1
|
Chen C, Ji L, Huang G, Liu X, Chen H, Wang Y, Yu L, Liu Y, Hong X, Wei C, Wu C, Luo L, Zhu X, Li W. Comparative analysis of the mitochondrial genomes of the soft-shelled turtles Palea steindachneri and Pelodiscus axenaria and phylogenetic implications for Trionychia. Sci Rep 2025; 15:7138. [PMID: 40021811 PMCID: PMC11871352 DOI: 10.1038/s41598-025-90985-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 02/17/2025] [Indexed: 03/03/2025] Open
Abstract
Soft-shelled turtles, or Trionychia, are an enigmatic and fascinating group due to their specific morphological features and ecological adaptations. Based on mitochondrial DNA (mtDNA) and/or nuclear markers, previous studies showed the incongruent phylogenetic topologies within Trionychia (e.g., the Palea and its closely related species). In order to resolve the equivocal relationships and obtain some "genome-level" common evolutionary characters of soft-shelled turtles, in this study, we assembled and annotated the complete mitochondrial genomes of Palea steindachneri and Pelodiscus axenaria, both naturally distributed in Asia. The sizes of the two mitochondrial genomes were 16,811 bp and 17,143 bp, respectively. Typical vertebrate animal mtDNA features were observed, such as the usual gene components and arrangements (37 genes with a non-coding control region) and the A + T biased nucleotide compositions on the light strand (61.5% and 62.7%, respectively). All conserved blocks common to the vertebrates control region except for the extended terminal associated sequences (ETAS2) were found in the two soft-shelled turtles. The ω ratio averaged over all sites of each protein-coding gene (PCG) was below 1, which indicated purifying selection at the gene-wide level. However, a positive selection site at the 350-codon position in the cytb gene was detected, as estimated by Bayes empirical Bayes (BEB) analysis. Compared with the gene subsets, the mitogenomes provided the most robust phylogenetic resolution. The monophyly of the clades Amydona, Gigantaesuarochelys, and Apalonia was well supported. Topology discrepancies were observed among different datasets (e.g., the positions of Lissemys and Palea), reflecting the heterogeneous phylogenetic signals in the soft-shelled turtle mitogenomes. Precise date estimation based on Bayesian relaxed clock analyses indicated that the crown group age of extant Trionychia was approximately 115.84 Ma (95% HPD: 91.33-142.18 Ma). Paleoclimate changes, especially the Eocene - Oligocene transition, could be responsible for the speciation in these groups. Our results reiterated the necessity and effectiveness of incorporating entire mitochondrial genomes to delineate phylogenetic relationships in chelonian phylogeny studies.
Collapse
Affiliation(s)
- Chen Chen
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Liqin Ji
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Guiyun Huang
- Department of Agriculture of Guangdong Province, Agro-Tech Extension Center of Guangdong Province, Guangzhou, China
| | - Xiaoli Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Haigang Chen
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Yakun Wang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Lingyun Yu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Yihui Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Xiaoyou Hong
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Chengqing Wei
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Congcong Wu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Laifu Luo
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Xinping Zhu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
| | - Wei Li
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
| |
Collapse
|
2
|
Das SP, Krishnan R, Sunil M, Majhi A, Yakshita, Nan FH, Srivastava A. Low depth sequencing reveals the critically endangered Batagur kachuga (Red-crowned roofed turtle) mitochondrial genome and its evolutionary implications. Gene 2024; 927:148671. [PMID: 38866260 DOI: 10.1016/j.gene.2024.148671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/24/2024] [Accepted: 06/07/2024] [Indexed: 06/14/2024]
Abstract
The Batagur kachuga (B. kachuga), commonly known as the Red-crowned roofed turtle, is a critically endangered species native to India and its neighboring countries like Bangladesh, and Nepal. The present study is the first report of the complete mitochondrial genome of B. kachuga (16,517 bp) construed via the next-generation sequencing (NGS) approach from eggshell DNA. There are 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), 13 protein-coding genes (PCGs), and one putative control region (CR/D-loop) in the mitogenome. The CR region from the current study reveals conserved TAS, CD, and CSB domains and two AT-rich tandem repeat regions. Most genes are encoded in the heavy strand except the NADH dehydrogenase subunit 6 (ND6) gene and seven tRNA genes. Most PCGs start with the initiation codon ATG, except the COI (Cytochrome Oxidase Subunit-I) gene, which starts with the GTG codon. The present investigation also predicts the distinctive cloverleaf structures of tRNAs except for tRNA-Ser1 and tRNA-Ser-2, which lack a DHU arm. The comparative analysis of Ka/Ks with other 33 species from Order Testudines, in relation to B. kachuga, revealed negative selection in most PCGs, indicating a process of preservation and purification that aids in eliminating undesirable or detrimental substitutes. Phylogenetic analysis of this species has been analysed using the complete mitogenome of 33 turtle species. The maximum likelihood phylogenetic tree strongly supports each family in different clades and also reveals a close relationship between the Pangashura and Batagur genera. Our study suggests the generation of genome-wide molecular data, in terms of mitogenomes, SNPs, and SSRs, is needed to improve the understanding of this species and their phylogenetics and evolutionary relationships, which will help to improve the conservation efforts of this species.
