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Ma F, Zheng C. Single-cell phylotranscriptomics of developmental and cell type evolution. Trends Genet 2024; 40:495-510. [PMID: 38490933 DOI: 10.1016/j.tig.2024.02.005] [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: 11/23/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 03/17/2024]
Abstract
Single-cell phylotranscriptomics is an emerging tool to reveal the molecular and cellular mechanisms of evolution. We summarize its utility in studying the hourglass pattern of ontogenetic evolution and for understanding the evolutionary history of cell types. The developmental hourglass model suggests that the mid-embryonic stage is the most conserved period of development across species, which is supported by morphological and molecular studies. Single-cell phylotranscriptomic analysis has revealed previously underappreciated heterogeneity in transcriptome ages among lineages and cell types throughout development, and has identified the lineages and tissues that drive the whole-organism hourglass pattern. Single-cell transcriptome age analyses also provide important insights into the origin of germ layers, the different selective forces on tissues during adaptation, and the evolutionary relationships between cell types.
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Affiliation(s)
- Fuqiang Ma
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Chaogu Zheng
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.
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2
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Nagashima A, Torii K, Ota C, Kato A. slc26a12-A novel member of the slc26 family, is located in tandem with slc26a2 in coelacanths, amphibians, reptiles, and birds. Physiol Rep 2024; 12:e16089. [PMID: 38828713 PMCID: PMC11145369 DOI: 10.14814/phy2.16089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
Solute carrier family 26 (Slc26) is a family of anion exchangers with 11 members in mammals (named Slc26a1-a11). Here, we identified a novel member of the slc26 family, slc26a12, located in tandem with slc26a2 in the genomes of several vertebrate lineages. BLAST and synteny analyses of various jawed vertebrate genome databases revealed that slc26a12 is present in coelacanths, amphibians, reptiles, and birds but not in cartilaginous fishes, lungfish, mammals, or ray-finned fishes. In some avian and reptilian lineages such as owls, penguins, egrets, and ducks, and most turtles examined, slc26a12 was lost or pseudogenized. Phylogenetic analysis showed that Slc26a12 formed an independent branch with the other Slc26 members and Slc26a12, Slc26a1 and Slc26a2 formed a single branch, suggesting that these three members formed a subfamily in Slc26. In jawless fish, hagfish have two genes homologous to slc26a2 and slc26a12, whereas lamprey has a single gene homologous to slc26a2. African clawed frogs express slc26a12 in larval gills, skin, and fins. These results show that slc26a12 was present at least before the separation of lobe-finned fish and tetrapods; the name slc26a12 is appropriate because the gene duplication occurred in the distant past.
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Affiliation(s)
- Ayumi Nagashima
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Kota Torii
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Chihiro Ota
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Akira Kato
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
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3
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Hassan NT, Galbraith JD, Adelson DL. Multiple horizontal transfer events of a DNA transposon into turtles, fishes, and a frog. Mob DNA 2024; 15:7. [PMID: 38605364 PMCID: PMC11008031 DOI: 10.1186/s13100-024-00318-9] [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: 09/13/2023] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
Horizontal transfer of transposable elements (HTT) has been reported across many species and the impact of such events on genome structure and function has been well described. However, few studies have focused on reptilian genomes, especially HTT events in Testudines (turtles). Here, as a consequence of investigating the repetitive content of Malaclemys terrapin terrapin (Diamondback turtle) we found a high similarity DNA transposon, annotated in RepBase as hAT-6_XT, shared between other turtle species, ray-finned fishes, and a frog. hAT-6_XT was notably absent in reptilian taxa closely related to turtles, such as crocodiles and birds. Successful invasion of DNA transposons into new genomes requires the conservation of specific residues in the encoded transposase, and through structural analysis, these residues were identified indicating some retention of functional transposition activity. We document six recent independent HTT events of a DNA transposon in turtles, which are known to have a low genomic evolutionary rate and ancient repeats.
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Affiliation(s)
- Nozhat T Hassan
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - James D Galbraith
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - David L Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, Australia.
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4
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Garg KM, Gwee CY, Chattopadhyay B, Ng NS, Prawiradilaga DM, David G, Fuchs J, Hung Le Manh, Martinez J, Olsson U, Vuong Tan Tu, Chhin S, Alström P, Lei F, Rheindt FE. When colors mislead: Genomics and bioacoustics prompt re-classification of Asian flycatcher radiation (Aves: Niltavinae). Mol Phylogenet Evol 2024; 193:107999. [PMID: 38160993 DOI: 10.1016/j.ympev.2023.107999] [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: 09/11/2023] [Revised: 11/10/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
Traditional classification of many animals, including birds, has been highly dependent on external morphological characters like plumage coloration. However, both bioacoustics and genetic or genomic data have revolutionized our understanding of the relationships of certain lineages and led to sweeping taxonomic re-organizations. In this study, we present a case of erroneous delimitation of genus boundaries in the species-rich flycatcher subfamily Niltavinae. Genera within this subfamily have historically been delineated based on blue versus brown male body plumage until recent studies based on a few mitochondrial and nuclear loci unearthed several cases of generic misclassification. Here we use extensive bioacoustic data from 43 species and genomic data from 28 species for a fundamental reclassification of species in the Niltavinae. Our study reveals that song is an important trait to classify these birds even at the genus level, whereas plumage traits exhibit ample convergence and have led to numerous historic misattributions. Our taxonomic re-organization leads to new biogeographic limits of major genera, such that the genus Cyornis now only extends as far east as the islands of Sulawesi, Sula, and Banggai, whereas Eumyias is redefined to extend far beyond Wallace's Line to the islands of Seram and Timor. Our conclusions advise against an over-reliance on morphological traits and underscore the importance of integrative datasets.
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Affiliation(s)
- Kritika M Garg
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Centre for Interdisciplinary Archaeological Research, Ashoka University, Sonipat, India; Department of Biology, Ashoka University, Sonipat, India
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany
| | - Balaji Chattopadhyay
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Department of Biology, Ashoka University, Sonipat, India; Trivedi School of Biosciences, Ashoka University, Sonipat, India
| | - Nathaniel S Ng
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Dewi M Prawiradilaga
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Bogor-Cibinong, West Java, Indonesia
| | - Gabriel David
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, 22 S U, EPHE, UA CP51, Paris, France
| | - Hung Le Manh
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | | | - Urban Olsson
- Systematics and Biodiversity, Department of Biology and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Center, Göteborg, Sweden
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Sophea Chhin
- Department of Biodiversity, General Directorate of Policy and Strategy, Ministry of Environment, Phnom Penh, Cambodia
| | - Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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5
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Li Y, Liu Y, Zheng J, Wu B, Cui X, Xu W, Zhu C, Qiu Q, Wang K. A chromosome-level genome assembly of the pig-nosed turtle (Carettochelys insculpta). Sci Data 2024; 11:311. [PMID: 38521795 PMCID: PMC10960847 DOI: 10.1038/s41597-024-03157-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/15/2024] [Indexed: 03/25/2024] Open
Abstract
The pig-nosed turtle (Carettochelys insculpta) represents the only extant species within the Carettochelyidae family, is a unique Trionychia member fully adapted to aquatic life and currently facing endangerment. To enhance our understanding of this species and contribute to its conservation efforts, we employed high-fidelity (HiFi) and Hi-C sequencing technology to generate its genome assembly at the chromosome level. The assembly result spans 2.18 Gb, with a contig N50 of 126 Mb, encompassing 34 chromosomes that account for 99.6% of the genome. The assembly has a BUSCO score above 95% with different databases and strong collinearity with Yangtze giant softshell turtles (Rafetus swinhoei), indicating its completeness and continuity. A total of 19,175 genes and 46.86% repetitive sequences were annotated. The availability of this chromosome-scale genome represents a valuable resource for the pig-nosed turtle, providing insights into its aquatic adaptation and serving as a foundation for future turtle research.
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Affiliation(s)
- Ye Li
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Yuxuan Liu
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Jiangmin Zheng
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Baosheng Wu
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Xinxin Cui
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wenjie Xu
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Chenglong Zhu
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Qiang Qiu
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
| | - Kun Wang
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
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6
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Kohsokabe T, Kuratanai S, Kaneko K. Developmental hourglass: Verification by numerical evolution and elucidation by dynamical-systems theory. PLoS Comput Biol 2024; 20:e1011867. [PMID: 38422161 PMCID: PMC10903806 DOI: 10.1371/journal.pcbi.1011867] [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: 06/17/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
Determining the general laws between evolution and development is a fundamental biological challenge. Developmental hourglasses have attracted increased attention as candidates for such laws, but the necessity of their emergence remains elusive. We conducted evolutionary simulations of developmental processes to confirm the emergence of the developmental hourglass and unveiled its establishment. We considered organisms consisting of cells containing identical gene networks that control morphogenesis and evolved them under selection pressure to induce more cell types. By computing the similarity between the spatial patterns of gene expression of two species that evolved from a common ancestor, a developmental hourglass was observed, that is, there was a correlation peak in the intermediate stage of development. The fraction of pleiotropic genes increased, whereas the variance in individuals decreased, consistent with previous experimental reports. Reduction of the unavoidable variance by initial or developmental noise, essential for survival, was achieved up to the hourglass bottleneck stage, followed by diversification in developmental processes, whose timing is controlled by the slow expression dynamics conserved among organisms sharing the hourglass. This study suggests why developmental hourglasses are observed within a certain phylogenetic range of species.
