Complete mitochondrial genome sequence of Japanese forest green tree frog (Rhacophorus arboreus)

Abstract

We determined the complete mitochondrial genome sequence of the Japanese forest green tree frog (Rhacophorus arboreus). The mitochondrial genome is 22,236 bp in length, which encodes 13 proteincoding genes, 2 rRNA, and 22 tRNA genes, and two control regions (D-loops). The whole gene arrangement of R. arboreus was the same as that of Rhacophorus omeimontis and Rhacophorus schlegelii.

Complete Mitogenomes of Polypedates Tree Frogs Unveil Gene Rearrangement and Concerted Evolution within Rhacophoridae

“…Eight tRNA genes ( tRNA Pro , tRNA Gln , tRNA Ala , tRNA Asn , tRNA Cys , tRNA Tyr , tRNA Ser(UCN) , and tRNA Glu ), and one PCG ( ND6 ) were encoded on the light strand (L-strand), while the remaining 14 tRNAs and 11 PCGs were encoded on the heavy strand (H-strand) ( Figure 1 ; Table S3 ). This H&L-strand gene distribution is congruent with all seven previously published rhacophorid mitogenomes [ 20 , 21 , 22 , 23 , 24 , 36 , 42 ]. Similar to the mitogenome of two other Polypedates frogs ( P. braueri and P. megacephalus ) [ 21 , 22 , 30 ], there was an NCR situated between gene tRNA Lys and ATP6 that is thought to be the original position of the absent ATP8 gene [ 22 , 30 ].…”

“…The length of the 16S rRNA gene was 1537 bp for P. impresus and P. mutus , and the size of 12S rRNA gene was 930 bp for P. impresus and 931 bp for P. mutus ( Table S3 ). As shown in Table 2 and Table S4 , both rRNA genes presented a high A+T preference of 59.0% for P. impresus and 59.9% for P. mutus , which was in line with the other seven rhacophorids [ 20 , 21 , 22 , 23 , 24 , 30 , 36 , 42 ]. Furthermore, the comparative analysis indicated that all nine Rhacophoridae species possessed a positive AT skew and a negative GC skew for both the 12S rRNA gene and 16S rRNA gene ( Table S4 ).…”

“…Protein genes were also re-identified using NCBI’s ORF Finder ( , accessed on 10 February 2021) to ensure the correct reading frame. Seven known mitogenome sequences of rhacophorids [ 20 , 21 , 22 , 23 , 24 , 30 , 36 , 42 ] were used to manually correct the gene boundaries by aligning the orthologous genes using MEGA-X ( accessed on 10 February 2021) [ 43 ]. The putative origins of replication on the light strand (O L ) sequences were identified using the MITOS web server, and then the O L sequences and the flanking sequences were uploaded to Mfold ( , accessed on 10 February 2021) [ 44 ] and Forna (force-directed RNA; , accessed on 10 February 2021) [ 45 ] to determine the secondary structures.…”

“…To ensure the accuracy and extensiveness of the phylogenetic analyses, we downloaded the mitogenomes of all 178 anuran species that have been characterized to date (28 October 2021) from the NCBI reference sequence (RefSeq) database [ 49 ], as well as one recently determined Rhacophoridae mitogenome [ 24 ] ( Zhangixalus arboreus , GenBank ID: LC565708) that is not archived yet and our two new rhacophorid mitogenomes ( P. impresus , GenBank ID: MT869008; P. mutus , GenBank ID: MT869009). Four non-anuran vertebrates ( Aptenodytes forsteri , A. patagonicus , Alligator sinensis, and A. mississippiensis ) served as outgroups to root the phylogenetic tree.…”

“…Overall, frog mitogenomes are fast-evolving. The mitochondrial genes of the Archaeobatrachia suborder retain the canonical vertebrate arrangement, whereas many neobatrachian frogs have been split into multiple novel derived orders with duplicated CR copies (e.g., Dicroglossidae [ 16 , 17 ], Mantellidae [ 18 , 19 ], and Rhacophoridae [ 20 , 21 , 22 , 23 , 24 ]). This duplication pattern seems to be phylogenetically conserved and is thought to result from either independent evolution [ 25 , 26 ] or concerted evolution [ 27 , 28 , 29 ].…”