Dataset Information

The Chloroplast Genome of the Lichen Photobiont Trebouxiophyceae sp. DW1 and Its Phylogenetic Implications.

ABSTRACT: 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 (Trebouxiophyceae 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 Trebouxiophyceae sp. DW1 is sister to the clade of Koliella longiseta and Pabia signiensis.

SUBMITTER: Wang L

PROVIDER: S-EPMC9601494 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature

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The Chloroplast Genome of the Lichen Photobiont <i>Trebouxiophyceae</i> sp. DW1 and Its Phylogenetic Implications.

Wang Lidan L Zhang Shenglu S Fang Jinjin J Jin Xinjie X Mamut Reyim R Li Pan P

Genes 20221012 10

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 ...[more]

PMID: 36292725

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Project description:The green algal genus Trebouxia is the most frequently encountered photobiont of the lichen symbiosis. The single-celled symbionts have a worldwide distribution, including all continents and climate zones. The vast, largely undescribed, diversity of Trebouxia lineages is currently grouped into four phylogenetic clades (A, C, I, and S), based on a multilocus phylogeny. Genomes are still scarce, however, and it is unclear how the phylogenetic diversity, the broad ecological tolerances, and the ability to form symbioses with many different fungal host species are reflected in genome-wide differences. Here, we generated PacBio-based de novo genomes of six Trebouxia lineages belonging to the Clades A and S, isolated from lichen individuals of the genus Umbilicaria. Sequences belonging to Clade S have been reported in a previous study, but were reassembled and reanalyzed here. Genome sizes ranged between 63.08 and 73.88 Mb. Repeat content accounted for 9% to 16% of the genome sequences. Based on RNA evidence, we predicted 14,109 to 16,701 gene models per genome, of which 5,203 belonged to a core set of gene families shared by all 6 lineages. Between 121 and 454, gene families are specific to each lineage. About 53% of the genes could be functionally annotated. The presence of biosynthetic gene clusters (6 to 17 per genome) suggests that Trebouxia algae are able to synthesize alkaloids, saccharides, terpenes, NRPSs, and T3PKSs. Phylogenomic comparisons of the six strains indicate prevalent gene gain during Trebouxia evolution. Some of the gene families that exhibited significant evolutionary changes (i.e. gene expansion and contraction) are associated with metabolic processes linked to protein phosphorylation, which is known to have a role in photosynthesis regulation, particularly under changing light conditions. Overall, there is substantial genomic divergence within the algal genus Trebouxia, which may contribute to the genus' large ecological amplitude concerning fungal host diversity and climatic niches.

Dataset Information

The Chloroplast Genome of the Lichen Photobiont Trebouxiophyceae sp. DW1 and Its Phylogenetic Implications.

Publications

The Chloroplast Genome of the Lichen Photobiont <i>Trebouxiophyceae</i> sp. DW1 and Its Phylogenetic Implications.

Similar Datasets

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