Collapse
Affiliation(s)
- Sofia Priyadarsani Das
- Department of Aquaculture, College of Life Science, National Taiwan Ocean University, Keelung, Taiwan; Amity Institute of Marine Science and Technology, Amity University Uttar Pradesh, Sector-125, Noida, India.
| | - Rama Krishnan
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, United Kingdom
| | - Mohit Sunil
- Bharathidasan University, Trichy, Tamil Nadu, India
| | - Ashutosh Majhi
- Amity Institute of Marine Science and Technology, Amity University Uttar Pradesh, Sector-125, Noida, India
| | - Yakshita
- Amity Institute of Marine Science and Technology, Amity University Uttar Pradesh, Sector-125, Noida, India
| | - Fan-Hua Nan
- Department of Aquaculture, College of Life Science, National Taiwan Ocean University, Keelung, Taiwan
| | - Ashutosh Srivastava
- Amity Institute of Marine Science and Technology, Amity University Uttar Pradesh, Sector-125, Noida, India; Siddhart University, Kapilvastu, Siddhart Nagar, Uttar Pradesh, India.
| |
Collapse
|
3
|
Jiang H, Wang Z, Zhai X, Ma G, Wang T, Kong F, Luo W, Yu Z, Li H, Ren Y, Guo R, Jian L, Zhao L, Zuo Z, Pan S, Qi Z, Zhang Y, Liu Z, Rao D, Li Y, Wang J. Chromosome-level genome of diamondback terrapin provides insight into the genetic basis of salinity adaptation. Integr Zool 2024. [PMID: 39391967 DOI: 10.1111/1749-4877.12898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Diamondback terrapins (Malaclemys terrapin centrata) exhibit strong environmental adaptability and live in both freshwater and saltwater. However, the genetic basis of this adaptability has not been the focus of research. In this study, we successfully constructed a ∼2.21-Gb chromosome-level genome assembly for M. t. centrata using high-coverage and high-depth genomic sequencing data generated on multiple platforms. The M. t. centrata genome contains 25 chromosomes and the scaffold N50 of ∼143.75 Mb, demonstrating high continuity and accuracy. In total, 53.82% of the genome assembly was composed of repetitive sequences, and 22 435 protein-coding genes were predicted. Our phylogenetic analysis indicated that M. t. centrata was closely related to the red-eared slider turtle (Trachemys scripta elegans), with divergence approximately ∼23.6 million years ago (Mya) during the early Neogene period of the Cenozoic era. The population size of M. t. centrata decreased significantly over the past ∼14 Mya during the Cenozoic era. Comparative genomic analysis indicated that 36 gene families related to ion transport were expanded and several genes (AQP3, solute carrier subfamily, and potassium channel genes) underwent specific amino acid site mutations in the M. t. centrata genome. Changes to these ion transport-related genes may have contributed to the remarkable salinity adaptability of diamondback terrapin. The results of this study not only provide a high-quality reference genome for M. t. centrata but also elucidate the possible genetic basis for salinity adaptation in this species.
Collapse
Affiliation(s)
- Hui Jiang
- College of Life Science, Hainan Normal University, Haikou, China
| | - Zhongkai Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Xiaofei Zhai
- College of Life Science, Hainan Normal University, Haikou, China
| | - Guangwei Ma
- College of Life Science, Hainan Normal University, Haikou, China
| | - Tongliang Wang
- College of Life Science, Hainan Normal University, Haikou, China
| | - Fei Kong
- Shaanxi Institute of Zoology, Xian, China
| | - Wenkai Luo
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Ziwei Yu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Haorong Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yandong Ren
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Rui Guo
- College of Life Science, Hainan Normal University, Haikou, China
| | - Li Jian
- College of Life Science, Hainan Normal University, Haikou, China
| | - Longhui Zhao
- College of Life Science, Hainan Normal University, Haikou, China
| | - Ziye Zuo
- College of Life Science, Hainan Normal University, Haikou, China
| | - Shoupeng Pan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Zan Qi
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yuxin Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Zhuoya Liu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Dingqi Rao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yongxin Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Jichao Wang
- College of Life Science, Hainan Normal University, Haikou, China
| |
Collapse
|
4
|
Park J, Cheon SJ, Choi JH, Park SM, Sung HC, Lee DH. Complete mitochondrial genome of the razor-backed musk turtle ( Sternotherus carinatus, testudines: emydidae) in Korea. Mitochondrial DNA B Resour 2023; 8:1396-1400. [PMID: 38189026 PMCID: PMC10768728 DOI: 10.1080/23802359.2023.2292744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Sternotherus carinatus has been considered as a potential invasive species in Korea. However, the mitochondrial genome information of S. carinatus which can be used to control its effect on ecosystem is lacking. In this study, the complete mitochondrial genome of S. carinatus in Korea was sequenced and characterized. The mitochondrial genome consists of 37 genes (13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes) and a noncoding region. Phylogenetic analysis based on the mitochondrial genome sequences showed that S. carinatus from Korea is separated from other turtles which are the invasive species in Korea. Sequence divergence calculations indicated near-zero divergence between S. carinatus populations in Korea, the USA, and China, suggesting limited genetic differentiation. In the context of the broader issue of invasive species disrupting ecosystems, this research contributes to the identification of mitochondrial genomes for various freshwater turtle species, emphasizing the need for extended data collection to discern genetic mixing trends between native and non-native species. This study is a significant step toward managing S. carinatus as a potential invasive species in Korea.
