Complete mitochondrial genome of Saltator similis (Aves, Passeriformes)

Abstract

Saltator similis, popularly known as Green-winged Saltator, is one of the most trafficked species in Brazil. DNA from a muscle tissue sample was sequenced on MiSeq (Illumina) sequencer. The reads were assembled to reference using Geneious. The mtDNA consisted of 16,750 base pairs containing 2 ribosomal RNA, 22 transporter RNA, 13 protein-coding genes, and 1 control region. Most of the tRNA and PCGs were encoded on the heavy strand.

Keywords:

• Wildlife trafficking
• green-winged saltator
• next-generation sequencing
• mtDNA

Saltator similis (d'Orbigny & Lafresnaye, 1837 in Guala & Döring 2019) popularly known as Green-winged Saltator, is a member of order Passeriformes. It inhabits in parts of Brazil, Bolivia, Uruguay, Paraguay and Argentina (BirdLife International 2018). The current decrease in population is due to the loss of habitats and the illegal capture (UFV 2009, Manhães & Loures-Ribeiro 2011). Saltator similis is one of the most seized species in actions to combat the illegal trade of wild animals in Brazil (Borges et al. 2006; SEMA/PMA 2006; Gogliath et al. 2010; Destro 2012; Nunes et al. 2012; Franco et al. 2012; Felker et al. 2013; Zocche and Vianna 2013; Silva 2015; Freitas et al. 2015). In Brazilian legislation, captive breeding is permitted. To be a legal bird, it must be born in captivity and have an official inviolable band.

A population of female individual from Saltator similis species deceased as a consequence of illegal trafficking. It was identified and donated by IBAMA (Brazilian Environmental Agency) with proper licensing from the competent authorities (SISBIO 56471-1, IEF 024/2016 and CEUA-UFMG 37/2017) and mitochondrial DNA was extracted following the protocol from Françoso et al. (2015). The specimen was taxidermized and is in the Center of Taxonomic Collections of Federal University of Minas Gerais (voucher DZ7289).

DNA library was constructed and sequenced using a single-read 300-bp strategy on a MiSeq system (Illumina, San Diego, CA) using MiSeq Reagent Kit V2-300. Reads were trimmed with Phred 30 and assembled to reference (mtDNA of Geospiza magnirostris – GenBank MG682351.1) using Geneious 11.1.5 (https://www.geneious.com). The complete mitochondrial DNA of S. similis (GenBank accession number MK419316) was found to be circular in shape with 16,750 bp length, with average coverage of 148 reads. mtDNA was submitted to nucleotide BLAST (Altschul et al. 1990), which resulted in high similarity with the mitogenome of other Passeriformes species. The mtDNA displayed a GC content of 46.93% and base frequencies were 30% A, 14.36% G, 23% T, and 32.57% C.

The mitogenome was annotated with MITOS (Bernt et al. 2013) and verified with ExPASy (Gasteiger et al. 2003). Genes in S. similis were arranged similarly to other avian mitogenomes (Raposo do Amaral et al. 2015; Ludwig et al. 2017; Liang et al. 2018), with a different organization of the genes near the control region when compared to typical vertebrate mitogenome (Quinn and Wilson 1993). The mtDNA structure contained 2 rRNA, 22 tRNA, 13 protein-coding genes (PCGs), and 1 control region (D-loop). Protein-coding genes commonly had ATG as start codon (11 PCGs). Nine of the 13 PCGs contained a TAA stop codon. Eight of the 22 tRNAs and one PCG (Nd6) were encoded on the light (L) strand. The remaining genes were encoded on the heavy (H) strand. We found 10 overlapping regions.

Phylogenetic analyses were conducted using MEGA version 6.06 (MEGA Inc., Englewood, NJ) (Tamura et al. 2013) using the neighbor-joining method (Saitou and Nei 1987). D-loop region was excluded from phylogenetic analysis due to its hypervariability (Gonder et al. 2007) (Figure 1).

Figure 1. Consensus neighbor-joining tree of 10 avian species. Analyses were conducted in MEGA6 (Tamura et al. 2013). The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches (Felsenstein 1985). The evolutionary distances were computed using the Kimura 2-parameter method (Kimura 1980) and are in the units of the number of base substitutions per site. The analysis involved 10 nucleotide sequences. Codon positions included were 1st + 2nd + 3rd. Thraupidae Family grouped together with a high boostrap value including Saltator similis. Turdidae and Laniidae Family were grouped in separate clades. Tree was rooted using Ara ararauna as the outgroup.

Acknowledgments

We thank IBAMA, IEF and colleagues of the Laboratory of Biotechnology and Molecular Markers for their partnership. We thank Jean Oliveira and team of Taxonomy Collection Center for their collaborations.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This study was supported by CAPES [Edital Ciências Forenses n⁰ 25/2014, Processo 23038.006839/2014-33, 3405/2014] and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) [307550/2015-0].