Complete mitochondrial genome and phylogenetic analysis of the marine red alga Polyopes affinis (Rhodophyta: Halymeniales)

Abstract

Polyopes affinis ((Harvey) Kawaguchi & Wang, 2002) is a red alga in the order Halymeniales of the phylum Rhodophyta. The entire mitogenome of P. affinis was sequenced and compared to related Halymeniales species. The entire circular-mitogenome is 25,988 bp long, has 27.59% GC content, and comprises 25 protein-coding genes (CDS), 23 transfer RNA (tRNA) genes, and three ribosomal RNA (rRNA) genes. In terms of gene synteny and tRNA composition, the P. affinis mitogenome differs significantly from that of P. lancifolius . Phylogenetic analysis shows P. affinis mitogenome in a branch sister to P. lancifolius , indicating a close relationship with other Halymeniales species.

Complete Mitogenome Sequencing, Annotation, and Phylogeny of Grateloupia turuturu, a Red Alga with Intronic cox1 Gene

“…Each PCG was initiated by a canonical ATG codon, except for tatC , which was initiated by a TTG codon ( Table 2 ). Similar results have been demonstrated in G. cornea (OQ910480), G. elliptica [ 7 ], and P. affinis [ 10 ]. Furthermore, out of 26 PCGs, 21 terminated with the TAA codon, except 5 PCGs ( sdh2 , cox2 , atp8 , atp6 , and rps11 ) which terminated with the TAG codon, which was typical for Grateloupia [ 6 , 7 , 8 , 9 ] and P. lancifolius [ 11 ].…”

“…Hypothetical genes orf641 and orf173 ( Table 2 ) with an unknown function were identified and encoded hypothetical proteins. Similar outcomes have been documented for all G. angusta, G. cornea, G. elliptica, G. filicina, and G. taiwanensis , but not for P. affinis and P. lancifolius ( Table 1 ) [ 6 , 7 , 8 , 9 , 10 , 11 ]. Group II intronic cox1 and trnI are the unique features of red algal mitogenomes [ 12 , 13 , 15 ].…”

“…The ymf39 gene is transcribed between cox3 and trnG genes in the mitogenome of G. turuturu and encodes an ATP synthase B chain precursor. Similar annotations were reported for Grateloupia species [ 6 , 7 , 8 , 9 ] and P. lancifolius [ 11 ], but the annotation for P. affinis is atp4 [ 10 ]. In recent studies, a reanalysis of red mitogenome sequences revealed that the atp4 gene was annotated with the name, ymf39 , instead of its original name [ 12 , 34 ].…”

“…The positive AT skew (0.049) and GC skew (0.032) were observed in this study with the presence of more A and G than T and C, respectively ( Table 1 ). In comparison to Grateloupia [ 6 , 7 , 8 , 9 ] and Polyopes [ 10 , 11 ] species with complete mitogenome features, the mitogenome of G. turuturu demonstrates no significant gene losses; however, G. elliptica (OP479979) [ 7 ] has closer mitogenome features in terms of nucleotide composition, bias AT content, and gene compositions. In Halymeniales, the typical complete mitogenome was circular and approximately 25 to 30 kb in length with correspondingly conserved gene content, which encoded 24 PCGs (excluding intronic and hypothetical genes), 2–3 rRNAs, and 18–23 tRNAs with A + T bias nucleotides ( Table 1 ) [ 6 , 7 , 8 , 9 , 10 , 11 ].…”

“…taiwanensis , Polyopes affinis, and P . lancifolius ) with complete mitogenome have been reported [ 6 , 7 , 8 , 9 , 10 , 11 ], as listed in Table 1 .…”