Collapse
Affiliation(s)
- Jaehong Park
- School of Biological Sciences and Biotechnology, Chonnam National University, Gwangju, Korea
| | - Seung-Ju Cheon
- School of Biological Sciences and Biotechnology, Chonnam National University, Gwangju, Korea
| | - Jae-Hyuk Choi
- School of Biological Sciences and Biotechnology, Chonnam National University, Gwangju, Korea
| | - Seung-Min Park
- School of Biological Sciences and Biotechnology, Chonnam National University, Gwangju, Korea
| | - Ha-Cheol Sung
- Research Center of Ecomimetics, Chonnam National University, Gwangju, Korea
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, Korea
| | - Dong-Hyun Lee
- Research Center of Ecomimetics, Chonnam National University, Gwangju, Korea
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, Korea
| |
Collapse
|
5
|
Chroust M, Mazuch M, Ivanov M, Alba DM, Luján ÀH. Redescription of the soft-shell turtle Rafetus bohemicus (Testudines, Trionychidae) from the Early Miocene of Czechia. PeerJ 2023; 11:e15658. [PMID: 37525660 PMCID: PMC10387236 DOI: 10.7717/peerj.15658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 06/07/2023] [Indexed: 08/02/2023] Open
Abstract
The taxonomy of the soft-shell turtle Rafetus bohemicus (Liebus, 1930), family Trionychidae, subfamily Trionychinae, is revised based on new and previously mentioned material (including the type material) from the Early Miocene (Burdigalian, MN 3) sites of the Most Basin, Czechia. Given that the diagnosis was so far based only on plastral elements, here we focused on the cranial material and combined our study with previously published data on postcranial elements. 3D models of the skulls derived from CT scans allow us to provide the first complete skull description of R. bohemicus, including several new cranial diagnostic characters of the species. Our results not only enable the distinction of the trionychid genera Trionyx and Rafetus, both recorded from Central Europe during the Early Miocene, but further allow us to provide an emended diagnosis for R. bohemicus. We confirm the conclusions of a previous study according to which Trionyx pontanus, T. preschenensis, T. aspidiformis, and T. elongatus are nomina dubia. R. bohemicus from Břešt'any (MN 3) represents the oldest record of this genus in Europe as well as the oldest occurrence of the genus.
Collapse
Affiliation(s)
- Milan Chroust
- Charles University, Institute of Geology and Palaeontology, Prague, Czech Republic
- Institute of Geology of the Czech Academy of Sciences, Department of Paleobiology and Paleoecology, Prague, Czech Republic
| | - Martin Mazuch
- Charles University, Institute of Geology and Palaeontology, Prague, Czech Republic
| | - Martin Ivanov
- Masaryk University, Department of Geological Sciences, Brno, Czech Republic
| | - David M. Alba
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Àngel H. Luján
- Masaryk University, Department of Geological Sciences, Brno, Czech Republic
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| |
Collapse
|
6
|
Verneau O, Johnston GR, Du Preez L. A quantum leap in the evolution of platyhelminths: host-switching from turtles to hippopotamuses illustrated from a phylogenetic meta-analysis of polystomes (Monogenea, Polystomatidae). Int J Parasitol 2023; 53:317-325. [PMID: 37004735 DOI: 10.1016/j.ijpara.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 04/03/2023]
Abstract
While monogenean worms are mainly parasites of the gills and skin of fish, and to a lesser extent parasites of the oral cavity, urinary bladder, and/or conjunctival sacs of amphibians and freshwater turtles, Oculotrema hippopotami Stunkard, 1924 is the single monogenean polystome reported from a mammal, the common hippopotamus (Hippopotamus amphibius Linnaeus). Several hypotheses have been suggested in the last decade to explain the origin of this enigmatic parasite which infects the conjunctival sacs of H. amphibius. Based on a molecular phylogeny inferred from nuclear (28S and 18S) and mitochondrial (12S and COI) sequences of O. hippopotami and chelonian polystomes, we found a sister group relationship between O. hippopotami and Apaloneotrema moleri (Du Preez & Morrison, 2012). This result suggests lateral parasite transfer between freshwater turtles and hippopotamuses, thus likely reflecting one of the most exceptional known examples of host-switching in the course of vertebrate evolution. It also demonstrates that the proximity in the ecological habitat of parasites within host species is an important feature for their speciation and diversification. Because A. moleri and its host, the Florida softshell turtle (Apalone ferox (Schneider)), are restricted to the USA, we suggest that an ancestral stock of parasites may have been isolated on primitive African trionychids after they diverged from their American relatives, and then switched to hippopotamuses or anthracotheres in Africa.