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Affiliation(s)
| | | | - Kunihiko Kaneko
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
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7
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Zhu J, Wang Y, Chen C, Ji L, Hong X, Liu X, Chen H, Wei C, Zhu X, Li W. Identification of Sex-Specific Markers and Candidate Genes Using WGS Sequencing Reveals a ZW-Type Sex-Determination System in the Chinese Soft-Shell Turtle ( Pelodiscus sinensis). Int J Mol Sci 2024; 25:819. [PMID: 38255893 PMCID: PMC10815769 DOI: 10.3390/ijms25020819] [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: 11/24/2023] [Revised: 01/02/2024] [Accepted: 01/07/2024] [Indexed: 01/24/2024] Open
Abstract
Male and female Chinese soft-shelled turtles (Pelodiscus sinensis) have sex-dimorphic growth patterns, and males have higher commercial value because of their larger size and thicker calipash. Thus, developing sex-specific markers is beneficial to studies on all-male breeding in P. sinensis. Here, we developed an accurate and efficient workflow for the screening of sex-specific sequences with ZW or XY sex determination systems. Based on this workflow, female and male P. sinensis reference genomes of 2.23 Gb and 2.26 Gb were obtained using de novo assembly. After aligning and filtering, 4.01 Mb female-specific sequences were finally identified. Subsequently, the seven developed sex-specific primer pairs were 100% accurate in preliminary, population, and embryonic validation. The presence and absence of bands for the primers of P44, P45, P66, P67, P68, and P69, as well as two and one bands for the PB1 primer, indicate that the embryos are genetically female and male, respectively. NR and functional annotations identified several sex-determining candidate genes and related pathways, including Ran, Eif4et, and Crkl genes, and the insulin signaling pathway and the cAMP signaling pathway, respectively. Collectively, our results reveal that a ZW-type sex-determination system is present in P. sinensis and provide novel insights for the screening of sex-specific markers, sex-control breeding, and the studies of the sex determination mechanism of P. sinensis.
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Affiliation(s)
- Junxian Zhu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China;
- 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Yongchang 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Xinping Zhu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China;
- 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Wei Li
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China;
- 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
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8
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Nakamuta S, Itoh M, Mori M, Kurita M, Zhang Z, Nikaido M, Miyazaki M, Yokoyama T, Yamamoto Y, Nakamuta N. In situ hybridization analysis of odorant receptor expression in the olfactory organ of the pig-nosed turtle Carettochelys insculpta. Tissue Cell 2023; 85:102255. [PMID: 37922676 DOI: 10.1016/j.tice.2023.102255] [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: 06/18/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/07/2023]
Abstract
The turtle olfactory organ consists of upper (UCE) and lower (LCE) chamber epithelium, which send axons to the ventral and dorsal portions of the olfactory bulbs, respectively. Generally, the UCE is associated with glands and contains ciliated olfactory receptor neurons (ORNs), while the LCE is devoid of glands and contains microvillous ORNs. However, the olfactory organ of the pig-nosed turtle Carettochelys insculpta appears to be a single olfactory system morphologically: there are no associated glands; ciliated ORNs are distributed throughout the olfactory organ; and the olfactory bulb is not divided into ventral and dorsal portions. In this study, we analyzed the expression of odorant receptors (ORs), the major olfactory receptors in turtles, in the pig-nosed turtle olfactory organ, via in situ hybridization. Of 690 ORs, 375 were classified as class I and 315 as class II. Some class II ORs were expressed predominantly in the posterior dorsomedial walls of the nasal cavity, while other class II ORs and all class I ORs examined were expressed in the remaining region. These results suggest that the pig-nosed turtle olfactory organ can be divided into two regions according to the expression of ORs.
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Affiliation(s)
- Shoko Nakamuta
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Miho Itoh
- Port of Nagoya Public Aquarium, 1-3 Minato-machi, Minato-ku, Nagoya, Aichi 455-0033, Japan
| | - Masanori Mori
- Port of Nagoya Public Aquarium, 1-3 Minato-machi, Minato-ku, Nagoya, Aichi 455-0033, Japan
| | - Masanori Kurita
- Port of Nagoya Public Aquarium, 1-3 Minato-machi, Minato-ku, Nagoya, Aichi 455-0033, Japan
| | - Zicong Zhang
- Institute for the Advanced Study of Human Biology, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Masao Miyazaki
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Takuya Yokoyama
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Yoshio Yamamoto
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Nobuaki Nakamuta
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan.
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9
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Guo Y, Tang J, Zhuo Z, Huang J, Fu Z, Song J, Liu M, Dong Z, Wang Z. The first high-quality chromosome-level genome of Eretmochelys imbricata using HiFi and Hi-C data. Sci Data 2023; 10:604. [PMID: 37689728 PMCID: PMC10492850 DOI: 10.1038/s41597-023-02522-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/30/2023] [Indexed: 09/11/2023] Open
Abstract
Eretmochelys imbricata, a critically endangered sea turtle inhabiting tropical oceans and protected across the world, had an unknown genome sequence until now. In this study, we used HiFi reads and Hi-C technology to assemble a high-quality, chromosome-level genome of E. imbricata. The genome size was 2,138.26 Mb, with contig N50 length of 123.49 Mb and scaffold N50 of 137.21 Mb. Approximately 97.52% of the genome sequence was anchored to 28 chromosomes. A total of 20,206 protein-coding genes were predicted. We also analyzed the evolutionary relationships, gene family expansions, and positive selection of E. imbricata. Our results revealed that E. imbricata diverged from Chelonia mydas 38 million years ago and had enriched olfactory receptors and aging-related genes. Our genome will be useful for studying E. imbricata and its conservation.
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Affiliation(s)
- Yusong Guo
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Jiao Tang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Zixuan Zhuo
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Jingru Huang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Zhenli Fu
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Jiahao Song
- State Key Laboratory of Marine Environmental Science and College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Min Liu
- State Key Laboratory of Marine Environmental Science and College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Zhongdian Dong
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Zhongduo Wang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China.
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China.
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10
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Kondoh D, Kaneoya Y, Tonomori W, Kitayama C. Histological features and Gα olf expression patterns in the nasal cavity of sea turtles. J Anat 2023; 243:486-503. [PMID: 37042468 PMCID: PMC10439381 DOI: 10.1111/joa.13873] [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: 11/09/2022] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/13/2023] Open
Abstract
Sea turtles use olfaction to detect volatile and water-soluble substances. The nasal cavity of green turtles (Chelonia mydas) comprises morphologically defined the anterodorsal, anteroventral, and posterodorsal diverticula, as well as a single posteroventral fossa. Here, we detailed the histological features of the nasal cavity of a mature female green turtle. The posterodorsal diverticulum contained spongy-like venous sinuses and a wave-shaped sensory epithelium that favored ventilation. Secretory structures that were significant in sensory and non-sensory epithelia were probably involved in protection against seawater. These findings suggested that green turtles efficiently intake airborne substances and dissolve water-soluble substances in mucous, while suppressing the effects of salts. In addition, positive staining of Gαs/olf that couples with olfactory, but not vomeronasal, receptors was predominant in all three types of sensory epithelium in the nasal cavity. Both of airborne and water-soluble odorants seemed to be detected in cells expressing Gαolf and olfactory receptors.
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Affiliation(s)
- Daisuke Kondoh
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
| | - Yuka Kaneoya
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
| | - Wataru Tonomori
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
| | - Chiyo Kitayama
- Everlasting Nature of Asia (ELNA), Yokohama, Kanagawa, Japan
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11
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Gable SM, Mendez JM, Bushroe NA, Wilson A, Byars MI, Tollis M. The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order. Genes (Basel) 2023; 14:1387. [PMID: 37510292 PMCID: PMC10379679 DOI: 10.3390/genes14071387] [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: 06/06/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Squamates include more than 11,000 extant species of lizards, snakes, and amphisbaenians, and display a dazzling diversity of phenotypes across their over 200-million-year evolutionary history on Earth. Here, we introduce and define squamates (Order Squamata) and review the history and promise of genomic investigations into the patterns and processes governing squamate evolution, given recent technological advances in DNA sequencing, genome assembly, and evolutionary analysis. We survey the most recently available whole genome assemblies for squamates, including the taxonomic distribution of available squamate genomes, and assess their quality metrics and usefulness for research. We then focus on disagreements in squamate phylogenetic inference, how methods of high-throughput phylogenomics affect these inferences, and demonstrate the promise of whole genomes to settle or sustain persistent phylogenetic arguments for squamates. We review the role transposable elements play in vertebrate evolution, methods of transposable element annotation and analysis, and further demonstrate that through the understanding of the diversity, abundance, and activity of transposable elements in squamate genomes, squamates can be an ideal model for the evolution of genome size and structure in vertebrates. We discuss how squamate genomes can contribute to other areas of biological research such as venom systems, studies of phenotypic evolution, and sex determination. Because they represent more than 30% of the living species of amniote, squamates deserve a genome consortium on par with recent efforts for other amniotes (i.e., mammals and birds) that aim to sequence most of the extant families in a clade.
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Affiliation(s)
- Simone M Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jasmine M Mendez
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Nicholas A Bushroe
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Adam Wilson
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Michael I Byars
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
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12
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Gong S, Ge Y, Wei Y, Gao Y. Genomic insights into the genetic basis of eagle-beak jaw, large head, and long tail in the big-headed turtle. Ecol Evol 2023; 13:e10361. [PMID: 37502307 PMCID: PMC10368965 DOI: 10.1002/ece3.10361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/15/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
The big-headed turtle (Platysternon megacephalum) is an endemic chelonian species in Asia. Unlike most other turtles in the world, P. megacephalum is characterized with eagle-beak jaw, large head, and long tail. Although these unique characteristics are well recognized, the underlying genetic basis remains largely elusive. Here, we performed comparative genomic analysis between P. megacephalum and other representative species, aiming to reveal the genetic basis of the unique morphological features. Our results revealed that the eagle-beak jaw is most likely enabled by combined effects of expansion of SFRP5, extraction of FGF11, and mutation of both ZFYVE16 and PAX6. Large head is supported by mutations of SETD2 and FGRF2 and copy number variations of six head circumference modulation-related genes (TGFBR2, Twist2, Rdh10, Gas1, Chst11, and SNAP25). The long tail is probably involved in a genetic network comprising Gdf11, Lin 28, and HoxC12, two of which showed a consistent expression pattern with a model organism (mice). These findings suggest that expansion, extraction, and mutation of those genes may have profound effects on unique phenotypes of P. megacephalum.
