Mitochondrial genome of bronze-winged jacana (Metopidius indicus, Latham 1790)

Abstract

We reported the mitochondrial genome (mitogenome) of bronze-winged jacana (Metopidius indicus, Latham 1790). The circular mitogenome was 17,208 base pairs (bp) in length, containing 13 protein-coding genes, two rRNAs, 22 tRNAs, and a non-coding control region. A DNA spacer 109 bp long was also detected between ND5 and Cytb. Phylogenetic analysis indicated that M. indicus was more closely related with the genera Himantopus, Jacana and Hydrophasianus. This annotated mitogenome reference can be utilized as a data resource for comparative mitogenomics of waders or shorebirds, with possible use in ecological and evolutionary studies.

Keywords:

• Metopidius
• next-generation sequencing
• mitogenome
• phylogenetics

The bronze-winged jacana (Metopidius indicus, Latham 1790) is a wader in the family Jacanidae. It is an ideal species for the study of polyandry (Miller et al. 2016) and widely distributed across the Indian subcontinent and Southeast Asia (Ali and Ripley 1980; IUCN 2013). The bronze-winged jacana shows greater reversed sexual size dimorphism than any other group of birds (Jenni 1996). The genus Metopidius was introduced by the German zoologist Johann Georg Wagler in 1832 (Wagler 1832). According to the World Bird List Version 9.2. International Ornithologists’ Union, Metopidius indicus is the only species within the genus (Avibase 2019; Frank and David 2019); however, the genetic features of this species have not been previously studied. Here, a complete mitochondrial genome of M. indicus was determined. The bronze-winged jacana specimen was collected as a carcass found at Kasetsart University, Bangkok, Thailand (13.847331°N, 100.572067°E). Animal ethics were submitted to the supervisory committee of Kasetsart University (ACKU63-SCI-022) and the specimen was stored in the Thailand Natural History Museum (No. THM21090; Contact person: Sunchai Makchai, E-mail: [email protected]). Whole genomic DNA was extracted from the liver using the standard salting-out protocol (Supikamolseni et al. 2015). Next-generation sequencing was performed using an Illumina HiSeq3000 platform at Vishuo Biomedical Ltd., Bangkok, Thailand, with a coverage of 50×. The quality of Illumina reads was evaluated with FastQC and the raw reads were trimmed to discard adapters using Trimmomatic software V0.32 (Bolger et al. 2014). The cleaned reads were then assembled to construct the mtgenome using MitoZ version_2.4-alpha (Meng et al. 2019). We set the multi-Kmer mode, ‘–genetic_code 2,’ ‘–clade chordata’ in MitoZ pipeline to identify the mitogenomic sequences, de novo assembly and annotations. Complete mitogenome sequences consisted of 17,208 bp for bronze-winged jacana (GenBank Accession no. MW482963, SRA: SSR13451235, BioProject: PRJNA692351), comprising 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region, similar to the mitogenome structure of birds (Desjardins and Morais 1990). Non-coding spacers were detected with 109 bp between ND5 and Cytb, which differed from other species in the family Jacanidae. Overall AT content value for the M. indicus mitogenome was 53.7%, with an average nucleotide diversity of 0.190 ± 0.002. The methodology of community phylogenetics was used to compare the phylogenetic dispersion of Charadriiformes. A phylogenetic tree was constructed based on twelve concatenated protein-coding genes of 21 species from Charadriiformes and Galliformes, using Bayesian inference with MrBayes version 3.2.6. (Huelsenbeck and Ronquist 2001). ND6 sequences were excluded in the phylogenetic analysis because of high bias toward transitions reported from previous tests of substitution models (Duchêne et al. 2011). Phylogenetic analysis of bronze-winged jacana showed an ancestral relationship with genera Himantopus, Jacana and Hydrophasianus, corresponding to a similar tree structure derived from TimeTree (Figure 1). These complete mitogenomes will allow the creation of a reference annotated genome, and provide valuable information at the molecular level that can be utilized to sustain conservation management of the bronze-winged jacana.

Figure 1. Phylogenetic relationships among 12 concatenated mitochondrial protein-coding genes, without ND6 sequences of 21 mitochondrial genomes, including Syrmaticus humiae as the outgroup, using Bayesian inference analysis. The complete mitochondrial genome sequence was downloaded from GenBank. Accession numbers are indicated in parentheses after the scientific names of each species. Support values at each node are Bayesian posterior probabilities, while branches length represents the number of nucleotide substitutions per site.

Ethical approval

Animal care and all experimental procedures were approved by the Animal Experiment Committee, Kasetsart University, Thailand (Approval no. ACKU63-SCI-021) and conducted in accordance with the Regulations on Animal Experiments at Kasetsart University.

Acknowledgments

The authors would like to thank Sunchai Makchai (E-mail: [email protected]; Thailand Natural History Museum) for advice on specimen collection. The authors are also indebted to Vishuo Biomedical (Thailand) Ltd. for excellent service collaboration. The Center for Agricultural Biotechnology (CAB) at Kasetsart University Kamphaeng Saen Campus provided support with server analysis services, while the Faculty of Science and the Faculty of Forestry at Kasetsart University provided research facilities. The National Biobank of Thailand (NBT) under the National Science and Technology Development Agency (NSTDA), Thailand supported this study through the use of a high-performance computer.

Disclosure statement

The authors report no conflicts of interest and are entirely responsible for the contents of this article.

Data availability statement

Data supporting the study findings are available in GenBank through the NCBI at https://www.ncbi.nlm.nih.gov. Isolated mitogenome reads were deposited at NCBI SRA database (accession ID: SSR13451235), and the assembled mitogenome sequences are available in GenBank (accession ID: MW482963).

Additional information

Funding

This research was financially supported by a grant from the National Research Council of Thailand [NRCT/16/2563] (awarded to S. F. A., W. S., N. L., A. S., T. P., P. D., and K. S.), the Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (awarded to K. S.), the Thailand Research Fund [Nos. RSA6180075, PHD60I0014, and PHD60I0082] through a grant awarded to K. S., W. S., and A. S., the Science Achievement Scholarship of Thailand [No. 5917400296] through a grant from the Office of the Higher Education Commission awarded to N. L., the Royal Golden Jubilee Ph.D. program under the Thailand Research Fund (TRF) awarded to D. H. M. N. and K. S. [no. PHD01392561], The degree of Bachelor of Science with major in biology, Ubon Ratchathani University, a grant from the Graduate Scholarship Program of the Graduate School, Kasetsart University, Thailand awarded to J. T., T. P., and K. S., and a Postdoctoral Researcher award at Kasetsart University awarded to S. F. A. and K. S. The funding agencies did not have a role in the design of the study or in the collection, analysis, and interpretation of data, or in writing the manuscript.