Collapse
|
7
|
Diversity of Underwater Vocalizations in Chinese Soft-Shelled Turtle ( Pelodiscus sinensis). Animals (Basel) 2023; 13:ani13050812. [PMID: 36899669 PMCID: PMC10000088 DOI: 10.3390/ani13050812] [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: 01/04/2023] [Revised: 02/11/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
Sound communication is important for underwater species. The wild population of the Chinese soft-shelled turtle (Pelodiscus sinensis) is listed as vulnerable. However, its vocalization, which can serve as the basis for ecological and evolutionary research, has not been studied. Here, we performed underwater recordings of 23 Chinese soft-shelled turtles of different ages and sexes and identified 720 underwater calls. The turtle calls were manually divided into 10 call types according to visual and aural inspection properties. The similarity test indicated that the manual division was reliable. We described the acoustic properties of the calls and the statistical analysis showed that the peak frequency of calls was significantly different between adult females and males, and also between subadults and adults. Similar to other aquatic turtles that prefer to live in deep water, Chinese soft-shelled turtles have a high vocal diversity and many harmonic calls, indicating that this highly aquatic species developed a variety of vocalizations to enhance their underwater communication, which helped them adapt to the complex and dim underwater environment. Furthermore, the turtles showed a tendency for vocalization to become more diverse with age.
Collapse
|
8
|
Baek HJ, Kim P, Kim YC, Kim A, Kim S, Min MS, Lee H. The complete mitochondrial genome of the Amur soft-shelled turtle ( Pelodiscus maackii Brandt, 1858), from South Korea. Mitochondrial DNA B Resour 2022; 7:498-500. [PMID: 35311211 PMCID: PMC8928817 DOI: 10.1080/23802359.2022.2051759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In this study, we use a specimen from wild-caught individual to determine the complete mitochondrial genome of the Amur soft-shelled turtle (Pelodiscus maackii). The complete mitogenome of P. maackii has 16,258 bp in length and consists of 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and one control region. The arrangement of genes of P. maackii is identical with previously reported mitogenomes in the family Trionychoidea. According to our result, the ML tree for the phylogenetic reconstruction revealed that the individuals used in present study is closely related with the previously reported sequences of P. sinensis (AY962573 and MG431983) in p-distance 0.7% and 2.5%.
Collapse
Affiliation(s)
- Hae-jun Baek
- Conservation Genome Resources Bank for Korean Wildlife (CGRB) and Research Institute for Veterinary Science College of Veterinary Medicine, Seoul National University, Seoul, South Korea
- Invasive Alien Species Research Team, Bureau of Survey and Safety Research, National Institute of Ecology, SeoCheon, Chungcheongnam-do, South Korea
| | - Philjae Kim
- Invasive Alien Species Research Team, Bureau of Survey and Safety Research, National Institute of Ecology, SeoCheon, Chungcheongnam-do, South Korea
| | - Young-Chae Kim
- Mammal Research Team, Research Center for Endangered Species, National Institute of Ecology, YeongYang, Gyeongsangbuk-do, South Korea
| | - Areum Kim
- Mammal Research Team, Research Center for Endangered Species, National Institute of Ecology, YeongYang, Gyeongsangbuk-do, South Korea
- Department of Life Sciences, College of Natural Science, Yeungnam University, Gyeongsan, Gyeongsangbuk-do, South Korea
| | - Suhwan Kim
- Invasive Alien Species Research Team, Bureau of Survey and Safety Research, National Institute of Ecology, SeoCheon, Chungcheongnam-do, South Korea
| | - Mi-Sook Min
- Conservation Genome Resources Bank for Korean Wildlife (CGRB) and Research Institute for Veterinary Science College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Hang Lee
- Conservation Genome Resources Bank for Korean Wildlife (CGRB) and Research Institute for Veterinary Science College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| |
Collapse
|
9
|
Liu J, Liu S, Zheng K, Tang M, Gu L, Young J, Wang Z, Qiu Y, Dong J, Gu S, Xiong L, Zhou R, Nie L. Chromosome-level genome assembly of the Chinese three-keeled pond turtle (Mauremys reevesii) provides insights into freshwater adaptation. Mol Ecol Resour 2021; 22:1596-1605. [PMID: 34845835 DOI: 10.1111/1755-0998.13563] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 11/27/2022]
Abstract
Mauremys reevesii is an endangered freshwater turtle that symbolizes longevity in Chinese culture. Despite its importance, genetic studies of this species remain limited, with no genomic sequence reported to date. Here, we report a high-quality, chromosome-level genomic sequence of M. reevesii obtained using a combination of Nanopore and Hi-C sequencing technologies. The 2.37 Gb M. reevesii genome was assembled from a total of ~226.80 Gb of Nanopore sequencing data. The M. reevesii genome contig N50 is 34.73 Mb, the highest value in published turtle genomes. In total, 18,238 genes were functionally annotated. The contigs were clustered and ordered onto 27 pseudochromosomes covering ~96.55% of the genome assembled with Hi-C data. To explore genome evolution, synteny analysis was performed between M. reevesii (freshwater turtle) and Gopherus evgoodei (terrestrial turtle) genomes. In general, each chromosome of M. reevesii corresponded to one chromosome of Gopherus evgoodei, but some interchromosomal rearrangements occurred between the two species based on the assembled genomes. These interchromosomal rearrangements were further confirmed by mapping of the long-read nanopore data to the assembly. The reconstructed demographic history showed varied effective population size among freshwater, marine and terrestrial turtles. We also discovered expansion of genes related to the innate immune system in M. reevesii that may provide defence against freshwater pathogens. The high-quality genomic sequence provides a valuable genetic resource for further studies of genetics and genome evolution in turtles.
