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Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles. Animals (Basel) 2023; 13:ani13030471. [PMID: 36766360 PMCID: PMC9913427 DOI: 10.3390/ani13030471] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles-lizards and snakes-recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.
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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: 2] [Impact Index Per Article: 0.7] [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.
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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
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Ueno S, Kamezaki N, Mine K, Suzuki D, Hosoya S, Kikuchi K, Okamoto K, Torii M, Kadowaki K, Okamoto K, Sano M. Reproductive Ability of Hybrids between Japanese Pond Turtle (Mauremys japonica) and Reeves' Pond Turtle (Mauremys reevesii). Zoolog Sci 2021; 39:186-192. [DOI: 10.2108/zs210047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/17/2021] [Indexed: 11/17/2022]
Affiliation(s)
- Shintaro Ueno
- Department of Ecosystem Studies, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Naoki Kamezaki
- Department of Biosphere-Geosphere Science, Okayama University of Science, Kita Ward, Okayama 700-0005, Japan
| | - Kanako Mine
- Nature Recovery Co. Ltd., Nagata, Kobe, Hyogo 653-0844, Japan
| | - Dai Suzuki
- Department of Biology, School of Biological Sciences, Tokai University, Sapporo, Hokkaido 005-8601, Japan
| | - Sho Hosoya
- Fisheries Laboratory, The University of Tokyo, Hamamatsu, Shizuoka 431-0214, Japan
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, The University of Tokyo, Hamamatsu, Shizuoka 431-0214, Japan
| | - Kei Okamoto
- Department of Ecosystem Studies, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | | | | | - Ken Okamoto
- Department of Ecosystem Studies, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Mitsuhiko Sano
- Department of Ecosystem Studies, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
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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: 1.8] [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.
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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
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Detecting coevolution of positively selected in turtles sperm-egg fusion proteins. Mech Dev 2019; 156:1-7. [DOI: 10.1016/j.mod.2019.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/15/2019] [Accepted: 02/15/2019] [Indexed: 12/12/2022]
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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
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Wang M, Lu Y, Nie L. The complete mitochondrial genome of the Cyclemys fusca (Chelonia: Geoemydidae). Mitochondrial DNA B Resour 2018; 3:805-806. [PMID: 33474329 PMCID: PMC7800475 DOI: 10.1080/23802359.2018.1481786] [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: 04/25/2018] [Accepted: 05/09/2018] [Indexed: 11/29/2022] Open
Abstract
The complete mitochondrial genome (mitogenome) of Cyclemys fusca was obtained and characterized in this study. The circular molecule is 16,491 bp in length and contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and one non-coding region (control region). Its gene arrangement type is identical to the type of most vertebrate. All protein-coding genes initiate with ATG as start codon, except for COI started with GTG. Interestingly, COI and ND6 end up with AGG. The complete mitogenome of C. fusca provides the basic data to research molecular systematics of Geoemydidea.
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Affiliation(s)
- Meng Wang
- Life Science College, Anhui Normal University, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| | - Yuanhua Lu
- Life Science College, Anhui Normal University, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| | - Liuwang Nie
- Life Science College, Anhui Normal University, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
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Shi Q, Wang J, Liu J, Jiang H, Nie L. The complete mitochondrial genome of Geochelone sulcata. MITOCHONDRIAL DNA PART B-RESOURCES 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] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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.
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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
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Wang Y, Dai X, Wang M, Nie L. The complete mitochondrial genome of the Heosemys depressa (Testudines, Geoemydidae). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:437-438. [PMID: 33473854 PMCID: PMC7800218 DOI: 10.1080/23802359.2017.1357438] [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: 12/05/2022]
Abstract
The complete mitochondrial genome of Heosemys depressa was obtained and characterized in this study. The mitochondrial genome is a circular molecule of 16,773bp in length, and harbours 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 non-coding D-loop region (control region). Its gene arrangement type is identical to the type of most vertebrate. Phylogenetic analysis suggests that H. depressa is closely related to H. annandalii than to the other species. Our data provide a useful resource for the phylogenetic studies of genus Heosemys.
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Affiliation(s)
- Yuqin Wang
- Life Science College, Anhui Normal University, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| | - Xueting Dai
- Life Science College, Anhui Normal University, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| | - Meng Wang
- Life Science College, Anhui Normal University, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| | - Liuwang Nie
- Life Science College, Anhui Normal University, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
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Li J, Lu Y, Zan J, Nie L. Complete mitochondrial genome of the Cyclemys pulchristriata (Chelonia: Geoemydidae). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:403-404. [PMID: 33473841 PMCID: PMC7800075 DOI: 10.1080/23802359.2017.1347836] [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: 11/17/2022]
Abstract
In this study, we obtained complete mitochondrial genome sequence of Cyclemys pulchristriata. The mitochondrial genome reaches a length of 16,527 bp, containing 13 protein-coding genes (PCGs), 22tRNA genes, 2 rRNA genes and 1 control region. All protein-coding genes initiate with ATG as start codon, except for CO1 started with GTG. Most protein-coding genes ended by TAA as stop codon. Interestingly, there is an extra nucleotide A insertion in ND3 gene in C. pulchristriata. This study provides information on the genetic resources of C. pulchristriata that will contribute to protect this species.
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Affiliation(s)
- Jun Li
- College of Life Science, Anhui Normal University, Wuhu, China.,The Laboratory of Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, Anhui, China
| | - Yuanhua Lu
- College of Life Science, Anhui Normal University, Wuhu, China.,The Laboratory of Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, Anhui, China
| | - Jiawei Zan
- College of Life Science, Anhui Normal University, Wuhu, China.,The Laboratory of Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, Anhui, China
| | - Liuwang Nie
- College of Life Science, Anhui Normal University, Wuhu, China.,The Laboratory of Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, Anhui, China
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The complete mitochondrial genome of the Burmese roofed turtle (Batagur trivittata) (Testudines: Geoemydidae). CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0629-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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