The first complete organellar genomes of an Antarctic red alga, Pyropia endiviifolia: insights into its genome architecture and phylogenetic position within genus Pyropia (Bangiales, Rhodophyta)

Pyropia species grow in the intertidal zone and are cold-water adapted. To date, most of the information about the whole plastid and mitochondrial genomes (ptDNA and mtDNA) of this genus is limited to Northern Hemisphere species. Here, we report the sequencing of the ptDNA and mtDNA of the Antarctic...

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Bibliographic Details
Published in:Journal of oceanology and limnology 2018-07, Vol.36 (4), p.1315-1328
Main Authors: Xu, Kuipeng, Tang, Xianghai, Bi, Guiqi, Cao, Min, Wang, Lu, Mao, Yunxiang
Format: Article
Language:English
Subjects:
Algae
Bayesian analysis
Biology
Collinearity
Earth and Environmental Science
Earth Sciences
Genes
Genomes
Intertidal environment
Intertidal zone
Introns
Mitochondrial DNA
Northern Hemisphere
Oceanography
Operons
Phylogenetics
Phylogeny
Plastids
Probability theory
Proteins
Pyropia
rRNA
Species
Transfer RNA
tRNA
Water temperature
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Summary:Pyropia species grow in the intertidal zone and are cold-water adapted. To date, most of the information about the whole plastid and mitochondrial genomes (ptDNA and mtDNA) of this genus is limited to Northern Hemisphere species. Here, we report the sequencing of the ptDNA and mtDNA of the Antarctic red alga Pyropia endiviifolia using the Illumina platform. The plastid genome (195 784 bp, 33.28% GC content) contains 210 protein-coding genes, 37 tRNA genes and 6 rRNA genes. The mitochondrial genome (34 603 bp, 30.5% GC content) contains 26 protein-coding genes, 25 tRNA genes and 2 rRNA genes. Our results suggest that the organellar genomes of Py. endiviifolia have a compact organization. Although the collinearity of these genomes is conserved compared with other Pyropia species, the genome sizes show significant differences, mainly because of the different copy numbers of rDNA operons in the ptDNA and group II introns in the mtDNA. The other Pyropia species have 2–3 distinct intronic ORFs in their cox 1 genes, but Py. endiviifolia has no introns in its cox 1 gene. This has led to a smaller mtDNA than in other Pyropia species. The phylogenetic relationships within Pyropia were examined using concatenated gene sets from most of the available organellar genomes with both the maximum likelihood and Bayesian methods. The analysis revealed a sister taxa affiliation between the Antarctic species Py. endiviifolia and the North American species Py. kanakaensis .
ISSN:2096-5508
2523-3521
DOI:10.1007/s00343-018-7088-7