Collapse
Affiliation(s)
- Jianjun Liu
- Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Science, Anhui Normal University, Wuhu, China.,Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
| | - Siqi Liu
- Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Science, Anhui Normal University, Wuhu, China
| | - Kai Zheng
- Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Science, Anhui Normal University, Wuhu, China
| | - Min Tang
- Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Science, Anhui Normal University, Wuhu, China
| | - Liping Gu
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
| | - James Young
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
| | - Ziming Wang
- Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Science, Anhui Normal University, Wuhu, China
| | - Yeyan Qiu
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
| | - Jinxiu Dong
- Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Science, Anhui Normal University, Wuhu, China
| | | | | | - Ruanbao Zhou
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
| | - Liuwang Nie
- Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Science, Anhui Normal University, Wuhu, China
| |
Collapse
|
10
|
A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins. Proc Natl Acad Sci U S A 2021; 118:2012215118. [PMID: 33558231 DOI: 10.1073/pnas.2012215118] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Living turtles are characterized by extraordinarily low species diversity given their age. The clade's extensive fossil record indicates that climate and biogeography may have played important roles in determining their diversity. We investigated this hypothesis by collecting a molecular dataset for 591 individual turtles that, together, represent 80% of all turtle species, including representatives of all families and 98% of genera, and used it to jointly estimate phylogeny and divergence times. We found that the turtle tree is characterized by relatively constant diversification (speciation minus extinction) punctuated by a single threefold increase. We also found that this shift is temporally and geographically associated with newly emerged continental margins that appeared during the Eocene-Oligocene transition about 30 million years before present. In apparent contrast, the fossil record from this time period contains evidence for a major, but regional, extinction event. These seemingly discordant findings appear to be driven by a common global process: global cooling and drying at the time of the Eocene-Oligocene transition. This climatic shift led to aridification that drove extinctions in important fossil-bearing areas, while simultaneously exposing new continental margin habitat that subsequently allowed for a burst of speciation associated with these newly exploitable ecological opportunities.
Collapse
|
11
|
Kundu S, Kumar V, Tyagi K, Chandra K. The complete mitochondrial genome of the endangered Assam Roofed Turtle, Pangshura sylhetensis (Testudines: Geoemydidae): Genomic features and phylogeny. PLoS One 2020; 15:e0225233. [PMID: 32324729 PMCID: PMC7179895 DOI: 10.1371/journal.pone.0225233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 04/08/2020] [Indexed: 12/02/2022] Open
Abstract
The Assam Roofed Turtle, Pangshura sylhetensis is an endangered and least studied species endemic to India and Bangladesh. The present study decodes the first complete mitochondrial genome of P. sylhetensis (16,568 bp) by using next-generation sequencing. The assembly encodes 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). Most of the genes were encoded on the majority strand, except NADH dehydrogenase subunit 6 (nad6) and eight tRNAs. All PCGs start with an ATG initiation codon, except for Cytochrome oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 5 (nad5), which both start with GTG codon. The study also found the typical cloverleaf secondary structures in most of the predicted tRNA structures, except for serine (trnS1) which lacks of conventional DHU arm and loop. Both Bayesian and maximum-likelihood phylogenetic inference using 13 concatenated PCGs demonstrated strong support for the monophyly of all 52 Testudines species within their respective families and revealed Batagur trivittata as the nearest neighbor of P. sylhetensis. The mitogenomic phylogeny with other amniotes is congruent with previous research, supporting the sister relationship of Testudines and Archosaurians (birds and crocodilians). Additionally, the mitochondrial Gene Order (GO) analysis indicated plesiomorphy with the typical vertebrate GO in most of the Testudines species.