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Affiliation(s)
- Shiping Gong
- College of Life Science and TechnologyJinan UniversityGuangzhouChina
| | - Yan Ge
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of ZoologyGuangdong Academy of SciencesGuangzhouChina
| | - Yufeng Wei
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of ZoologyGuangdong Academy of SciencesGuangzhouChina
| | - Yangchun Gao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of ZoologyGuangdong Academy of SciencesGuangzhouChina
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13
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Liu X, Liu H, Wang Y, Li M, Ji L, Wang K, Wei C, Li W, Chen C, Yu L, Zhu X, Hong X. Chromosome-Level Analysis of the Pelochelys cantorii Genome Provides Insights to Its Immunity, Growth and Longevity. BIOLOGY 2023; 12:939. [PMID: 37508370 PMCID: PMC10376104 DOI: 10.3390/biology12070939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/19/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023]
Abstract
The Asian giant soft-shelled turtle, Pelochelys cantorii (Trionychidae), is one of the largest aquatic turtles in China and was designated as a First-Grade Protected Animal in China in 1989. Previous investigation based on a combination of Illumina short-read, PacBio long-read and Hi-C scaffolding technologies acquired a high-quality chromosome-level genome of Pc. cantorii. In this study, comparative genomic analysis between Pc. cantorii and 16 other vertebrate genomes indicated that turtles separated from the ancestor of archosaurians approximately 256.6 (95% highest posterior density interval, 263.6-251.9) million years ago (Mya) (Upper Permian to Triassic) and that Pc. cantorii separated from the ancestor of Pd. sinensis and R. swinhoei approximately 59.3 (95% highest posterior density interval, 64.3-54.3) Mya. Moreover, several candidate genes, such as VWA5A, ABCG2, A2M and IGSF1, associated with tumor suppression, growth and age were expanded, implicating their potential roles in the exceptional longevity of turtles. This new chromosome-level assembly has important scientific value in the study of conservation of Pc. cantorii and also enriches the evolutionary investigation of turtle species.
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Affiliation(s)
- 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
| | - Haiyang 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
| | - 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
| | - Mingzhi Li
- Guangzhou Bio & Data Technology Co., Ltd., Guangzhou 510555, 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
| | - Kaikuo 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
- College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, 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
| | - 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
| | - 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
| | - 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
| | - 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
- College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, 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
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14
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Chang G, Jones S, Leelakumari S, Ashkani J, Culibrk L, O'Neill K, Tse K, Cheng D, Chuah E, McDonald H, Kirk H, Pandoh P, Pari S, Angelini V, Kyle C, Bertorelle G, Zhao Y, Mungall A, Moore R, Vilaça S, Jones S. The genome sequence of the Loggerhead sea turtle, Caretta caretta Linnaeus 1758. F1000Res 2023; 12:336. [PMID: 37455852 PMCID: PMC10338980 DOI: 10.12688/f1000research.131283.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
We present a genome assembly of Caretta caretta (the Loggerhead sea turtle; Chordata, Testudines, Cheloniidae), generated from genomic data from two unrelated females. The genome sequence is 2.13 gigabases in size. The assembly has a busco completion score of 96.1% and N50 of 130.95 Mb. The majority of the assembly is scaffolded into 28 chromosomal representations with a remaining 2% of the assembly being excluded from these.
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Affiliation(s)
- Glenn Chang
- Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Samantha Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Sreeja Leelakumari
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Jahanshah Ashkani
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Luka Culibrk
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Kieran O'Neill
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Kane Tse
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Dean Cheng
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Helen McDonald
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Heather Kirk
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Pawan Pandoh
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Sauro Pari
- Fondazione Cetacea Onlus, Riccione, RN, 47838, Italy
| | | | - Christopher Kyle
- Forensic Science Department, Trent University, Peterborough, Ontario, K9L 0G2, Canada
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, K9L 0G2, Canada
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, FE, 44121, Italy
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Andrew Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Sibelle Vilaça
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, K9L 0G2, Canada
| | - Steven Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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15
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Nakamuta S, Mori M, Ito M, Kurita M, Miyazaki M, Yamamoto Y, Nakamuta N. In situ hybridization analysis of olfactory receptor expression in the sea turtle olfactory organ. Cell Tissue Res 2023:10.1007/s00441-023-03782-6. [PMID: 37266727 DOI: 10.1007/s00441-023-03782-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 05/08/2023] [Indexed: 06/03/2023]
Abstract
The olfactory organ of turtles consists of an upper chamber epithelium (UCE) with associated glands, and a lower chamber epithelium (LCE) devoid of glands. The UCE and LCE are referred to as the air-nose and the water-nose, respectively, because the UCE is thought to detect airborne odorants, while the LCE detects waterborne odorants. However, it is not clear how the two are used in the olfactory organ. Odorant receptors (ORs) are the major olfactory receptors in turtles; they are classified as class I and II ORs, distinguished by their primary structure. Class I ORs are suggested to be receptive to water-soluble ligands and class II ORs to volatile ligands. This study analyzed the expression of class I and II ORs in hatchlings of the green sea turtle, Chelonia mydas, through in situ hybridization, to determine the localization of OR-expressing cells in the olfactory organ. Class I OR-expressing cells were distributed mainly in the LCE, implying that the LCE is receptive to waterborne odorants. Class II OR-expressing cells were distributed in both the UCE and LCE, implying that the entire olfactory organ is receptive to airborne odorants. The widespread expression of class II ORs may increase opportunities for sea turtles to sense airborne odorants.
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Affiliation(s)
- Shoko Nakamuta
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan
| | - Masanori Mori
- Port of Nagoya Public Aquarium, 1-3 Minato-machi, Minato-ku, Nagoya, Aichi, 455-0033, Japan
| | - Miho Ito
- Port of Nagoya Public Aquarium, 1-3 Minato-machi, Minato-ku, Nagoya, Aichi, 455-0033, Japan
| | - Masanori Kurita
- Port of Nagoya Public Aquarium, 1-3 Minato-machi, Minato-ku, Nagoya, Aichi, 455-0033, Japan
| | - Masao Miyazaki
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan
| | - Yoshio Yamamoto
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan
| | - Nobuaki Nakamuta
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan.
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16
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Reiner A. Could theropod dinosaurs have evolved to a human level of intelligence? J Comp Neurol 2023; 531:975-1006. [PMID: 37029483 PMCID: PMC10106414 DOI: 10.1002/cne.25458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 04/09/2023]
Abstract
Noting that some theropod dinosaurs had large brains, large grasping hands, and likely binocular vision, paleontologist Dale Russell suggested that a branch of these dinosaurs might have evolved to a human intelligence level, had dinosaurs not become extinct. I offer reasons why the likely pallial organization in dinosaurs would have made this improbable, based on four assumptions. First, it is assumed that achieving human intelligence requires evolving an equivalent of the about 200 functionally specialized cortical areas characteristic of humans. Second, it is assumed that dinosaurs had an avian nuclear type of pallial organization, in contrast to the mammalian cortical organization. Third, it is assumed that the interactions between the different neuron types making up an information processing unit within pallium are critical to its role in analyzing information. Finally, it is assumed that increasing axonal length between the neuron sets carrying out this operation impairs its efficacy. Based on these assumptions, I present two main reasons why dinosaur pallium might have been unable to add the equivalent of 200 efficiently functioning cortical areas. First, a nuclear pattern of pallial organization would require increasing distances between the neuron groups corresponding to the separate layers of any given mammalian cortical area, as more sets of nuclei equivalent to a cortical area are interposed between the existing sets, increasing axon length and thereby impairing processing efficiency. Second, because of its nuclear organization, dinosaur pallium could not reduce axon length by folding to bring adjacent areas closer together, as occurs in cerebral cortex.
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Affiliation(s)
- Anton Reiner
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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17
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Uchida Y, Takeda H, Furusawa C, Irie N. Stability in gene expression and body-plan development leads to evolutionary conservation. EvoDevo 2023; 14:4. [PMID: 36918942 PMCID: PMC10015717 DOI: 10.1186/s13227-023-00208-w] [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: 11/06/2022] [Accepted: 03/01/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND Phenotypic evolution is mainly explained by selection for phenotypic variation arising from factors including mutation and environmental noise. Recent theoretical and experimental studies have suggested that phenotypes with greater developmental stability tend to have a constant phenotype and gene expression level within a particular genetic and environmental condition, and this positively correlates with stronger evolutionary conservation, even after the accumulation of genetic changes. This could reflect a novel mechanism that contributes to evolutionary conservation; however, it remains unclear whether developmental stability is the cause, or whether at least it contributes to their evolutionary conservation. Here, using Japanese medaka lines, we tested experimentally whether developmental stages and gene expression levels with greater stability led to their evolutionary conservation. RESULTS We first measured the stability of each gene expression level and developmental stage (defined here as the whole embryonic transcriptome) in the inbred F0 medaka population. We then measured their evolutionary conservation in the F3 generation by crossing the F0 line with the distantly related Japanese medaka line (Teradomori), followed by two rounds of intra-generational crossings. The results indicated that the genes and developmental stages that had smaller variations in the F0 generation showed lower diversity in the hybrid F3 generation, which implies a causal relationship between stability and evolutionary conservation. CONCLUSIONS These findings suggest that the stability in phenotypes, including the developmental stages and gene expression levels, leads to their evolutionary conservation; this most likely occurs due to their low potential to generate phenotypic variation. In addition, since the highly stable developmental stages match with the body-plan-establishment stage, it also implies that the developmental stability potentially contributed to the strict conservation of animal body plan.
