The complete sequence of the mitochondrial DNA and phylogenetic analysis of the marine red alga Grateloupia elliptica (Rhodophyta: Halymeniales)

Abstract

Grateloupia elliptica (Holmes, 1896) is a red alga belonging to the order Halymeniales and phylum Rhodophyta. In this study, the complete mitochondrial DNA (mtDNA) of G. elliptica has been described. The complete circular mtDNA of G. elliptica was 28,503 bp in length, with an A + T content of 68.78%; it encoded a total of 49 genes, including 20 tRNA, three rRNA, and 26 protein-coding ( CDS ) genes. Phylogenetic analysis based on complete mitochondrial genomes revealed that G. elliptica was most closely related to G. angusta . The complete mitochondrial sequence of G. elliptica will enrich the mitochondrial genome database and provide useful resources for population genetics and evolution analyses.

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 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 .…”

“…In addition, mitogenomes have a specific sequence that gives reliable data for studying the gene order, makeup, contents, and secondary structures of the encoded RNA [ 14 , 15 ], and it is also useful for making molecular kits (barcoding markers) for economically important species identification [ 16 ]. The Grateloupia species contain a characteristic intronic cox1 gene ( Table 1 ), and such features are useful to understand evolutionary and phylogenetic studies [ 3 , 6 , 7 , 8 , 9 , 17 ]. Algae mitogenomes consist of introns in the genic region, tandem repeats, and large intergenic repeats, which create challenges for assembling complete circular mitogenomes [ 15 ] but due to revolutionary advances in sequencing technologies and bioinformatics tools, such issues can be overcome.…”