Collapse
Affiliation(s)
- Shantanu Kundu
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| |
Collapse
|
12
|
Kundu S, Kumar V, Tyagi K, Chakraborty R, Chandra K. The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): Characterization and comparative analysis. Ecol Evol 2019; 9:10854-10868. [PMID: 31624586 PMCID: PMC6787814 DOI: 10.1002/ece3.5606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/24/2019] [Accepted: 08/07/2019] [Indexed: 11/09/2022] Open
Abstract
The characterization of a complete mitogenome is widely used in genomics studies for systematics and evolutionary research. However, the sequences and structural motifs contained within the mitogenome of Testudines taxa have rarely been examined. The present study decodes the first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (16,657 bp) by using next-generation sequencing. This denovo assembly encodes 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA, and one control region (CR). Most of the genes were encoded on majority strand, except for one PCG (NADH dehydrogenase subunit 6) and eight tRNAs. Most of the PCGs were started with an ATG initiation codon, except for Cytochrome oxidase subunit 1 with "GTG" and NADH dehydrogenase subunit 5 with "ATA." The termination codons, "TAA" and "AGA" were observed in two subunits of NADH dehydrogenase gene. The relative synonymous codon usage analysis revealed the maximum abundance of alanine, isoleucine, leucine, and threonine. The nonsynonymous/synonymous ratios were <1 in all PCGs, which indicates strong negative selection among all Geoemydid species. The study also found the typical cloverleaf secondary structure in most of the tRNA genes, except for serine with the lack of the conventional DHU arm. The comparative study of Geoemydid mitogenomes revealed the occurrence of tandem repeats was frequent in the 3' end of CR. Further, two copies of a unique tandem repeat "TTCTCTTT" were identified in P. tentoria. The Bayesian and maximum-likelihood phylogenetic trees using concatenation of 13 PCGs revealed the close relationships of P. tentoria with Batagur trivittata in the studied dataset. All the Geoemydid species showed distinct clustering with high bootstrap support congruent with previous evolutionary hypotheses. We suggest that the generations of more mitogenomes of Geoemydid species are required, to improve our understanding of their in-depth phylogenetic and evolutionary relationships.
Collapse
Affiliation(s)
- Shantanu Kundu
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
| | - Vikas Kumar
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
| | - Kaomud Tyagi
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
| | - Rajasree Chakraborty
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
| | - Kailash Chandra
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
| |
Collapse
|
13
|
Yu P, Yang X, Zhou W, Yang W, Zhou L, Liu X, Wan Q, Zhang J. Comparative mitogenomic and phylogenetic analysis of Apalone spinifera and Apalone ferox (Testudines: Trionychidae). Genetica 2019; 147:165-176. [PMID: 30887216 DOI: 10.1007/s10709-019-00059-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 03/12/2019] [Indexed: 10/27/2022]
Abstract
The soft-shell turtles Apalone spinifera (AS) and Apalone ferox (AF) are two important economic species. AF is found in the Yellow River of China, and is a confirmed member of the Trionychidae family. However, the classification of AS was in dispute. Mitochondrial genomes (mitogenomes) have been widely used for species identification, as well as population and phylogenetic analysis. In order to understand the phylogenetic and mitogenomic features of AS and AF, the complete mitogenomes were sequenced, annotated and analyzed in this study. The complete mitogenomes of AS and AF are 16,817 bp and 16,756 bp in length, respectively. Both mitogenomes contain 37 genes, seven short intergenic spacers and two long intergenic spacers. Comparative analysis showed that there are 1,137 variation sites (6.79%) between the two mitogenomes. AS and AF mitogenomes both show a usage preference in terms of nucleotides, codons and amino acids. In addition, the non-synonymous substitution rate/synonymous substitution rate indicates that all protein-coding genes (PCGs) have undergone a strong purifying selection. Phylogenetic trees constructed by 13 PCGs show a clear phylogenetic relationship of the soft-shell turtles and suggest that AS is a sister species to AF of the genus Apalone. The data could be useful for further research of species identification, population analysis and the mitogenomic features of soft-shell turtles.
