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Asaeda Y, Shiraga K, Suzuki M, Sambongi Y, Ogino H, Igawa T. Rapid and collective determination of the complete "hot-spring frog" mitochondrial genome containing long repeat regions using Nanopore sequencing. PLoS One 2023; 18:e0280090. [PMID: 37906558 PMCID: PMC10617713 DOI: 10.1371/journal.pone.0280090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/25/2023] [Indexed: 11/02/2023] Open
Abstract
The mitochondrial genome (mt-genome) is one of the promising molecular markers for phylogenetics and population genetics. Recently, various mt-genomes have been determined rapidly by using massively parallel sequencers. However, the control region (CR, also called D-loop) in mt-genomes remain difficult to precisely determine due to the presence of repeat regions. Here, using Nanopore sequencing, we succeeded in rapid and collective determination of complete mt-genome of the hot-spring frog, Buergeria japonica, and found that its mt-genome size was 22,274 bp including CR (6,929 bp) with two types of tandem repeat motifs forming repeat regions. Comparison of assembly strategies revealed that the long- and short-read data combined together enabled efficient determination of the CR, but the short-read data alone did not. The B. japonica CR was longer than that of a congenic species inhabiting cooler climate areas, Buergeria buergeri, because of the long repeat regions in the former. During the thermal adaptation of B. japonica, the longer repeat regions in its CR may have accumulated within a period after divergence from B. buergeri.
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Affiliation(s)
- Yuka Asaeda
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kento Shiraga
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Makoto Suzuki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yoshihiro Sambongi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hajime Ogino
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Japan
| | - Takeshi Igawa
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Japan
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Cohen O, Ram Y, Hadany L, Geffen E, Gafny S. The effect of habitat and climatic on microsatellite diversity and allele length variation. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.893856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microsatellite loci have been shown to vary according to environment. We studied allelic length variation and diversity in eight microsatellite loci along a sharp climatic and habitat gradient in Israel, using the eastern spadefoot toad (Pelobates syriacus) as our model system. We found a gradual increase in allele lengths from north to south. We used a distance-based redundancy analysis (dbRDA) to associate between allele length and habitat and climatic measures and found that geography and annual climate explained the significant variation in allele length. We also used additional measurements pertaining to demography, heterozygosity and allelic diversity to explore four different hypotheses that might explain the variations in allele length. Our results suggest that the changes we observed in allele lengths may not be purely random but could be influenced by the differential mutation rate and/or local environmental conditions operating at the different locations.
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Quantitative species-level ecology of reef fish larvae via metabarcoding. Nat Ecol Evol 2017; 2:306-316. [PMID: 29255297 DOI: 10.1038/s41559-017-0413-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 11/13/2017] [Indexed: 11/08/2022]
Abstract
The larval pool of coral reef fish has a crucial role in the dynamics of adult fish populations. However, large-scale species-level monitoring of species-rich larval pools has been technically impractical. Here, we use high-throughput metabarcoding to study larval ecology in the Gulf of Aqaba, a region that is inhabited by >500 reef fish species. We analysed 9,933 larvae from 383 samples that were stratified over sites, depth and time. Metagenomic DNA extracted from pooled larvae was matched to a mitochondrial cytochrome c oxidase subunit I barcode database compiled for 77% of known fish species within this region. This yielded species-level reconstruction of the larval community, allowing robust estimation of larval spatio-temporal distributions. We found significant correlations between species abundance in the larval pool and in local adult assemblages, suggesting a major role for larval supply in determining local adult densities. We documented larval flux of species whose adults were never documented in the region, suggesting environmental filtering as the reason for the absence of these species. Larvae of several deep-sea fishes were found in shallow waters, supporting their dispersal over shallow bathymetries, potentially allowing Lessepsian migration into the Mediterranean Sea. Our method is applicable to any larval community and could assist coral reef conservation and fishery management efforts.
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He X, Chen X, Zhang W, Pu Y, Song S, Han J, Dong K, Zhao Q, Guan W, Ma Y, Jiang L. High occurrence of length heteroplasmy in domestic Bactrian camel (Camelus bactrianus). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:851-854. [PMID: 27937010 DOI: 10.1080/24701394.2016.1197219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Heteroplasmy is the presence of more than one mitochondrial DNA (mtDNA) variant within a cell, tissue, or individual. In this study, sequence variation was investigated in the control region (CR) of mitochondrial DNA (mtDNA) from 135 individuals belonging to five primary domestic Bactrian camel breeds in China and Mongolia. Due to variation of the repeat unit G(T/C)(AC)n, length heteroplasmy was detected within each camel by direct sequencing and fragment analysis. A high occurrence of mtDNA heteroplasmy, up to 100 percentages was observed in five camel populations. Our study provides the first evidence of extensive length heteroplasmy in Bactrian camels.
