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Das G, Das SP, Sahoo L, Swain SK, Raghavendra CH, Sahoo SK, Jayasankar P, Sundaray JK, Das P. High Genetic Differentiation and Genetic Diversity in Endangered Mahseer Tor khudree (Sykes, 1839) as Revealed from Concatenated ATPase 6/8 and Cyt b Mitochondrial Genes. Biochem Genet 2024:10.1007/s10528-023-10623-2. [PMID: 38231360 DOI: 10.1007/s10528-023-10623-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 12/06/2023] [Indexed: 01/18/2024]
Abstract
The Deccan mahseer, Tor khudree (Sykes 1839), belonging to family Cyprinidae is an important food and a game fish distributed in peninsular India. Due to overfishing and habitat destruction, the species is declared endangered and placed on the IUCN red list. Therefore, a well-designed conservation program may be essential to get this species protected in its natural habitat. We used a total of 152 samples from four rivers of peninsular India to assess the genetic diversity and structure of the mahseer using concatenated sequences of two mitochondrial genes, ATPase 6/8 (790 bp) and Cyt b (1000 bp). High haplotypic diversity was seen with 44 haplotypes. Individual gene wise haplotypes included 10 and 21 haplotypes for ATPase6/8 and Cyt b, respectively. AMOVA revealed most of the genetic variations (71.02%) to be within the populations. Significant genetic differentiation was observed between all population pairs, with FST values ranging from 0.121 to 0.372, with minimum between Tunga and Tungabhadra population and maximum between Tunga and Periyar population. Haplotype network showed one ancestral haplotype (TKACH04). Significant negative Fu's F and unimodal mismatch distribution suggested recent demographic expansion. The results of the present study would serve as a useful resource for further research on population genetics and conservation programs of the species.
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Affiliation(s)
- Gargee Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | | | - Lakshman Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Subrat Kumar Swain
- Institute of Medical Sciences & SUM Hospital, Siksha O Anusandhan University, Bhubaneswar, India
| | | | - Sangram Ketan Sahoo
- Aquaculture Production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Pallipuram Jayasankar
- Department of Marine Biotechnology, Fish Nutrition and Health, ICAR-Central Marine Fisheries Research Institute, Kochi, India
| | - Jitendra Kumar Sundaray
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Paramananda Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India.
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Kim MJ, Park JS, Kim H, Kim SR, Kim SW, Kim KY, Kwak W, Kim I. Phylogeographic Relationships among Bombyx mandarina (Lepidoptera: Bombycidae) Populations and Their Relationships to B. mori Inferred from Mitochondrial Genomes. BIOLOGY 2022; 11:68. [PMID: 35053066 PMCID: PMC8773246 DOI: 10.3390/biology11010068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/19/2021] [Accepted: 12/30/2021] [Indexed: 02/01/2023]
Abstract
We report 37 mitochondrial genome (mitogenome) sequences of Bombyx mori strains (Lepidoptera: Bombycidae) and four of B. mandarina individuals, each preserved and collected, respectively, in South Korea. These mitogenome sequences combined with 45 public data showed a substantial genetic reduction in B. mori strains compared to the presumed ancestor B. mandarina, with the highest diversity detected in the Chinese origin B. mori. Chinese B. mandarina were divided into northern and southern groups, concordant to the Qinling-Huaihe line, and the northern group was placed as an immediate progenitor of monophyletic B. mori strains in phylogenetic analyses, as has previously been detected. However, one individual that was in close proximity to the south Qinling-Huaihe line was exceptional, belonging to the northern group. The enigmatic South Korean population of B. mandarina, which has often been regarded as a closer genetic group to Japan, was most similar to the northern Chinese group, evidencing substantial gene flow between the two regions. Although a substantial genetic divergence is present between B. mandarina in southern China and Japan, a highly supported sister relationship between the two regional populations may suggest the potential origin of Japanese B. mandarina from southern China instead of the Korean peninsula.
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Affiliation(s)
- Min-Jee Kim
- Experiment and Analysis Division, Honam Regional Office, Animal and Plant Quarantine Agency, Gunsan 54096, Korea;
- Department of Applied Biology, College of Agriculture & Life Sciences, Chonnam National University, Gwangju 61186, Korea; (J.-S.P.); (H.K.)
| | - Jeong-Sun Park
- Department of Applied Biology, College of Agriculture & Life Sciences, Chonnam National University, Gwangju 61186, Korea; (J.-S.P.); (H.K.)
| | - Hyeongmin Kim
- Department of Applied Biology, College of Agriculture & Life Sciences, Chonnam National University, Gwangju 61186, Korea; (J.-S.P.); (H.K.)
| | - Seong-Ryul Kim
- Department of Agricultural Biology, National Academy of Agricultural Science, Rural Development Administration, Wanju Gun 55365, Korea; (S.-R.K.); (S.-W.K.); (K.-Y.K.)
| | - Seong-Wan Kim
- Department of Agricultural Biology, National Academy of Agricultural Science, Rural Development Administration, Wanju Gun 55365, Korea; (S.-R.K.); (S.-W.K.); (K.-Y.K.)
| | - Kee-Young Kim
- Department of Agricultural Biology, National Academy of Agricultural Science, Rural Development Administration, Wanju Gun 55365, Korea; (S.-R.K.); (S.-W.K.); (K.-Y.K.)
| | | | - Iksoo Kim
- Department of Applied Biology, College of Agriculture & Life Sciences, Chonnam National University, Gwangju 61186, Korea; (J.-S.P.); (H.K.)
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Complete Mitochondrial Genomes of Metcalfa pruinosa and Salurnis marginella (Hemiptera: Flatidae): Genomic Comparison and Phylogenetic Inference in Fulgoroidea. Curr Issues Mol Biol 2021; 43:1391-1418. [PMID: 34698117 PMCID: PMC8929015 DOI: 10.3390/cimb43030099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 12/30/2022] Open
Abstract
The complete mitochondrial genomes (mitogenomes) of two DNA barcode-defined haplotypes of Metcalfa pruinosa and one of Salurnis marginella (Hemiptera: Flatidae) were sequenced and compared to those of other Fulgoroidea species. Furthermore, the mitogenome sequences were used to reconstruct phylogenetic relationships among fulgoroid families. The three mitogenomes, including that of the available species of Flatidae, commonly possessed distinctive structures in the 1702-1836 bp A+T-rich region, such as two repeat regions at each end and a large centered nonrepeat region. All members of the superfamily Fulgoroidea, including the Flatidae, consistently possessed a motiflike sequence (TAGTA) at the ND1 and trnS2 junction. The phylogenetic analyses consistently recovered the familial relationships of (((((Ricaniidae + Issidae) + Flatidae) + Fulgoridae) + Achilidae) + Derbidae) in the amino acid-based analysis, with the placement of Cixiidae and Delphacidae as the earliest-derived lineages of fulgoroid families, whereas the monophyly of Delphacidae was not congruent between tree-constructing algorithms.
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