Comparative genomics and systematics of Betaphycus, Eucheuma, and Kappaphycus (Solieriaceae: Rhodophyta) based on mitochondrial genome
Betaphycus Doty, Eucheuma J. Agardh, and Kappaphycus Doty (Solieriaceae, Gigartinales) are the three most commercially important seaweed genera that produce carrageenan. In the present study we provide mitogenomes of Betaphycus gelatinus, Eucheuma denticulatum and Kappaphycus alvarezii. The mitogenomes of these three species contain a set of 50 genes, including 24 protein-coding genes, 2 rRNA genes, and 24 tRNA genes. The mitogenome length ranges from 25,198 bp (Kappaphycus alvarezii) to 25,327 bp (Eucheuma denticulatum). As compared with the previous published mitogenomes of Florideophyceae species, only the species in Gelidiaceae and Pterocladiaceae have smaller mitochondrial genome size than these reported here. At the junction of two transcription units, we identified a stem-loop structure in six representative Gigartinales species, which is presumed to play an important role in the replication and transcription of mitochondrial genes. In Gigartinales the difference in gene order among the four Solieriaceae (B. gelatinus, E. denticulatum, K. alvarezii, K. striatus) and other two Gigartinales species (Chondrus crispus and Mastocarpus papillatus) can be explained by inversion of two tRNA genes. Collinearity analysis of the 12 mitochondrial genomes of Florideophyceae showed considerable sequence synteny across all the species compared, with the exception of a highly variable region between atp6 and rpl20 genes. Phylogenetic analyses based on 21 shared mitochondrial genes showed that the four Solieriaceae species form one clade (Solieriaceae clade). Within this clade, B. gelatinae is basal relative to the other three species. The genus Kappaphycus is more closely related to Eucheuma than Betaphycus.
KeywordsCollinearity analysis Mitochondrial genome Phylogenetic analyses Solieriaceae Stem-loop
This work was supported by the China-ASEAN Maritime Cooperation Fund, by Public Science and Technology Research Funds Projects of Ocean (Grant No. 201405020), and by the Fundamental Research Funds for the Central Universities.
- Doty MS, Norris JN (1985) Eucheuma species (Solieriaceae, Rhodophyta) that are major sources of carrageenan. In: Abbott IA (ed) Taxonomy of economic seaweeds. California Sea Grant College Program, La Jolla, pp 47–61Google Scholar
- Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT; Nucl Acids Symp Ser 41:95–98Google Scholar
- Pereira L, Meireles F, Abreu HT, Ribeiro-Claro PJA (2015) A comparative analysis of carrageenans produced by underutilized versus industrially utilized macroalgae (Gigartinales, Rhodophyta). In: Kim S-K, Chojnacka K (eds) Marine algae extracts: processes, products, and applications. Wiley-VCH, Weinheim, pp 277–294Google Scholar
- Sissini MN, Navarrete-Fernández TM, Murray EMC, Freese JM, Gentilhomme AS, Huber SR, Mumford TF, Hughey JR (2016) Mitochondrial and plastid genome analysis of the heteromorphic red alga Mastocarpus papillatus (C. Agardh) Kützing (Phyllophoraceae, Rhodophyta) reveals two characteristic florideophyte organellar genomes. Mitochondrial DNA B 1:676–677CrossRefGoogle Scholar
- Sun YY, Luo D, Zhao C, Li W, Liu T (2011) DNA extraction and PCR analysis of five kinds of large seaweed under different preservation conditions. Mol Plant Breed 9:1680–1691Google Scholar
- Zuccarello GC, Critchley AT, Smith J, Sieber V, Lhonneur GB, West JA (2007) Systematics and genetic variation in commercial Kappaphycus and Eucheuma (Solieriaceae, Rhodophyta). In: Anderson R, Brodie J, Onsøyen E, Critchley AT (eds) Proceedings of the Eighteenth International Seaweed Symposium. Springer, Dordrecht, pp 417–425CrossRefGoogle Scholar