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)
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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.
KeywordAntarctic Pyropia endiviifolia plastid and mitochondrial genomes genome structure phylogenetic
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- Brodie J A, Irvine L M. 2003. Seaweeds of the British Isles. Volume 1 Rhodophyta. Part 3B Bangiophycidae. Natural History Museum, London.Google Scholar
- Buschiazzo E, Ritland C, Bohlmann J, Ritland K. 2012. Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms. BMC Evolutionary Biology, 12: 8.Google Scholar
- Chamberlain Y M. 1963. The identity of Monostroma endiviifolium A. and E.S. Gepp. Nova Hedwigia, 5: 151–155.Google Scholar
- Gray M W, Burger G, Lang B F. 2001. The origin and early evolution of mitochondria. Genome Biology, 2 (6): reviews1018.1.Google Scholar
- Guiry M D, Guiry G M. 2017. AlgaeBase. World-Wide Electronic Publication, National University of Ireland, Galway, https://doi.org/www.marinespecies.org/aphia.php?p=sourcedetails&id=37. Google Scholar
- Hagopian J C, Reis M, Kitajima J P, Bhattacharya D, De Oliveira M C. 2004. Comparative analysis of the complete plastid genome sequence of the red alga Gracilaria tenuistipitata var. liui provides insights into the evolution of rhodoplasts and their relationship to other plastids. Journal of Molecular Evolution, 59 (4): 464–477.CrossRefGoogle Scholar
- Mumford Jr T F, Miura A. 1988. Porphyra as food: cultivation and economics. In: Lembi C A, Waaland J R eds. Algae and Human Affairs. Cambridge University Press, Cambridge.Google Scholar
- Niwa K, Kikuchi N, Iwabuchi M, Aruga Y. 2004. Morphological and AFLP variation of Porphyra yezoensis Ueda form, narawaensis Miura (Bangiales, Rhodophyta). Phycological Research, 52 (2): 180–190.Google Scholar
- Ogihara Y, Yamazaki Y, Murai K, Kanno A, Terachi T, Shiina T, Miyashita N, Nasuda S, Nakamura C, Mori N, Takumi S, Murata N, Futo S, Tsunewaki K. 2005. Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome. Nucleic A cids Research, 33 (19): 6 235–6 250.CrossRefGoogle Scholar
- Sutherland J E, Lindstrom S C, Nelson W A, Brodie J, Lynch M D J, Hwang M S, Choi H G, Miyata M, Kikuchi N, Oliveira M C, Farr T, Neefus C, Mols-Mortensen A, Milstein D, Müller K M. 2011. A new look at an ancient order: generic revision of the Bangiales (Rhodophyta). Journal of Phycology, 47 (5): 1 131–1 151.CrossRefGoogle Scholar
- Yang E C, Kim K M, Kim S Y, Lee J, Boo G H, Lee J H, Nelson W A, Yi G M, Schmidt W E, Fredericq S, Boo S M, Bhattacharya D, Yoon H S. 2015. Highly conserved mitochondrial genomes among multicellular red algae of the Florideophyceae. Genome Biology and E volution, 7 (8): 2 394–2 406.CrossRefGoogle Scholar