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DNA Res. 2016 Aug;23(4):325-38. doi: 10.1093/dnares/dsw023. Epub 2016 Jun 21.

Whole genomic DNA sequencing and comparative genomic analysis of Arthrospira platensis: high genome plasticity and genetic diversity.

Author information

1
School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou 325035, China.
2
Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
3
School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou 325035, China BGI-Shenzhen, Shenzhen 518083, China.
4
BGI-Shenzhen, Shenzhen 518083, China.
5
BGI-Shenzhen, Shenzhen 518083, China James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China.
6
School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou 325035, China BGI-Shenzhen, Shenzhen 518083, China baoqy@genomics.org.cn.

Abstract

Arthrospira platensis is a multi-cellular and filamentous non-N2-fixing cyanobacterium that is capable of performing oxygenic photosynthesis. In this study, we determined the nearly complete genome sequence of A. platensis YZ. A. platensis YZ genome is a single, circular chromosome of 6.62 Mb in size. Phylogenetic and comparative genomic analyses revealed that A. platensis YZ was more closely related to A. platensis NIES-39 than Arthrospira sp. PCC 8005 and A. platensis C1. Broad gene gains were identified between A. platensis YZ and three other Arthrospira speices, some of which have been previously demonstrated that can be laterally transferred among different species, such as restriction-modification systems-coding genes. Moreover, unprecedented extensive chromosomal rearrangements among different strains were observed. The chromosomal rearrangements, particularly the chromosomal inversions, were analysed and estimated to be closely related to palindromes that involved long inverted repeat sequences and the extensively distributed type IIR restriction enzyme in the Arthrospira genome. In addition, species from genus Arthrospira unanimously contained the highest rate of repetitive sequence compared with the other species of order Oscillatoriales, suggested that sequence duplication significantly contributed to Arthrospira genome phylogeny. These results provided in-depth views into the genomic phylogeny and structural variation of A. platensis, as well as provide a valuable resource for functional genomics studies.

KEYWORDS:

chromosomal rearrangement; comparative genomics; evolution; lateral gene transfer

PMID:
27330141
PMCID:
PMC4991836
DOI:
10.1093/dnares/dsw023
[Indexed for MEDLINE]
Free PMC Article

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