Mitochondrial genome analysis and systematics of Halymeniaceae (Halymeniales, Rhodophyta)

Abstract

Halymeniaceae Bory is one of the largest family in Rhodophyta, including 35 genera and 332 species. Previous rbcL analysis showed promising utility for the taxonomy of Halymeniacean species, although it showed limitation to resolve deep phylogeny. Based on the rbcL (207 taxa) phylogeny, we selected 6 representatives for the 4 major clades of Halymeniaceae as follow i) Grateloupia angusta & Kintokiocolax agregato-cerantha, ii) Halymenia maculata, iii) Polyopes affinis & P. lancifolious, iv) Pacymenia lanciniata. We determined new six mitochondrial genomes using Ion Torrent Personal Genome Machine (Life Technology, USA), and assembled using MIRA assembler. The overall mitochondrial gene synteny is highly conserved among the halymeniacean species with a few differences such as total size of mitogenome, intron positions, and numbers of tRNAs. The mitogenome variation mostly caused by intron and intronic-ORF of rrl and cox1. The other variations arefollowed as: 1) structural differences of intron and intronic ORFs in cox1 and rrl 2) absence of ymf39 in H. maculata and atp8 and ymf39 in P. lanciniata 3) different positions of two t-RNAs (trnG and trnL) among species and independent gain and loss of tRNA, i.e., two gain (trnD and trnH) and one loss (trnL) in H. maculata one gain (trnR) and one loss (trnM) in P. lanciniata. Various combinations of mitochondrial genes were tested to resolve the relationships among 4 majo