Collapse
Affiliation(s)
- Peng Yu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoli Yang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Weishang Zhou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Wentao Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xuan Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Quan Wan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Jun Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China. .,Mingguang Modern Agricultural Science and Technology Cooperation Promotion Service Center, Mingguang, 239400, China.
| |
Collapse
|
14
|
Xiong L, Wang J, Nie L. The complete mitochondrial genome of the Madagascan plowshare tortoise Astrochelys yniphora (Testudines, Testudinidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1605860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Lei Xiong
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Life Science College, Anhui Normal University, Wuhu, P.R. China
- Provincial Key Laboratory of Biological Macro-molecules Research, Biochemistry Department, Wannan Medical College, Wuhu, P.R. China
| | - Jue Wang
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Life Science College, Anhui Normal University, Wuhu, P.R. China
| | - Liuwang Nie
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Life Science College, Anhui Normal University, Wuhu, P.R. China
| |
Collapse
|
15
|
Kundu S, Kumar V, Tyagi K, Chakraborty R, Singha D, Rahaman I, Pakrashi A, Chandra K. Complete mitochondrial genome of Black Soft-shell Turtle (Nilssonia nigricans) and comparative analysis with other Trionychidae. Sci Rep 2018; 8:17378. [PMID: 30478342 PMCID: PMC6255766 DOI: 10.1038/s41598-018-35822-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/09/2018] [Indexed: 11/08/2022] Open
Abstract
The characterization of mitochondrial genome has been evidenced as an efficient field of study for phylogenetic and evolutionary analysis in vertebrates including turtles. The aim of this study was to distinguish the structure and variability of the Trionychidae species mitogenomes through comparative analysis. The complete mitogenome (16796 bp) of an endangered freshwater turtle, Nilssonia nigricans was sequenced and annotated. The mitogenome encoded for 37 genes and a major non-coding control region (CR). The mitogenome was A + T biased (62.16%) and included six overlapping and 19 intergenic spacer regions. The Relative synonymous codon usage (RSCU) value was consistent among all the Trionychidae species; with the exception of significant reduction of Serine (TCG) frequency in N. nigricans, N. formosa, and R. swinhoei. In N. nigricans, most of the transfer RNAs (tRNAs) were folded into classic clover-leaf secondary structures with Watson-Crick base pairing except for trnS1 (GCT). The comparative analysis revealed that most of the tRNAs were structurally different, except for trnE (TTC), trnQ (TTG), and trnM (CAT). The structural features of tRNAs resulted ≥ 10 mismatched or wobble base pairings in 12 tRNAs, which reflects the nucleotide composition in both H- and L-strands. The mitogenome of N. nigricans also revealed two unique tandem repeats (ATTAT)8, and (TATTA)20 in the CR. Further, the conserved motif 5'-GACATA-3' and stable stem-loop structure was detected in the CRs of all Trionychidae species, which play an significant role in regulating transcription and replication in the mitochondrial genome. Further, the comparative analysis of Ka/Ks indicated negative selection in most of the protein coding genes (PCGs). The constructed Maximum Likelihood (ML) phylogeny using all PCGs showed clustering of N. nigricans with N. formosa. The resulting phylogeny illustrated the similar topology as described previously and consistent with the taxonomic classification. However, more sampling from different taxonomic groups of Testudines and studies on their mitogenomics are desirable for better understanding of the phylogenetic and evolutionary relationships.
Collapse
Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India.
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Rajasree Chakraborty
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Devkant Singha
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Iftikar Rahaman
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Avas Pakrashi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| |
Collapse
|
16
|
Liu XL, Wang YK, Ouyang S, Zhu YY, Li W, Hong XY, Xu HY, Zhu XP. Evolutionary conservation of transferrin genomic organization and expression characterization in seven freshwater turtles. Biochem Biophys Res Commun 2018; 506:874-882. [PMID: 30392910 DOI: 10.1016/j.bbrc.2018.10.168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 10/27/2018] [Indexed: 01/28/2023]
Abstract
Serum transferrin (tf), encoding an iron-binding glycoprotein, has been revealed to play important roles in iron transportation and immune response, and it also has been demonstrated to be valuable for phylogenetic analysis in vertebrates. However, the evolutionary conservation, expression profiles and positive selection of transferrin genes among freshwater turtle species remain largely unclear. Here, the genomic DNA and coding sequences of transferrin genes were cloned and characterized in seven freshwater turtles including Mauremys mutica, Mauremys sinensis, Cyclemys dentate, Mauremyssi reevesi, Heosemys grandis, Trachemys scripta and Chrysemys picta. The isolated coding sequences of turtles' tf genes were 2118 bp or 2121 bp, encoding 706 or 707 amino acids. The predicted Tf proteins of turtles share high identities with M. mutica Tf, up to 91%-98% and the M. mutica Tf has the highest identity (91%) in amino acid with the Chelomia mydas Tf, the moderate with other reptiles' Tfs (65%-59%), chicken (58%), and Human Tf (∼55%), and the lowest with zebrafish Tf (41%). Additionally, tf genes were consistently composed of 17 exons and 16 introns with the same splicing sites in introns in all the turtles examined. Moreover, 12 positive selected sites were detected in these turtles' Tf and mainly distributed on the surface of transferrin protein. Importantly, it was found that transferrin genes in all turtles examined were predominantly expressed in adult liver via real-time quantitative PCR. The molecular characterizations and expression profiles of transferrin would shed new insights into understanding the conversations and divergences of transferrin genes in turtles, even in vertebrates.