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Affiliation(s)
- Yui Uchida
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Chikara Furusawa
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.,Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Naoki Irie
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan. .,Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan.
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18
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Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories. Proc Natl Acad Sci U S A 2023; 120:e2201076120. [PMID: 36749728 PMCID: PMC9962930 DOI: 10.1073/pnas.2201076120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.
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19
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Yenmiş M, Ayaz D. The Story of the Finest Armor: Developmental Aspects of Reptile Skin. J Dev Biol 2023; 11:jdb11010005. [PMID: 36810457 PMCID: PMC9944452 DOI: 10.3390/jdb11010005] [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: 12/15/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/31/2023] Open
Abstract
The reptile skin is a barrier against water loss and pathogens and an armor for mechanical damages. The integument of reptiles consists of two main layers: the epidermis and the dermis. The epidermis, the hard cover of the body which has an armor-like role, varies among extant reptiles in terms of structural aspects such as thickness, hardness or the kinds of appendages it constitutes. The reptile epithelial cells of the epidermis (keratinocytes) are composed of two main proteins: intermediate filament keratins (IFKs) and corneous beta proteins (CBPs). The outer horny layer of the epidermis, stratum corneum, is constituted of keratinocytes by means of terminal differentiation or cornification which is a result of the protein interactions where CBPs associate with and coat the initial scaffold of IFKs. Reptiles were able to colonize the terrestrial environment due to the changes in these epidermal structures, which led to various cornified epidermal appendages such as scales and scutes, a beak, claws or setae. Developmental and structural aspects of the epidermal CBPs as well as their shared chromosomal locus (EDC) indicate an ancestral origin that gave rise to the finest armor of reptilians.
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20
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Tokita M, Sato H. Creating morphological diversity in reptilian temporal skull region: A review of potential developmental mechanisms. Evol Dev 2023; 25:15-31. [PMID: 36250751 DOI: 10.1111/ede.12419] [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: 02/11/2022] [Revised: 09/18/2022] [Accepted: 09/20/2022] [Indexed: 01/13/2023]
Abstract
Reptilian skull morphology is highly diverse and broadly categorized into three categories based on the number and position of the temporal fenestrations: anapsid, synapsid, and diapsid. According to recent phylogenetic analysis, temporal fenestrations evolved twice independently in amniotes, once in Synapsida and once in Diapsida. Although functional aspects underlying the evolution of tetrapod temporal fenestrations have been well investigated, few studies have investigated the developmental mechanisms responsible for differences in the pattern of temporal skull region. To determine what these mechanisms might be, we first examined how the five temporal bones develop by comparing embryonic cranial osteogenesis between representative extant reptilian species. The pattern of temporal skull region may depend on differences in temporal bone growth rate and growth direction during ontogeny. Next, we compared the histogenesis patterns and the expression of two key osteogenic genes, Runx2 and Msx2, in the temporal region of the representative reptilian embryos. Our comparative analyses suggest that the embryonic histological condition of the domain where temporal fenestrations would form predicts temporal skull morphology in adults and regulatory modifications of Runx2 and Msx2 expression in osteogenic mesenchymal precursor cells are likely involved in generating morphological diversity in the temporal skull region of reptiles.
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Affiliation(s)
- Masayoshi Tokita
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Hiromu Sato
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
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21
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Field EK, Hartzheim A, Terry J, Dawson G, Haydt N, Neuman-Lee LA. Reptilian Innate Immunology and Ecoimmunology: What Do We Know and Where Are We Going? Integr Comp Biol 2022; 62:1557-1571. [PMID: 35833292 DOI: 10.1093/icb/icac116] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 01/05/2023] Open
Abstract
Reptiles, the only ectothermic amniotes, employ a wide variety of physiological adaptations to adjust to their environments but remain vastly understudied in the field of immunology and ecoimmunology in comparison to other vertebrate taxa. To address this knowledge gap, we assessed the current state of research on reptilian innate immunology by conducting an extensive literature search of peer-reviewed articles published across the four orders of Reptilia (Crocodilia, Testudines, Squamata, and Rhynchocephalia). Using our compiled dataset, we investigated common techniques, characterization of immune components, differences in findings and type of research among the four orders, and immune responses to ecological and life-history variables. We found that there are differences in the types of questions asked and approaches used for each of these reptilian orders. The different conceptual frameworks applied to each group has led to a lack of unified understanding of reptilian immunological strategies, which, in turn, have resulted in large conceptual gaps in the field of ecoimmunology as a whole. To apply ecoimmunological concepts and techniques most effectively to reptiles, we must combine traditional immunological studies with ecoimmunological studies to continue to identify, characterize, and describe the reptilian immune components and responses. This review highlights the advances and gaps that remain to help identify targeted and cohesive approaches for future research in reptilian ecoimmunological studies.
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Affiliation(s)
- Emily K Field
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72401, USA
| | - Alyssa Hartzheim
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72401, USA
| | - Jennifer Terry
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72401, USA
| | - Grant Dawson
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72401, USA
| | - Natalie Haydt
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72401, USA
| | - Lorin A Neuman-Lee
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72401, USA
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22
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Jiang YJ, Gao JF, Lin LH, Li H, Meng QG, Qu YF, Ji X. Single-cell transcriptomes from turtle livers reveal sensitivity of hepatic immune cells to bacteria-infection. FISH & SHELLFISH IMMUNOLOGY 2022; 131:847-854. [PMID: 36273515 DOI: 10.1016/j.fsi.2022.10.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/10/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
The liver is important in the synthesis, metabolism and storage of nutrients, detoxification and immune response of the body, and the liver immune response against exogenous pathogens from the intestinal tract plays a key role in the immune activities. However, the cellular composition of the liver immune atlas remains sparsely studied in reptiles. We used single-cell RNA sequencing to identify the cellular profile of the liver of the Chinese soft-shelled turtle (Pelodiscus sinensis). We obtained the transcriptional landscape based on 9938 cells from the fractionation of fresh hepatic tissues from two individuals, uninfected and infected with bacteria (Aeromonas hydrophila). We identified seven hepatic immune cell subsets, including plasma, erythroid, T/NK, B, endothelial, dendritic and Kupffer cells. Bacteria-infection altered the number of liver immune cells, as revealed by the fact that the infected turtle had more plasma, endothelial and Kupffer cells and fewer T/NK, dendritic and erythroid cells than did the uninfected turtle. Our study is the first to provide a comprehensive view of the hepatic immune landscape of P. sinensis at the single-cell resolution that outlines the characteristics of immune cells in the turtle liver and provides a liver transcriptome baseline for turtle immunology.
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Affiliation(s)
- Yi-Jin Jiang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Jian-Fang Gao
- Hangzhou Key Laboratory for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Long-Hui Lin
- Hangzhou Key Laboratory for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Qing-Guo Meng
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Yan-Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.
| | - Xiang Ji
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, Zhejiang, China.
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23
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Jin L, Sun W, Bao H, Liang X, Li P, Shi S, Wang Z, Qian G, Ge C. The forkhead factor Foxl2 participates in the ovarian differentiation of Chinese soft-shelled turtle Pelodiscus sinensis. Dev Biol 2022; 492:101-110. [DOI: 10.1016/j.ydbio.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/24/2022] [Accepted: 10/05/2022] [Indexed: 11/30/2022]
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24
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Hoh DZ, Lee HH, Wada N, Liu WA, Lu MR, Lai CK, Ke HM, Sun PF, Tang SL, Chung WH, Chen YL, Chung CL, Tsai IJ. Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization. BMC Biol 2022; 20:236. [PMID: 36266645 PMCID: PMC9583462 DOI: 10.1186/s12915-022-01436-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The Fusarium solani species complex (FSSC) comprises fungal pathogens responsible for mortality in a diverse range of animals and plants, but their genome diversity and transcriptome responses in animal pathogenicity remain to be elucidated. We sequenced, assembled and annotated six chromosome-level FSSC clade 3 genomes of aquatic animal and plant host origins. We established a pathosystem and investigated the expression data of F. falciforme and F. keratoplasticum in Chinese softshell turtle (Pelodiscus sinensis) host. RESULTS Comparative analyses between the FSSC genomes revealed a spectrum of conservation patterns in chromosomes categorised into three compartments: core, fast-core (FC), and lineage-specific (LS). LS chromosomes contribute to variations in genomes size, with up to 42.2% of variations between F. vanettenii strains. Each chromosome compartment varied in structural architectures, with FC and LS chromosomes contain higher proportions of repetitive elements with genes enriched in functions related to pathogenicity and niche expansion. We identified differences in both selection in the coding sequences and DNA methylation levels between genome features and chromosome compartments which suggest a multi-speed evolution that can be traced back to the last common ancestor of Fusarium. We further demonstrated that F. falciforme and F. keratoplasticum are opportunistic pathogens by inoculating P. sinensis eggs and identified differentially expressed genes also associated with plant pathogenicity. These included the most upregulated genes encoding the CFEM (Common in Fungal Extracellular Membrane) domain. CONCLUSIONS The high-quality genome assemblies provided new insights into the evolution of FSSC chromosomes, which also serve as a resource for studies of fungal genome evolution and pathogenesis. This study also establishes an animal model for fungal pathogens of trans-kingdom hosts.
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Affiliation(s)
- Daphne Z Hoh
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, 116 Wenshan, Taipei, Taiwan
| | - Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan
| | - Naohisa Wada
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan
| | - Wei-An Liu
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan
| | - Min R Lu
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan
| | - Cheng-Kuo Lai
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan
| | - Pei-Feng Sun
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, 116 Wenshan, Taipei, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Wen-Hsin Chung
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Ying-Lien Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617, Taiwan
| | - Chia-Lin Chung
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617, Taiwan
| | - Isheng Jason Tsai
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan.