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Affiliation(s)
- Xiaohong He
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Xiaofei Chen
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Wenbin Zhang
- c Bactrian Camels Institute of Alxa League , Inner Mongolia Autonomous Region , China
| | - Yabin Pu
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Shen Song
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Jianlin Han
- b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,d International Livestock Research Institute (ILRI) , Nairobi , Kenya
| | - Kunzhe Dong
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Qianjun Zhao
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Weijun Guan
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Yuehui Ma
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Lin Jiang
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
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Pironon S, Papuga G, Villellas J, Angert AL, García MB, Thompson JD. Geographic variation in genetic and demographic performance: new insights from an old biogeographical paradigm. Biol Rev Camb Philos Soc 2016; 92:1877-1909. [DOI: 10.1111/brv.12313] [Citation(s) in RCA: 214] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 10/07/2016] [Accepted: 10/17/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Samuel Pironon
- Instituto Pirenaico de Ecología (IPE-CSIC); Box 1005 avenida Montañana 50059 Zaragoza, Spain
| | - Guillaume Papuga
- UMR 5175 Centre d'Ecologie Fonctionnelle et Evolutive, CNRS; Box 1019 route de Mende 34090 Montpellier France
- Dipartimento di Scienze della Natura e del Territorio; Università degli Studi di Sassari; Box 21 Piazza Universitá 07100 Sassari Italy
| | - Jesús Villellas
- Department of Biology; Duke University; Box 90338 Durham NC 27708-0338 U.S.A
| | - Amy L. Angert
- Departments of Botany and Zoology; University of British Columbia; Box 4200-6270 University Boulevard, Vancouver V6T 1Z4 Canada
| | - María B. García
- Instituto Pirenaico de Ecología (IPE-CSIC); Box 1005 avenida Montañana 50059 Zaragoza, Spain
| | - John D. Thompson
- UMR 5175 Centre d'Ecologie Fonctionnelle et Evolutive, CNRS; Box 1019 route de Mende 34090 Montpellier France
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He XL, Ding CQ, Han JL. Lack of Structural Variation but Extensive Length Polymorphisms and Heteroplasmic Length Variations in the Mitochondrial DNA Control Region of Highly Inbred Crested Ibis, Nipponia nippon. PLoS One 2013; 8:e66324. [PMID: 23805212 PMCID: PMC3689774 DOI: 10.1371/journal.pone.0066324] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 05/03/2013] [Indexed: 01/21/2023] Open
Abstract
The animal mitochondrial DNA (mtDNA) length polymorphism and heteroplasmy are accepted to be universal. Here we report the lack of structural variation but the presence of length polymorphism as well as heteroplasmy in mtDNA control region of an endangered avian species - the Crested Ibis (Nipponia nippon). The complete control region was directly sequenced while the distribution pattern and inheritance of the length variations were examined using both direct sequencing and genotyping of the PCR fragments from captive birds with pedigrees, wild birds and a historical specimen. Our results demonstrated that there was no structural variation in the control region, however, different numbers of short tandem repeats with an identical motif of CA3CA2CA3 at the 3'-end of the control region determined the length polymorphisms among and heteroplasmy within individual birds. There were one to three predominant fragments in every bird; nevertheless multiple minor fragments coexist in all birds. These extremely high polymorphisms were suggested to have derived from the 'replication slippage' of a perfect microsatellite evolution following the step-wise mutational model. The patterns of heteroplasmy were found to be shifted between generations and among siblings but rather stable between blood and feather samples. This study provides the first evidence of a very extensive mtDNA length polymorphism and heteroplasmy in the highly inbred Crested Ibis which carries an mtDNA genome lack of structural genetic diversity. The analysis of pedigreed samples also sheds light on the transmission of mtDNA length heteroplasmy in birds following the genetic bottleneck theory. Further research focusing on the generation and transmission of particular mtDNA heteroplasmy patterns in single germ line of Crested Ibis is encouraged by this study.
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Affiliation(s)
- Xue-Lian He
- College of Nature Conservation, Beijing Forestry University, Beijing, China
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Chang-Qing Ding
- College of Nature Conservation, Beijing Forestry University, Beijing, China
- * E-mail: (CQD); (JLH)
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- * E-mail: (CQD); (JLH)
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Tikochinski Y, Bendelac R, Barash A, Daya A, Levy Y, Friedmann A. Mitochondrial DNA STR analysis as a tool for studying the green sea turtle (Chelonia mydas) populations: the Mediterranean Sea case study. Mar Genomics 2012; 6:17-24. [PMID: 22578655 DOI: 10.1016/j.margen.2012.01.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 01/09/2012] [Accepted: 01/15/2012] [Indexed: 11/28/2022]
Abstract
The Mediterranean population of the green sea turtle Chelonia mydas is critically endangered. Genetic analysis of this population using the ordinary haplotyping system, based on sequence analysis of a segment of the mitochondrial DNA (mtDNA) D-loop (control region), revealed very little variation. The most common haplotype, CM-A13, was observed in all but three individuals in hundreds of samples in previous studies. In search for a more informative marker we sequenced the 3' of the mitochondrial control region which contains an AT-rich microsatellite. We found a unique pattern that consists of four AT short tandem repeats (STRs) with varying copy numbers. This allowed us to construct a new haplotyping system composed of four different STR sizes for each mtDNA sequence. Our new mitochondrial STR (mtSTR) haplotyping approach revealed 33 different haplotypes within the nesting and stranded sea turtles along the Mediterranean Israeli seashore. The Israeli coast nesting females had 10 different haplotypes that can be used for monitoring and conservation purposes. The mtSTR haplotyping system can clearly assist in fingerprinting of individual turtles. Moreover, it can be used for estimating phylogenetic distances within populations. This case study shows that the mtSTR haplotyping is applicable for the study of global green sea turtle populations and could also be considered as markers of genetic variability in other species.
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Affiliation(s)
- Y Tikochinski
- School of Marine Sciences, Ruppin Academic Center, Michmoret, Israel.
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