Dynamic evolution of mitochondrial genomes in Trebouxiophyceae, including the first completely assembled mtDNA from a lichen-symbiont microalga (Trebouxia sp. TR9)

Fernando Martínez-Alberola,Eva M Del Campo,Leonardo M Casano,Francisco Gasulla,Arántzazu Molins,Eva Barreno

doi:10.1038/s41598-019-44700-7

Fernando Martínez-Alberola, Eva M Del Campo + Show 4 more

Open Access

https://doi.org/10.1038/s41598-019-44700-7

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Journal: Scientific Reports	Publication Date: Jun 3, 2019
Citations: 12	License type: open-access

Affiliation: University of Valencia, University of Alcalá

Abstract

Trebouxiophyceae (Chlorophyta) is a species-rich class of green algae with a remarkable morphological and ecological diversity. Currently, there are a few completely sequenced mitochondrial genomes (mtDNA) from diverse Trebouxiophyceae but none from lichen symbionts. Here, we report the mitochondrial genome sequence of Trebouxia sp. TR9 as the first complete mtDNA sequence available for a lichen-symbiont microalga. A comparative study of the mitochondrial genome of Trebouxia sp. TR9 with other chlorophytes showed important organizational changes, even between closely related taxa. The most remarkable change is the enlargement of the genome in certain Trebouxiophyceae, which is principally due to larger intergenic spacers and seems to be related to a high number of large tandem repeats. Another noticeable change is the presence of a relatively large number of group II introns interrupting a variety of tRNA genes in a single group of Trebouxiophyceae, which includes Trebouxiales and Prasiolales. In addition, a fairly well-resolved phylogeny of Trebouxiophyceae, along with other Chlorophyta lineages, was obtained based on a set of seven well-conserved mitochondrial genes.

Highlights

The use of organelle genomic information has become a common practice for comparative studies and phylogenetic analyses of entire genomes
This imbalance is more remarkable among Trebouxiophyceae, since the availability of chloroplast genomes has increased in the few last years[1,5,6]
Regarding the tRNAs, a total of tRNA genes were identified with RNAweasel and tRNAscan-SE, whereas with ARAGORN, we found tRNAs, including an additional trnP

Summary

Introduction

The use of organelle genomic information has become a common practice for comparative studies and phylogenetic analyses of entire genomes (phylogenomics). Molecular data contributed to elucidating the evolution of chlorophytes, corroborating the initial hypothesis of the antiquity of Prasinophyceae, which gave rise to the remaining Chlorophyta classes[3,4] Regarding this issue, the phylogenetic relationships among chlorophytes remain controversial, especially at higher taxonomic levels (order, class). The number of complete sequences of organellar genomes in the NCBI databases is more than fifteen-fold greater in streptophytes than in chlorophytes (2,492 and 161 are available in the NCBI databases, respectively); among the 161 genomes from chlorophytes, only 56 correspond to mitogenomes This imbalance is more remarkable among Trebouxiophyceae, since the availability of chloroplast genomes has increased in the few last years (approximately 30 chloroplast genomes are available in the NCBI databases, most of them are published)[1,5,6]. Organization and gene content with other mitochondrial genomes reported for Trebouxiophyceae and other Chlorophyta microalgae and provide a phylogenetic reconstruction on the basis of seven selected mitochondrial genes (cob, cox[1], nad[1], nad[2], nad[4], nad[5] and nad[6])

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Conclusion