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.
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25
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Dyson CJ, Pfennig A, Ariano-Sánchez D, Lachance J, Mendelson III JR, Goodisman MAD. Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes. G3 GENES|GENOMES|GENETICS 2022; 12:6760128. [DOI: 10.1093/g3journal/jkac276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
Abstract
Many lizard species face extinction due to worldwide climate change. The Guatemalan Beaded Lizard, Heloderma charlesbogerti, is a member of the Family Helodermatidae that may be particularly imperiled; fewer than 600 mature individuals are believed to persist in the wild. In addition, H. charlesbogerti lizards are phenotypically remarkable. They are large in size, charismatically patterned, and possess a venomous bite. Here, we report the draft genome of the Guatemalan Beaded Lizard using DNA from a wild-caught individual. The assembled genome totals 2.31 Gb in length, similar in size to the genomes of related species. Single-copy orthologs were used to produce a novel molecular phylogeny, revealing that the Guatemalan Beaded Lizard falls into a clade with the Asian Glass Lizard (Anguidae) and in close association with the Komodo Dragon (Varanidae) and the Chinese Crocodile Lizard (Shinisauridae). In addition, we identified 31,411 protein-coding genes within the genome. Of the genes identified, we found 504 that evolved with a differential constraint on the branch leading to the Guatemalan Beaded Lizard. Lastly, we identified a decline in the effective population size of the Guatemalan Beaded Lizard approximately 400,000 years ago, followed by a stabilization before starting to dwindle again 60,000 years ago. The results presented here provide important information regarding a highly endangered, venomous reptile that can be used in future conservation, functional genetic, and phylogenetic analyses.
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Affiliation(s)
- Carl J Dyson
- School of Biological Sciences, Georgia Institute of Technology , Atlanta, GA 30332, USA
| | - Aaron Pfennig
- School of Biological Sciences, Georgia Institute of Technology , Atlanta, GA 30332, USA
| | - Daniel Ariano-Sánchez
- Centro de Estudios Ambientales y Biodiversidad, Universidad del Valle de Guatemala , Zona 15 01015, Guatemala
- Heloderma Natural Reserve , Zacapa 19007, Guatemala
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology , Atlanta, GA 30332, USA
| | - Joseph R Mendelson III
- School of Biological Sciences, Georgia Institute of Technology , Atlanta, GA 30332, USA
- Zoo Atlanta , Atlanta, GA 30315, USA
| | - Michael A D Goodisman
- School of Biological Sciences, Georgia Institute of Technology , Atlanta, GA 30332, USA
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Gene Regulation during Carapacial Ridge Development of Mauremys reevesii: The Development of Carapacial Ridge, Ribs and Scutes. Genes (Basel) 2022; 13:genes13091676. [PMID: 36140843 PMCID: PMC9498798 DOI: 10.3390/genes13091676] [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: 08/10/2022] [Revised: 08/26/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
The unique topological structure of a turtle shell, including the special ribs-scapula relationship, is an evolutionarily novelty of amniotes. The carapacial ridge is a key embryonic tissue for inducing turtle carapace morphologenesis. However, the gene expression profiles and molecular regulatory mechanisms that occur during carapacial ridge development, including the regulation mechanism of rib axis arrest, the development mechanism of the carapacial ridge, and the differentiation between soft-shell turtles and hard-shell turtles, are not fully understood. In this study, we obtained genome-wide gene expression profiles during the carapacial ridge development of Mauremys reevesii using RNA-sequencing by using carapacial ridge tissues from stage 14, 15 and 16 turtle embryos. In addition, a differentially expressed genes (DEGs) analysis and a gene set enrichment analysis (GSEA) of three comparison groups were performed. Furthermore, a Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was used to analyze the pathway enrichment of the differentially expressed genes of the three comparative groups. The result displayed that the Wnt signaling pathway was substantially enriched in the CrTK14 vs. the CrTK15 comparison group, while the Hedgehog signaling pathway was significantly enriched in the CrTK15 vs. the CrTK16 group. Moreover, the regulatory network of the Wnt signaling pathway showed that Wnt signaling pathways might interact with Fgfs, Bmps, and Shh to form a regulatory network to regulate the carapacial ridge development. Next, WGCNA was used to cluster and analyze the expression genes during the carapacial ridge development of M. reevesii and P. sinensis. Further, a KEGG functional enrichment analysis of the carapacial ridge correlation gene modules was performed. Interesting, these results indicated that the Wnt signaling pathway and the MAPK signaling pathway were significantly enriched in the gene modules that were highly correlated with the stage 14 and stage 15 carapacial ridge samples of the two species. The Hedgehog signaling pathway was significantly enriched in the modules that were strongly correlated with the stage 16 carapacial ridge samples of M. reevesii, however, the PI3K-Akt signaling and the TGF-β signaling pathways were significantly enriched in the modules that were strongly correlated with the stage 16 carapacial ridge samples of P. sinensis. Furthermore, we found that those modules that were strongly correlated with the stage 14 carapacial ridge samples of M. reevesii and P. sinensis contained Wnts and Lef1. While the navajo white 3 module which was strongly correlated with the stage 16 carapacial ridge samples of M. reevesii contained Shh and Ptchs. The dark green module strongly correlated with the stage 16 carapacial ridge samples of P. sinensis which contained Col1a1, Col1a2, and Itga8. Consequently, this study systematically revealed the signaling pathways and genes that regulate the carapacial ridge development of M. reevesii and P. sinensis, which provides new insights for revealing the molecular mechanism that is underlying the turtle's body structure.
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27
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Ecay TW, Stewart JR, Khambaty M. Functional complexity in the chorioallantoic membrane of an oviparous snake: Specializations for calcium uptake from the eggshell. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:331-341. [PMID: 35652464 DOI: 10.1002/jez.b.23146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 04/15/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
The chorioallantoic membrane of oviparous reptiles forms a vascular interface with the eggshell. The eggshell contains calcium, primarily as calcium carbonate. Extraction and mobilization of this calcium by the chorioallantoic membrane contributes importantly to embryonic nutrition. Development of the chorioallantoic membrane is primarily known from studies of squamates and birds. Although there are pronounced differences in eggshell structure, squamate and bird embryos each mobilize calcium from eggshells. Specialized cells in the chicken chorionic epithelium transport calcium from the eggshell aided by a second population of cells that secrete protons generated by the enzyme carbonic anhydrase. Calcium transporting cells also are present in the chorioallantoic membrane of corn snakes, although these cells function differently than those of chickens. We used histology and immunohistology to characterize the morphology and functional attributes of the chorioallantoic membrane of corn snakes. We identified two populations of cells in the outer layer of the chorionic epithelium. Calbindin-D28K , a cellular marker for calcium transport expressed in squamate chorioallantoic membranes, is localized in large, flattened cells that predominate in the chorionic epithelium. Smaller cells, interspersed among the large cells, express carbonic anhydrase 2, an enzyme not previously localized in the chorionic epithelium of an oviparous squamate. These findings indicate that differentiation of chorionic epithelial cells contributes to extraction and transport of calcium from the eggshell. The presence of specializations of chorioallantoic membranes for calcium uptake from eggshells in chickens and corn snakes suggests that eggshell calcium was a source of embryonic nutrition early in the evolution of Sauropsida.
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Affiliation(s)
- Tom W Ecay
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson, Tennessee, USA
| | - James R Stewart
- Department of Biological Sciences, East Tennessee State University, Johnson City, Tennessee, USA
| | - Maleka Khambaty
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson, Tennessee, USA
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28
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Chen SN, Huang L, Fu JP, Pang AN, Wang KL, Nie P. Gene synteny, evolution and antiviral activity of type I IFNs in a reptile species, the Chinese soft-shelled turtle Pelodiscus sinensis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 134:104461. [PMID: 35660570 DOI: 10.1016/j.dci.2022.104461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/21/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Type I interferons (IFNs) are critical cytokines for the establishment of antiviral status in fish, amphibian, avian and mammal, but the knowledge on type I IFNs is rather limited in reptile. In this study, seven type I IFN genes, designed as IFN1 to IFN7, were identified from a reptile species, the Chinese soft-shelled turtle (Pelodiscus sinensis). These identified type I IFNs have relatively low protein identity, when compared with those in human and chicken; but they possess conserved cysteines, predicted multi-helix structure and N-terminal signal peptide. The Chinese soft-shelled turtle IFN1 to IFN5 have two exons and one intron, but IFN6 and IFN7 are the single-exon genes. Chinese soft-shelled turtle type I IFNs are located respectively on the two conserved reptile-bird loci, named as Locus a and Locus c, and are clustered into the four of the five reptile-bird groups (named as Groups I-V) based on phylogenetic evidence, due to the lack of IFNK in the turtle. Moreover, the Chinese soft-shelled turtle type I IFNs can be induced by soft-shelled turtle iridovirus (STIV) infection and show antiviral activity in soft-shelled turtle artery (STA) cells, except IFN6. In addition, due to the difference in genome organizations, such as the number of exons and introns of type I IFN genes from fish to mammal, the definition and evolution of 'intronless' type I IFN genes were discussed in lineages of vertebrates. Thus, the finding of type I IFNs on two different loci in P. sinensis sheds light on the evolution of type I IFN genes in vertebrates.
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Affiliation(s)
- Shan Nan Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - Lin Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - Jian Ping Fu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - An Ning Pang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - Kai Lun Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - Pin Nie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong Province, 266237, China; School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China.
