Complete mitochondrial genome of the Japanese Cormorant Phalacrocorax capillatus (Temminck & Schlegel, 1850) (Suliformes: Phalacrocoracidae)

Abstract The complete sequencing of mitochondrial DNA of the Japanese Cormorant Phalacrocorax capillatus was performed using long PCR and primer walking methods. The assembled genome was 19,105 bp in length. It contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and two control regions. The phylogenetic analysis using the obtained sequence showed that P. capillatus is closest to P. carbo.

The Japanese Cormorant Phalacrocorax capillatus (Temminck & Schlegel, 1850) is native to Northeast Asia, from Taiwan, throughout the east coast of China, Korea, and Japan to Sakhalin (Orta et al. 2020). The phylogenetic position of P. capillatus in the family Phalacrocoracidae remains controversial as it forms a monophyletic group with some subspecies of P. carbo (Kennedy and Spencer 2014). This ambiguity in the phylogenetic position of P. capillatus is possibly be due to lack of genetic data. Therefore, the development of genetic markers for P. capillatus with varying evolutionary rates is needed to understand the evolution of Phalacrocoracidae.
A blood specimen of P. capillatus was obtained from a bird rescued in Aomori City, Japan (40 48 0 N, 140 46 0 E) on 1 February 2010, by the Aomori Wildlife Conservation Center; however, the bird died two days later. The genomic DNA extracted from the specimen was deposited at Hirosaki University (Dr. Atsushi Sogabe, e-mail: atsushi.sogabe@hirosaki-u.ac.jp) under voucher number HUA2103161. The complete mitogenome sequence was determined using primer walking for the five long PCR products (see Table S1 for a list of primers used for long PCR). The assembled mitogenome sequence was annotated using MITOS web server (Bernt et al. 2013).
The complete mitogenome of P. capillatus was 19,105 bp in length (DDBJ accession no. LC714913). It contained 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and two control regions. The gene arrangement of P. capillatus was identical to that of other Suliformes species, characterized by a duplicated region spanning from the latter half of cytochrome b to the control region (Gibb et al. 2013). Most mitochondrial genes are encoded on the H-strand, except for ND6 and eight tRNA genes (tRNA-Gln, -Ala, -Asn, -Cys, -Tyr, -Ser, -Glu, and -Pro). The overall nucleotide composition was as follows: A (31.9%), C (31.9%), G (13.2%), and T (22.9%).
The maximum-likelihood method was used to reconstruct the phylogenetic tree based on 13 PCGs from 11 species of Suliformes, with Grey Heron Ardea cinerea (Pelecaniformes) as an outgroup. The best-fitting model of sequence evolution was selected using ModelTest-NG 0.1.6 (Darriba et al. 2020). Phylogenetic analysis was conducted using RAxML-NG 1.0.1 (Kozlov et al 2019) with 1000 pseudoreplicates to estimate branch support values. The overall topology among the families of Suliformes was congruent with that of Gibb et al. (2013); however, the phylogenetic relationships within the family Phalacrocoracidae differed from those of Kennedy and Spencer (2014) (Figure 1). We also found that P. capillatus is a sister species of P. carbo. The present study provides useful genetic tools to facilitate further studies on the Phalacrocoracidae evolution, as well as the population genetics of the Japanese Cormorant. and Yukita Sato were involved in interpretation of the data; Rina Honda and Atsushi Sogabe drafted the paper; Mizue Inumaru and Yukita Sato revised it critically for intellectual content; all authors approved the final manuscript and agreed to be accountable for all aspects of the work.

Disclosure statement
No potential conflict of interest was reported by the author(s).

Funding
The author(s) reported there is no funding associated with the work featured in this article.

Data availability statement
The data that support the findings of this study are available in DDBJ at https://www.ddbj.nig.ac.jp/index-e.html (reference number: LC714913).