1
|
Thintip J, Ahmad SF, Singchat W, Laopichienpong N, Suntronpong A, Panthum T, Ho My Nguyen D, Ariyaraphong N, Muangmai N, Suksawet W, Duengkae P, Srikulnath K. Mitochondrial genome of bronze-winged jacana ( Metopidius indicus, Latham 1790). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2251-2253. [PMID: 34377794 PMCID: PMC8330700 DOI: 10.1080/23802359.2021.1945971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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.
Collapse
Affiliation(s)
- Jitmat Thintip
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Dung Ho My Nguyen
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Nattakan Ariyaraphong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Warong Suksawet
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Prateep Duengkae
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, Thailand (CAST NAR, NRU-KU, Thailand).,Center of Excellence on Agricultural Biotechnology: (AG-BIO/MHESI), Bangkok, Thailand
| |
Collapse
|
3
|
Raposo do Amaral F, Neves LG, Resende MFR, Mobili F, Miyaki CY, Pellegrino KCM, Biondo C. Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes. PLoS One 2015; 10:e0138446. [PMID: 26379155 PMCID: PMC4574942 DOI: 10.1371/journal.pone.0138446] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/31/2015] [Indexed: 02/06/2023] Open
Abstract
Sequence capture of ultraconserved elements (UCEs) associated with massively parallel sequencing has become a common source of nuclear data for studies of animal systematics and phylogeography. However, mitochondrial and microsatellite variation are still commonly used in various kinds of molecular studies, and probably will complement genomic data in years to come. Here we show that besides providing abundant genomic data, UCE sequencing is an excellent source of both sequences for microsatellite loci design and complete mitochondrial genomes with high sequencing depth. Identification of dozens of microsatellite loci and assembly of complete mitogenomes is exemplified here using three species of Poospiza warbling finches from southern and southeastern Brazil. This strategy opens exciting opportunities to simultaneously analyze genome-wide nuclear datasets and traditionally used mtDNA and microsatellite markers in non-model amniotes at no additional cost.
Collapse
Affiliation(s)
- Fábio Raposo do Amaral
- Universidade Federal de São Paulo, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório de Genética Evolutiva, Rua Professor Artur Riedel, 275, Diadema, SP, 09972–270, Brazil
| | - Leandro G. Neves
- RAPiD Genomics, LLC, 747 SW 2nd Avenue, Gainesville, FL, 32601, United States of America
| | - Márcio F. R. Resende
- RAPiD Genomics, LLC, 747 SW 2nd Avenue, Gainesville, FL, 32601, United States of America
| | - Flávia Mobili
- Universidade Federal de São Paulo, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório de Genética Evolutiva, Rua Professor Artur Riedel, 275, Diadema, SP, 09972–270, Brazil
| | - Cristina Y. Miyaki
- Universidade de São Paulo, Departamento de Genética e Biologia Evolutiva, Rua do Matão, 277, Cidade Universitária, São Paulo, SP, 05508–090, Brazil
| | - Katia C. M. Pellegrino
- Universidade Federal de São Paulo, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório de Genética Evolutiva, Rua Professor Artur Riedel, 275, Diadema, SP, 09972–270, Brazil
| | - Cibele Biondo
- Universidade Federal do ABC, Centro de Ciências Naturais e Humanas, Rua Arcturus 03, Jardim Antares, São Bernardo do Campo, SP, 09606–070, Brazil
| |
Collapse
|
4
|
López K, Angeli C, Aguilar C, Loaiza JR, De León LF, McMillan WO, Miller MJ. Extreme mitogenomic divergence between two syntopic specimens of Arremon aurantiirostris (Aves: Emberizidae) in central Panama suggests possible cryptic species. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3451-3. [PMID: 26367084 DOI: 10.3109/19401736.2015.1066344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We report the complete mitochondrial genome of two specimens of Orange-billed Sparrow Arremon aurantiirostris from Colón Province, in central Panama. The two specimens were collected on the same day, and at the same locality; however, they showed substantial divergence (6.3% average pairwise divergence among coding genes). A survey of ND2 sequence variation across Panama suggests that this divergence is the result of geographic differentiation and secondary contact. This high level of mitochondrial divergence among co-occurring individuals raises the possibility of multiple biological species in Orange-billed Sparrows. Our results are yet another demonstration that much remains to be discovered regarding avian biodiversity in Panama and throughout the Neotropics.
Collapse
Affiliation(s)
- Krisangel López
- a Department of Biology , Villanova University , Villanova , PA , USA
| | - Cody Angeli
- a Department of Biology , Villanova University , Villanova , PA , USA
| | - Celestino Aguilar
- b Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) , Panamá , República de Panamá , and.,c Smithsonian Tropical Research Institute , Panamá , República de Panamá
| | - Jose R Loaiza
- b Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) , Panamá , República de Panamá , and
| | - Luis Fernando De León
- b Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) , Panamá , República de Panamá , and
| | - W Owen McMillan
- c Smithsonian Tropical Research Institute , Panamá , República de Panamá
| | - Matthew J Miller
- a Department of Biology , Villanova University , Villanova , PA , USA .,b Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) , Panamá , República de Panamá , and.,c Smithsonian Tropical Research Institute , Panamá , República de Panamá
| |
Collapse
|
6
|
Aguilar C, De Léon LF, Loaiza JR, McMillan WO, Miller MJ. Extreme sequence divergence between mitochondrial genomes of two subspecies of White-breasted Wood-wren (Henicorhina leucosticta, Cabanis, 1847) from western and central Panamá. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:956-7. [PMID: 24938093 DOI: 10.3109/19401736.2014.926503] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Prior studies of mitochondrial variation in White-breasted Wood-Wrens (Henicorhina leucosticta) have suggested that populations in South American and Mesoamerica might represent multiple species. Here we report the complete mitochondrial genomes from two individuals of H. leucosticta, representing the Panamanian subspecies pittieri and alexandri. The two sequences were 16,721 and 16,726 base pairs in size with both genomes comprised of the usual 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes, and one displacement loop region in the standard avian order. Uncorrected pairwise divergence between mitogenome features was high, with the highest divergence occurring in protein-coding genes (average = 8.2%), followed by control region (6.7%). RNA features had lower pairwise divergences (average tRNA = 4.3%, average rRNA = 2.3%). The protein-coding ATPase 6 gene had a different stop codon between these two specimens. The high level of sequence variation between these subspecies suggests that Mesoamerican H. leucosticta might be comprised of multiple species. We urge a full phylogeographic survey of this widespread Neotropical forest bird.
Collapse
Affiliation(s)
- Celestino Aguilar
- a Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) , Panamá , República de Panamá .,b Department of Biotechnology , Acharya Nagarjuna University , Guntur , India , and
| | - Luis Fernando De Léon
- a Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) , Panamá , República de Panamá
| | - José R Loaiza
- a Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) , Panamá , República de Panamá
| | - W Owen McMillan
- c Smithsonian Tropical Research Institute , Panamá , República de Panamá
| | - Matthew J Miller
- a Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) , Panamá , República de Panamá .,c Smithsonian Tropical Research Institute , Panamá , República de Panamá
| |
Collapse
|