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29
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Yu M. Computational analysis on two putative mitochondrial protein-coding genes from the Emydura subglobosa genome: A functional annotation approach. PLoS One 2022; 17:e0268031. [PMID: 35981005 PMCID: PMC9387794 DOI: 10.1371/journal.pone.0268031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 04/21/2022] [Indexed: 11/19/2022] Open
Abstract
Rapid advancements in automated genomic technologies have uncovered many unique findings about the turtle genome and its associated features including olfactory gene expansions and duplications of toll-like receptors. However, despite the advent of large-scale sequencing, assembly, and annotation, about 40-50% of genes in eukaryotic genomes are left without functional annotation, severely limiting our knowledge of the biological information of genes. Additionally, these automated processes are prone to errors since draft genomes consist of several disconnected scaffolds whose order is unknown; erroneous draft assemblies may also be contaminated with foreign sequences and propagate to cause errors in annotation. Many of these automated annotations are thus incomplete and inaccurate, highlighting the need for functional annotation to link gene sequences to biological identity. In this study, we have functionally annotated two genes of the red-bellied short-neck turtle (Emydura subglobosa), a member of the relatively understudied pleurodire lineage of turtles. We improved upon initial ab initio gene predictions through homology-based evidence and generated refined consensus gene models. Through functional, localization, and structural analyses of the predicted proteins, we discovered conserved putative genes encoding mitochondrial proteins that play a role in C21-steroid hormone biosynthetic processes and fatty acid catabolism-both of which are distantly related by the tricarboxylic acid (TCA) cycle and share similar metabolic pathways. Overall, these findings further our knowledge about the genetic features underlying turtle physiology, morphology, and longevity, which have important implications for the treatment of human diseases and evolutionary studies.
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Affiliation(s)
- Megan Yu
- Department of Molecular, Cell & Developmental Biology, University of California–Los Angeles, Los Angeles, California, United States of America
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30
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Hussan MT, Sakai A, Matsui H. Glutamatergic pathways in the brains of turtles: A comparative perspective among reptiles, birds, and mammals. Front Neuroanat 2022; 16:937504. [PMID: 36059432 PMCID: PMC9428285 DOI: 10.3389/fnana.2022.937504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Glutamate acts as the main excitatory neurotransmitter in the brain and plays a vital role in physiological and pathological neuronal functions. In mammals, glutamate can cause detrimental excitotoxic effects under anoxic conditions. In contrast, Trachemys scripta, a freshwater turtle, is one of the most anoxia-tolerant animals, being able to survive up to months without oxygen. Therefore, turtles have been investigated to assess the molecular mechanisms of neuroprotective strategies used by them in anoxic conditions, such as maintaining low levels of glutamate, increasing adenosine and GABA, upregulating heat shock proteins, and downregulating KATP channels. These mechanisms of anoxia tolerance of the turtle brain may be applied to finding therapeutics for human glutamatergic neurological disorders such as brain injury or cerebral stroke due to ischemia. Despite the importance of glutamate as a neurotransmitter and of the turtle as an ideal research model, the glutamatergic circuits in the turtle brain remain less described whereas they have been well studied in mammalian and avian brains. In reptiles, particularly in the turtle brain, glutamatergic neurons have been identified by examining the expression of vesicular glutamate transporters (VGLUTs). In certain areas of the brain, some ionotropic glutamate receptors (GluRs) have been immunohistochemically studied, implying that there are glutamatergic target areas. Based on the expression patterns of these glutamate-related molecules and fiber connection data of the turtle brain that is available in the literature, many candidate glutamatergic circuits could be clarified, such as the olfactory circuit, hippocampal–septal pathway, corticostriatal pathway, visual pathway, auditory pathway, and granule cell–Purkinje cell pathway. This review summarizes the probable glutamatergic pathways and the distribution of glutamatergic neurons in the pallium of the turtle brain and compares them with those of avian and mammalian brains. The integrated knowledge of glutamatergic pathways serves as the fundamental basis for further functional studies in the turtle brain, which would provide insights on physiological and pathological mechanisms of glutamate regulation as well as neural circuits in different species.
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Affiliation(s)
- Mohammad Tufazzal Hussan
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, Japan
- Department of Anatomy and Histology, Patuakhali Science and Technology University, Barishal, Bangladesh
- *Correspondence: Mohammad Tufazzal Hussan,
| | - Akiko Sakai
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hideaki Matsui
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, Japan
- Hideaki Matsui,
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31
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Chromosome-level genome assembly of Asian yellow pond turtle (Mauremys mutica) with temperature-dependent sex determination system. Sci Rep 2022; 12:7905. [PMID: 35550586 PMCID: PMC9098631 DOI: 10.1038/s41598-022-12054-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/21/2022] [Indexed: 12/14/2022] Open
Abstract
Knowledge of sex determination has important implications in physiology, ecology and genetics, but the evolutionary mechanisms of sex determination systems in turtles have not been fully elucidated, due to a lack of reference genomes. Here, we generate a high-quality genome assembly of Asian yellow pond turtle (Mauremys mutica) using continuous long-read (PacBio platform), Illumina, and high-throughput chromatin conformation capture (Hi-C) technologies. The M. mutica haplotype has a genome size of 2.23 Gb with a contig N50 of 8.53 Mb and scaffold N50 of 141.98 Mb. 99.98% sequences of the total assembly are anchored to 26 pseudochromosomes. Comparative genomics analysis indicated that the lizard-snake-tuatara clade diverged from the bird-crocodilian-turtle clade at approximately 267.0-312.3 Mya. Intriguingly, positive selected genes are mostly enriched in the calcium signaling pathway and neuroactive ligand-receptor interaction, which are involved in the process of temperature-dependent sex determination. These findings provide important evolutionary insights into temperature-dependent sex determination system.
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32
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Mayne B, Mustin W, Baboolal V, Casella F, Ballorain K, Barret M, Vanderklift MA, Tucker AD, Korbie D, Jarman S, Berry O. Age prediction of green turtles with an epigenetic clock. Mol Ecol Resour 2022; 22:2275-2284. [DOI: 10.1111/1755-0998.13621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/29/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Benjamin Mayne
- Environomics Future Science Platform Indian Oceans Marine Research Centre Commonwealth Scientific and Industrial Research Organisation (CSIRO) Crawley Western Australia Australia
| | - Walter Mustin
- Cayman Turtle Conservation and Education Centre Grand Cayman KY1‐1301 Cayman Islands
| | - Vandanaa Baboolal
- Cayman Turtle Conservation and Education Centre Grand Cayman KY1‐1301 Cayman Islands
| | - Francesca Casella
- Cayman Turtle Conservation and Education Centre Grand Cayman KY1‐1301 Cayman Islands
| | - Katia Ballorain
- Centre d'Etude et de Découverte des Tortues Marines (CEDTM) 19 Cité des Frangipaniers 97424 Piton Saint‐Leu, La Réunion France
| | - Mathieu Barret
- Kélonia l’observatoire des tortues marines 46 Rue Général de Gaulle 97436 Saint‐Leu, La Réunion France
| | - Mathew A. Vanderklift
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Oceans and Atmosphere Crawley Western Australia Australia
| | - Anton D. Tucker
- Department of Biodiversity, Conservation and Attractions Marine Science Program Kensington Western Australia Australia
| | - Darren Korbie
- Australian Institute for Bioengineering and Nanotechnology The University of Queensland Brisbane Queensland Australia
| | - Simon Jarman
- School of Biological Sciences University of Western Australia 35 Stirling Highway Perth Western Australia Australia
| | - Oliver Berry
- Environomics Future Science Platform Indian Oceans Marine Research Centre Commonwealth Scientific and Industrial Research Organisation (CSIRO) Crawley Western Australia Australia
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33
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Uchida Y, Shigenobu S, Takeda H, Furusawa C, Irie N. Potential contribution of intrinsic developmental stability toward body plan conservation. BMC Biol 2022; 20:82. [PMID: 35399082 PMCID: PMC8996622 DOI: 10.1186/s12915-022-01276-5] [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: 11/15/2021] [Accepted: 03/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite the morphological diversity of animals, their basic anatomical patterns-the body plans in each animal phylum-have remained highly conserved over hundreds of millions of evolutionary years. This is attributed to conservation of the body plan-establishing developmental period (the phylotypic period) in each lineage. However, the evolutionary mechanism behind this phylotypic period conservation remains under debate. A variety of hypotheses based on the concept of modern synthesis have been proposed, such as negative selection in the phylotypic period through its vulnerability to embryonic lethality. Here we tested a new hypothesis that the phylotypic period is developmentally stable; it has less potential to produce phenotypic variations than the other stages, and this has most likely led to the evolutionary conservation of body plans. RESULTS By analyzing the embryos of inbred Japanese medaka embryos raised under the same laboratory conditions and measuring the whole embryonic transcriptome as a phenotype, we found that the phylotypic period has greater developmental stability than other stages. Comparison of phenotypic differences between two wild medaka populations indicated that the phylotypic period and its genes in this period remained less variational, even after environmental and mutational modifications accumulated during intraspecies evolution. Genes with stable expression levels were enriched with those involved in cell-cell signalling and morphological specification such as Wnt and Hox, implying possible involvement in body plan development of these genes. CONCLUSIONS This study demonstrated the correspondence between the developmental stage with low potential to produce phenotypic variations and that with low diversity in micro- and macroevolution, namely the phylotypic period. Whereas modern synthesis explains evolution as a process of shaping of phenotypic variations caused by mutations, our results highlight the possibility that phenotypic variations are readily limited by the intrinsic nature of organisms, namely developmental stability, thus biasing evolutionary outcomes.
