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Sequence analysis of Arthrospira maxima based on fosmid library

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Abstract

Arthrospira (Spirulina) (Setchell & Gardner) is an important cyanobacterium not only in its nutritional potential but in its special biological characteristics. An unbiased fosmid library of Arthrospira maxima FACHB438 that contains 4300 clones was constructed. The size distribution of insert fragments is from 15.5 to 48.9 kb and the average size is 37.6 kb. The recombination frequency is 100%. Therefore the library is 29.9 equivalents to the Arthrospira genome size of 5.4 Mb. A total of 719 sample clones were randomly chosen from the library and 602 available sequences, which consisted of 307,547 bases, covering 5.70% of the whole genome. The codon usage of A. maxima was not strongly biased. GC content at the first position of codons (46.9%) was higher than the second (39.8%) and the third (45.5%) positions. GC content of the genome was 43.6%. Of these sequences, 287 (47.7%) showed high similarities to known genes, 63 (10.5%) to hypothetical genes and the remaining 252 (41.8%) had no significant similarities. The assigned genes were classified into 22 categories with respect to different biological roles. Remarkably, the high presence of 25 sequences (4.2%) encoding reverse transcriptase indicates the RT gene may have multiple copies in the A. maxima genome and might play an important role in the evolutionary history and metabolic regulation. In addition, the sequences encoding the ATP-binding cassette transport system and the two-component signal transduction system were the second and third most frequent genes, respectively. These genomic features provide some clues as to the mechanisms by which this organism adapts to the high concentration of bicarbonate and to the high pH environment.

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Abbreviations

ABC:

ATP-binding cassette

FIGE:

Field inversion gel electrophoresis

KEGG:

Kyoto Encyclopedia of Genes and Genomes

RT:

Reverse transcriptase

TCST:

Two-component signal transduction system

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Acknowledgements

The work was supported by the National Natural Science Foundation of China (Grant No.30200208 and No.30571418) and the Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences. We thank Hangzhou Genomics Institute for performing the DNA sequencing under contract and Aruna kumara for valuable advice and critical reading of the manuscript.

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Authors and Affiliations

  1. Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China

    Na Ling, Yunxiang Mao, Xuecheng Zhang & Wei Liu

  2. Key Laboratory of Experimental Marine Biology Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China

    Zhaolan Mo & Guangce Wang

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  1. Na Ling
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  2. Yunxiang Mao
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  3. Xuecheng Zhang
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  5. Guangce Wang
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Correspondence to Yunxiang Mao.

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Ling, N., Mao, Y., Zhang, X. et al. Sequence analysis of Arthrospira maxima based on fosmid library. J Appl Phycol 19, 333–346 (2007). https://doi.org/10.1007/s10811-006-9140-9

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  • DOI: https://doi.org/10.1007/s10811-006-9140-9

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