Collapse
Affiliation(s)
- Xiao-Li Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Ya-Kun Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; College of Life Science, Nanchang University, Nanchang 330031, China
| | - Shu Ouyang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, China
| | - Yan-Yu Zhu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, China
| | - Wei Li
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Xiao-You Hong
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Hong-Yan Xu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
| | - Xin-Ping Zhu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
| |
Collapse
|
17
|
Shi Q, Wang J, Liu J, Jiang H, Nie L. The complete mitochondrial genome of Geochelone sulcata. Mitochondrial DNA B Resour 2017; 2:463-464. [PMID: 33473863 PMCID: PMC7800827 DOI: 10.1080/23802359.2017.1357437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/17/2017] [Indexed: 10/31/2022] Open
Abstract
The complete mitochondrial genome of Geochelone sulcata was determined using PCR, Long-PCR with length of 16,692 bp. The genome organization, gene order, and base composition was similar to typical vertebrate. Gene content included 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. Otherwise, the lack of C, as same as in the other species of Testudinidae, was detected in arms of tRNALys gene in G. sulcata. In addition, an extra nucleotide A was discovered in ND3 gene in G. sulcata. The complete mitogenome of G. sulcata provides the basic data to research molecular systematics of Testudinidae.
Collapse
Affiliation(s)
- Qiong Shi
- Life Science College, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, China
| | - Jue Wang
- Life Science College, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, China
| | - Jianjun Liu
- Life Science College, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, China
| | - Hui Jiang
- Life Science College, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, China
| | - Liuwang Nie
- Life Science College, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, China
| |
Collapse
|
18
|
Brinkman D, Rabi M, Zhao L. Lower Cretaceous fossils from China shed light on the ancestral body plan of crown softshell turtles (Trionychidae, Cryptodira). Sci Rep 2017; 7:6719. [PMID: 28751684 PMCID: PMC5532300 DOI: 10.1038/s41598-017-04101-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/08/2017] [Indexed: 12/04/2022] Open
Abstract
Pan-trionychids or softshell turtles are a highly specialized and widespread extant group of aquatic taxa with an evolutionary history that goes back to the Early Cretaceous. The earliest pan-trionychids had already fully developed the "classic" softshell turtle morphology and it has been impossible to resolve whether they are stem members of the family or are within the crown. This has hindered our understanding of the evolution of the two basic body plans of crown-trionychids. Thus it remains unclear whether the more heavily ossified shell of the cyclanorbines or the highly reduced trionychine morphotype is the ancestral condition for softshell turtles. A new pan-trionychid from the Early Cretaceous of Zhejiang, China, Perochelys hengshanensis sp. nov., allows a revision of softshell-turtle phylogeny. Equal character weighting resulted in a topology that is fundamentally inconsistent with molecular divergence date estimates of deeply nested extant species. In contrast, implied weighting retrieved Lower Cretaceous Perochelys spp. and Petrochelys kyrgyzensis as stem trionychids, which is fully consistent with their basal stratigraphic occurrence and an Aptian-Santonian molecular age estimate for crown-trionychids. These results indicate that the primitive morphology for soft-shell turtles is a poorly ossified shell like that of crown-trionychines and that shell re-ossification in cyclanorbines (including re-acquisition of peripheral elements) is secondary.
Collapse
Affiliation(s)
- Donald Brinkman
- Royal Tyrrell Museum of Palaeontology, Box 7500, Drumheller, Alberta, Canada, T0J 0Y0.
- Adjunct Professor, Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
| | - Márton Rabi
- Department of Earth Sciences, University of Torino, Via Valperga Caluso 35, 10125, Torino, Italy.
- Institute of Geosciences, University of Tübingen, Sigwartstr. 10, 72076, Tübingen, Germany.
| | - Lijun Zhao
- Zhejiang Museum of Natural History, No. 71 Jiaogong Road, Hangzhou, Zhejiang, China
- Zhejiang Museum of Natural History, 6 Westlake Culture Square, Hangzhou, Zhejiang Province, China
| |
Collapse
|