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Affiliation(s)
- Yui Uchida
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Chikara Furusawa
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
- Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Naoki Irie
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
- Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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Bianchi L, Casini S, Vantaggiato L, Di Noi A, Carleo A, Shaba E, Armini A, Bellucci F, Furii G, Bini L, Caliani I. A Novel Ex Vivo Approach Based on Proteomics and Biomarkers to Evaluate the Effects of Chrysene, MEHP, and PBDE-47 on Loggerhead Sea Turtles ( Caretta caretta). INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19074369. [PMID: 35410049 PMCID: PMC8998652 DOI: 10.3390/ijerph19074369] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/18/2022] [Accepted: 04/02/2022] [Indexed: 02/04/2023]
Abstract
The principal aim of the present study was to develop and apply novel ex vivo tests as an alternative to cell cultures able to evaluate the possible effects of emerging and legacy contaminants in Caretta caretta. To this end, we performed ex vivo experiments on non-invasively collected whole-blood and skin-biopsy slices treated with chrysene, MEHP, or PBDE-47. Blood samples were tested by oxidative stress (TAS), immune system (respiratory burst, lysozyme, and complement system), and genotoxicity (ENA assay) biomarkers, and genotoxic and immune system effects were observed. Skin slices were analyzed by applying a 2D-PAGE/MS proteomic approach, and specific contaminant signatures were delineated on the skin proteomic profile. These reflect biochemical effects induced by each treatment and allowed to identify glutathione S-transferase P, peptidyl-prolyl cis-trans isomerase A, mimecan, and protein S100-A6 as potential biomarkers of the health-threatening impact the texted toxicants have on C. caretta. Obtained results confirm the suitability of the ex vivo system and indicate the potential risk the loggerhead sea turtle is undergoing in the natural environment. In conclusion, this work proved the relevance that the applied ex vivo models may have in testing the toxicity of other compounds and mixtures and in biomarker discovery.
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Affiliation(s)
- Laura Bianchi
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Via A. Moro, 2, 53100 Siena, Italy; (L.B.); (L.V.); (E.S.); (L.B.)
| | - Silvia Casini
- Department of Physical, Earth and Environmental Sciences, University of Siena, Via Mattioli, 4, 53100 Siena, Italy; (F.B.); (I.C.)
- Correspondence:
| | - Lorenza Vantaggiato
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Via A. Moro, 2, 53100 Siena, Italy; (L.B.); (L.V.); (E.S.); (L.B.)
| | - Agata Di Noi
- Department of Life Sciences, University of Siena, Via P. Mattioli, 4, 53100 Siena, Italy;
| | - Alfonso Carleo
- Department of Pulmonology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany;
| | - Enxhi Shaba
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Via A. Moro, 2, 53100 Siena, Italy; (L.B.); (L.V.); (E.S.); (L.B.)
| | - Alessandro Armini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 2, 53100 Siena, Italy;
| | - Francesco Bellucci
- Department of Physical, Earth and Environmental Sciences, University of Siena, Via Mattioli, 4, 53100 Siena, Italy; (F.B.); (I.C.)
| | - Giovanni Furii
- Centro Recupero Tartarughe Marine Legambiente, Molo di Ponente, 71043 Manfredonia, Italy;
| | - Luca Bini
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Via A. Moro, 2, 53100 Siena, Italy; (L.B.); (L.V.); (E.S.); (L.B.)
| | - Ilaria Caliani
- Department of Physical, Earth and Environmental Sciences, University of Siena, Via Mattioli, 4, 53100 Siena, Italy; (F.B.); (I.C.)
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35
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Farrell JA, Whitmore L, Mashkour N, Rollinson Ramia DR, Thomas RS, Eastman CB, Burkhalter B, Yetsko K, Mott C, Wood L, Zirkelbach B, Meers L, Kleinsasser P, Stock S, Libert E, Herren R, Eastman S, Crowder W, Bovery C, Anderson D, Godfrey D, Condron N, Duffy DJ. Detection and population genomics of sea turtle species via non-invasive environmental DNA analysis of nesting beach sand tracks and oceanic water. Mol Ecol Resour 2022; 22:2471-2493. [PMID: 35377560 DOI: 10.1111/1755-0998.13617] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/12/2022] [Accepted: 03/23/2022] [Indexed: 11/27/2022]
Abstract
Elusive aquatic wildlife, such as endangered sea turtles, are difficult to monitor and conserve. As novel molecular and genetic technologies develop, it is possible to adapt and optimize them for wildlife conservation. One such technology is environmental (e)DNA - the detection of DNA shed from organisms into their surrounding environments. We developed species-specific green (Chelonia mydas) and loggerhead (Caretta caretta) sea turtle probe-based qPCR assays, which can detect and quantify sea turtle eDNA in controlled (captive tank water and sand samples) and free ranging (oceanic water samples and nesting beach sand) settings. eDNA detection complemented traditional in-water sea turtle monitoring by enabling detection even when turtles were not visually observed. Furthermore, we report that high throughput shotgun sequencing of eDNA sand samples enabled sea turtle population genetic studies and pathogen monitoring, demonstrating that non-invasive eDNA techniques are viable and efficient alternatives to biological sampling (e.g. biopsies and blood draws). Genetic information was obtained from sand many hours after nesting events, without having to observe or interact with the target individual. This greatly reduces the sampling stress experienced by nesting mothers and emerging hatchlings, and avoids sacrificing viable eggs for genetic analysis. The detection of pathogens from sand indicates significant potential for increased wildlife disease monitoring capacity and viral variant surveillance. Together, these results demonstrate the potential of eDNA approaches to ultimately help understand and conserve threatened species such as sea turtles.
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Affiliation(s)
- Jessica A Farrell
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Liam Whitmore
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biological Sciences, University of Limerick, Limerick, Ireland
| | - Narges Mashkour
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Devon R Rollinson Ramia
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Rachel S Thomas
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Catherine B Eastman
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Brooke Burkhalter
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,The Turtle Hospital, 2396 Overseas Highway, Marathon, FL, 33050, USA
| | - Kelsey Yetsko
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biological Sciences, Florida International University, Miami, FL, 33181, USA
| | - Cody Mott
- Inwater Research Group Inc, Jensen Beach, FL, 34957, USA
| | - Larry Wood
- Florida Hawksbill Project, National Save The Sea Turtle Foundation, Ft. Lauderdale, FL, 33308, USA
| | - Bette Zirkelbach
- The Turtle Hospital, 2396 Overseas Highway, Marathon, FL, 33050, USA
| | - Lucas Meers
- Mickler's Landing Turtle Patrol, Ponte Vedra Beach, FL, 32082, USA
| | - Pat Kleinsasser
- Crescent Beach Turtle Patrol, Crescent Beach, FL, 32080, USA
| | - Sharon Stock
- Flagler Turtle Patrol, Marineland Beach, FL, 32080, USA
| | | | | | - Scott Eastman
- Florida Department of Environmental Protection, St Augustine, FL, 32080, USA
| | | | | | | | - David Godfrey
- The Sea Turtle Conservancy, Gainesville, FL, 32609, USA
| | - Nancy Condron
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Mickler's Landing Turtle Patrol, Ponte Vedra Beach, FL, 32082, USA
| | - David J Duffy
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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36
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Distinguishing Evolutionary Conservation from Derivedness. Life (Basel) 2022; 12:life12030440. [PMID: 35330191 PMCID: PMC8954198 DOI: 10.3390/life12030440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 11/17/2022] Open
Abstract
While the concept of “evolutionary conservation” has enabled biologists to explain many ancestral features and traits, it has also frequently been misused to evaluate the degree of changes from a common ancestor, or “derivedness”. We propose that the distinction of these two concepts allows us to properly understand phenotypic and organismal evolution. From a methodological aspect, “conservation” mainly considers genes or traits which species have in common, while “derivedness” additionally covers those that are not commonly shared, such as novel or lost traits and genes to evaluate changes from the time of divergence from a common ancestor. Due to these differences, while conservation-oriented methods are effective in identifying ancestral features, they may be prone to underestimating the overall changes accumulated during the evolution of certain lineages. Herein, we describe our recently developed method, “transcriptomic derivedness index”, for estimating the phenotypic derivedness of embryos with a molecular approach using the whole-embryonic transcriptome as a phenotype. Although echinoderms are often considered as highly derived species, our analyses with this method showed that their embryos, at least at the transcriptomic level, may not be much more derived than those of chordates. We anticipate that the future development of derivedness-oriented methods could provide quantitative indicators for finding highly/lowly evolvable traits.
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37
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Gable SM, Byars MI, Literman R, Tollis M. A Genomic Perspective on the Evolutionary Diversification of Turtles. Syst Biol 2022; 71:1331-1347. [DOI: 10.1093/sysbio/syac019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
To examine phylogenetic heterogeneity in turtle evolution, we collected thousands of high-confidence single-copy orthologs from 19 genome assemblies representative of extant turtle diversity and estimated a phylogeny with multispecies coalescent and concatenated partitioned methods. We also collected next-generation sequences from 26 turtle species and assembled millions of biallelic markers to reconstruct phylogenies based on annotated regions from the western painted turtle (Chrysemys picta bellii) genome (coding regions, introns, untranslated regions, intergenic, and others). We then measured gene tree-species tree discordance, as well as gene and site heterogeneity at each node in the inferred trees, and tested for temporal patterns in phylogenomic conflict across turtle evolution. We found strong and consistent support for all bifurcations in the inferred turtle species phylogenies. However, a number of genes, sites, and genomic features supported alternate relationships between turtle taxa. Our results suggest that gene tree-species tree discordance in these datasets is likely driven by population-level processes such as incomplete lineage sorting. We found very little effect of substitutional saturation on species tree topologies, and no clear phylogenetic patterns in codon usage bias and compositional heterogeneity. There was no correlation between gene and site concordance, node age, and DNA substitution rate across most annotated genomic regions. Our study demonstrates that heterogeneity is to be expected even in well resolved clades such as turtles, and that future phylogenomic studies should aim to sample as much of the genome as possible in order to obtain accurate phylogenies for assessing conservation priorities in turtles.
