Abstract
Since 2007, the annual green tide disaster in the Yellow Sea has brought serious economic losses to China. There is no research on the genetic similarities of four constituent species of green tide algae at the genomic level. We previously determined the mitochondrial genomes of Ulva prolifera, Ulva linza and Ulva flexuosa. In the present work, the mitochondrial genome of another green tide (Ulva compressa) was sequenced and analyzed. With the length of 62,311 bp, it contained 29 encoding genes, 26 tRNAs and 10 open reading frames. By comparing these four mitochondrial genomes, we found that U. compressa was quite different from the other three types of Ulva species. However, there were similarities between U. prolifera and U. linza in the number, distribution and homology of open reading frames, evolutionary and codon variation of tRNA, evolutionary relationship and selection pressure of coding genes. Repetitive sequence analysis of simple sequence repeats, tandem repeat and forward repeats further supposed that they have evolved from the same origin. In addition, we directly analyzed gene homologies and translocation of four green tide algae by Mauve alignment. There were gene order rearrangements among them. With fast-evolving genomes, these four green algal mitochondria have both conservatism and variation, thus opening another window for the understanding of origin and evolution of Ulva.
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Abbreviations
- ORF:
-
Open reading frame
- PCG:
-
Protein-coding gene
- ML:
-
Maximum likelihood
- SSR:
-
Simple sequence repeat
- TR:
-
Tandem repeat
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Acknowledgements
We appreciate a lot the peer reviewers and editors for their constructive suggestions and revisions of this article. We thank Shanghai MAP Biotech Co., Ltd. for technical assistance. This work was supported by Shanghai Natural Science Fund (18ZR1417400), National Natural Science Foundation of China (41576163), National Key R&D Program of China (2016YFC1402105) and Key Laboratory of Integrated Marine Monitoring and Applied Technologies for Harmful Algal Blooms, S.O.A. (MATHAB2017010). The funders did not play a role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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CEC was responsible for the bioinformatics analysis of mitogenomes and wrote the manuscript. FL and KG were participated in bioinformatics analysis. TJ was participated in generation sequencing and assembling. LKW collected U. compressa, identified and cultivated the algae. LJZ was participated in U. compressa collection and identification. RJ was participated in U. compressa cultivation. JFR was participated in phylogenomic analysis. PMH, CEC and RJ conceived the study. PMH was responsible for generation sequencing and assembling. CEC and PMH were responsible for research funding. All authors reviewed the manuscript.
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Cai, C., Liu, F., Jiang, T. et al. Comparative study on mitogenomes of green tide algae. Genetica 146, 529–540 (2018). https://doi.org/10.1007/s10709-018-0046-7
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DOI: https://doi.org/10.1007/s10709-018-0046-7