengMDPI AGGenes2073-44252022-10-011310184010.3390/genes13101840The Chloroplast Genome of the Lichen Photobiont <i>Trebouxiophyceae</i> sp. DW1 and Its Phylogenetic ImplicationsLidan Wang0Shenglu Zhang1Jinjin Fang2Xinjie Jin3Reyim Mamut4Pan Li5College of Life Sciences and Technology, Xinjiang University, Urumchi 830046, ChinaCollege of Life Sciences, Zhejiang University, Hangzhou 310058, ChinaCollege of Life Sciences and Technology, Xinjiang University, Urumchi 830046, ChinaCollege of Life and Environmental Science, Wenzhou University, Wenzhou 325035, ChinaCollege of Life Sciences and Technology, Xinjiang University, Urumchi 830046, ChinaCollege of Life Sciences, Zhejiang University, Hangzhou 310058, ChinaLichens are symbiotic associations of algae and fungi. The genetic mechanism of the symbiosis of lichens and the influence of symbiosis on the size and composition of the genomes of symbiotic algae have always been intriguing scientific questions explored by lichenologists. However, there were limited data on lichen genomes. Therefore, we isolated and purified a lichen symbiotic alga to obtain a single strain (<i>Trebouxiophyceae</i> sp. DW1), and then obtained its chloroplast genome information by next-generation sequencing (NGS). The chloroplast genome is 129,447 bp in length, and the GC content is 35.2%. Repetitive sequences with the length of 30–35 bp account for 1.27% of the total chloroplast genome. The simple sequence repeats are all mononucleotide repeats. Codon usage analysis showed that the genome tended to use codon ending in A/U. By comparing the length of different regions of Trebouxiophyceae genomes, we found that the changes in the length of exons, introns, and intergenic sequences affect the size of genomes. Trebouxiophyceae had an unstable chloroplast genome structure, with IRs repeatedly losing during evolution. Phylogenetic analysis showed that Trebouxiophyceae is paraphyletic, and <i>Trebouxiophyceae</i> sp. DW1 is sister to the clade of <i>Koliella longiseta</i> and <i>Pabia signiensis</i>.https://www.mdpi.com/2073-4425/13/10/1840algaegenome size<i>Peltigera</i>Prasiolalesphylogeny |
| spellingShingle | Lidan Wang Shenglu Zhang Jinjin Fang Xinjie Jin Reyim Mamut Pan Li The Chloroplast Genome of the Lichen Photobiont <i>Trebouxiophyceae</i> sp. DW1 and Its Phylogenetic Implications Genes algae genome size <i>Peltigera</i> Prasiolales phylogeny |
| title | The Chloroplast Genome of the Lichen Photobiont <i>Trebouxiophyceae</i> sp. DW1 and Its Phylogenetic Implications |
| title_full | The Chloroplast Genome of the Lichen Photobiont <i>Trebouxiophyceae</i> sp. DW1 and Its Phylogenetic Implications |
| title_fullStr | The Chloroplast Genome of the Lichen Photobiont <i>Trebouxiophyceae</i> sp. DW1 and Its Phylogenetic Implications |
| title_full_unstemmed | The Chloroplast Genome of the Lichen Photobiont <i>Trebouxiophyceae</i> sp. DW1 and Its Phylogenetic Implications |
| title_short | The Chloroplast Genome of the Lichen Photobiont <i>Trebouxiophyceae</i> sp. DW1 and Its Phylogenetic Implications |
| title_sort | chloroplast genome of the lichen photobiont i trebouxiophyceae i sp dw1 and its phylogenetic implications |
| topic | algae genome size <i>Peltigera</i> Prasiolales phylogeny |
| url | https://www.mdpi.com/2073-4425/13/10/1840 |
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