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Affiliation(s)
- Simone M Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, PO Box 5693, Flagstaff, AZ 8601, USA
| | - Michael I Byars
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, PO Box 5693, Flagstaff, AZ 8601, USA
| | - Robert Literman
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingstown, RI, 0288, USA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, PO Box 5693, Flagstaff, AZ 8601, USA
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38
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Jacobs LF. How the evolution of air breathing shaped hippocampal function. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200532. [PMID: 34957846 PMCID: PMC8710879 DOI: 10.1098/rstb.2020.0532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/15/2021] [Indexed: 12/25/2022] Open
Abstract
To make maps from airborne odours requires dynamic respiratory patterns. I propose that this constraint explains the modulation of memory by nasal respiration in mammals, including murine rodents (e.g. laboratory mouse, laboratory rat) and humans. My prior theories of limbic system evolution offer a framework to understand why this occurs. The answer begins with the evolution of nasal respiration in Devonian lobe-finned fishes. This evolutionary innovation led to adaptive radiations in chemosensory systems, including the emergence of the vomeronasal system and a specialization of the main olfactory system for spatial orientation. As mammals continued to radiate into environments hostile to spatial olfaction (air, water), there was a loss of hippocampal structure and function in lineages that evolved sensory modalities adapted to these new environments. Hence the independent evolution of echolocation in bats and toothed whales was accompanied by a loss of hippocampal structure (whales) and an absence of hippocampal theta oscillations during navigation (bats). In conclusion, models of hippocampal function that are divorced from considerations of ecology and evolution fall short of explaining hippocampal diversity across mammals and even hippocampal function in humans. This article is part of the theme issue 'Systems neuroscience through the lens of evolutionary theory'.
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Affiliation(s)
- Lucia F. Jacobs
- Department of Psychology, University of California, 2121 Berkeley Way, Berkeley, CA 94720-1650, USA
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39
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Ren Y, Zhang Q, Yan X, Hou D, Huang H, Li C, Rao D, Li Y. Genomic insights into the evolution of the critically endangered soft‐shelled turtle
Rafetus swinhoei. Mol Ecol Resour 2022; 22:1972-1985. [DOI: 10.1111/1755-0998.13596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/07/2022] [Accepted: 02/07/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Yandong Ren
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
| | - Qiang Zhang
- Changsha Ecological Zoo Changsha 410002 China
| | - Xiahui Yan
- Changsha Ecological Zoo Changsha 410002 China
| | - Dongmin Hou
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
| | | | - Chunhui Li
- Changsha Ecological Zoo Changsha 410002 China
| | - Dingqi Rao
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
| | - Yongxin Li
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
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40
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Siddiqui R, Maciver SK, Khan NA. Gut microbiome-immune system interaction in reptiles. J Appl Microbiol 2022; 132:2558-2571. [PMID: 34984778 DOI: 10.1111/jam.15438] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/12/2021] [Accepted: 12/31/2021] [Indexed: 12/17/2022]
Abstract
Reptiles are ectothermic amniotes in a world dominated by endotherms. Reptiles originated more than 300 million years ago and they often dwell in polluted environments which may expose them to pathogenic micro-organisms, radiation and/or heavy metals. Reptiles also possess greater longevity and may live much longer than similar-sized land mammals, for example, turtles, tortoises, crocodiles and tuatara are long-lived reptiles living up to 100 years or more. Many recent studies have emphasized the pivotal role of the gut microbiome on its host; thus, we postulated that reptilian gut microbiome and/or its metabolites and the interplay with their robust immune system may contribute to their longevity and overall hardiness. Herein, we discuss the composition of the reptilian gut microbiome, immune system-gut microbiome cross-talk, antimicrobial peptides, reptilian resistance to infectious diseases and cancer, ageing, as well the current knowledge of the genome and epigenome of these remarkable species. Preliminary studies have demonstrated that microbial gut flora of reptiles such as crocodiles, tortoises, water monitor lizard and python exhibit remarkable anticancer and antibacterial properties, as well as comprise novel gut bacterial metabolites and antimicrobial peptides. The underlying mechanisms between the gut microbiome and the immune system may hold clues to developing new therapies overall for health, and possible extrapolation to exploit the ancient defence systems of reptiles for Homo sapiens benefit.
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Affiliation(s)
- Ruqaiyyah Siddiqui
- College of Arts and Sciences, American University of Sharjah, Sharjah, United Arab Emirates
| | - Sutherland K Maciver
- Centre for Discovery Brain Science, Edinburgh Medical School, Biomedical Sciences, University of Edinburgh, Edinburgh, UK
| | - Naveed Ahmed Khan
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
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41
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Zhu W, Yang J, Lu S, Huang Y, Jin D, Pu J, Liu L, Li Z, Shi M, Xu J. Novel pegiviruses infecting wild birds and rodents. Virol Sin 2022; 37:208-214. [PMID: 35234631 PMCID: PMC9170927 DOI: 10.1016/j.virs.2022.01.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/04/2021] [Indexed: 11/18/2022] Open
Abstract
Pegivirus (family Flaviviridae) is a genus of small enveloped RNA viruses that mainly causes blood infections in various mammals including human. Herein, we carried out an extensive survey of pegiviruses from a wide range of wild animals mainly sampled in the Qinghai-Tibet Plateau of China. Three novel pegiviruses, namely Passer montanus pegivirus, Leucosticte brandti pegivirus and Montifringilla taczanowskii pegivirus, were identified from different wild birds, and one new rodent pegivirus, namely Phaiomys leucurus pegivirus, was identified from Blyth's vole. Interestingly, the pegiviruses of non-mammalian origin discovered in this study substantially broaden the host range of Pegivirus to avian species. Co-evolutionary analysis showed virus-host co-divergence over long evolutionary timescales, and indicated that pegiviruses largely followed a virus-host co-divergence relationship. Overall, this work extends the biodiversity of the Pegivirus genus to those infecting wild birds and hence revises the host range and evolutionary history of genus Pegivirus. Novel pegiviruses were identified from wild-life animals in Qinghai-Tibet Plateau. The three divergent species of bird pegiviruses substantially broaden the host range of Pegivirus. A long-term evolutionary relationship was established between pegiviruses and their vertebrate hosts.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China; Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China; Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China; Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China; Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zhenjun Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Mang Shi
- School of Medicine, Sun Yat-sen University, Shenzhen, 510006, China.
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China; Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China; Research Institute of Public Heath, Nankai University, Tianjin, 300071, China.
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Kohsokabe T, Kaneko K. Dynamical systems approach to evolution-development congruence: Revisiting Haeckel's recapitulation theory. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:62-75. [PMID: 33600605 PMCID: PMC9291011 DOI: 10.1002/jez.b.23031] [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] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 11/16/2022]
Abstract
It is acknowledged that embryonic development has a tendency to proceed from common toward specific. Ernst Haeckel raised the question of why that tendency prevailed through evolution, and the question remains unsolved. Here, we revisit Haeckel's recapitulation theory, that is, the parallelism between evolution and development through numerical evolution and dynamical systems theory. By using intracellular gene expression dynamics with cell-to-cell interaction over spatially aligned cells to represent the developmental process, gene regulation networks (GRN) that govern these dynamics evolve under the selection pressure to achieve a prescribed spatial gene expression pattern. For most numerical evolutionary experiments, the evolutionary pattern changes over generations, as well as the developmental pattern changes governed by the evolved GRN exhibit remarkable similarity. Changes in both patterns consisted of several epochs where stripes are formed in a short time, whereas for other temporal regimes, the pattern hardly changes. In evolution, these quasi-stationary generations are needed to achieve relevant mutations, whereas, in development, they are due to some gene expressions that vary slowly and control the pattern change. These successive epochal changes in development and evolution are represented as common bifurcations in dynamical systems theory, regulating working network structure from feedforward subnetwork to those containing feedback loops. The congruence is the correspondence between successive acquisitions of subnetworks through evolution and changes in working subnetworks in development. Consistency of the theory with the segmentation gene-expression dynamics is discussed. Novel outlook on recapitulation and heterochrony are provided, testable experimentally by the transcriptome and network analysis.
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Affiliation(s)
- Takahiro Kohsokabe
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics ResearchRIKENKobeHyogoJapan
| | - Kunihiko Kaneko
- Research Center for Complex Systems Biology, Universal Biology InstituteThe University of TokyoTokyoJapan
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43
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OUP accepted manuscript. Syst Biol 2022; 71:973-985. [DOI: 10.1093/sysbio/syac014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 02/15/2022] [Accepted: 02/22/2022] [Indexed: 11/12/2022] Open
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44
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Leong JCK, Li Y, Uesaka M, Uchida Y, Omori A, Hao M, Wan W, Dong Y, Ren Y, Zhang S, Zeng T, Wang F, Chen L, Wessel G, Livingston BT, Bradham C, Wang W, Irie N. Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms. Front Cell Dev Biol 2021; 9:749963. [PMID: 34900995 PMCID: PMC8661034 DOI: 10.3389/fcell.2021.749963] [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: 07/30/2021] [Accepted: 11/03/2021] [Indexed: 11/13/2022] Open
Abstract
Species retaining ancestral features, such as species called living fossils, are often regarded as less derived than their sister groups, but such discussions are usually based on qualitative enumeration of conserved traits. This approach creates a major barrier, especially when quantifying the degree of phenotypic evolution or degree of derivedness, since it focuses only on commonly shared traits, and newly acquired or lost traits are often overlooked. To provide a potential solution to this problem, especially for inter-species comparison of gene expression profiles, we propose a new method named "derivedness index" to quantify the degree of derivedness. In contrast to the conservation-based approach, which deals with expressions of commonly shared genes among species being compared, the derivedness index also considers those that were potentially lost or duplicated during evolution. By applying our method, we found that the gene expression profiles of penta-radial phases in echinoderm tended to be more highly derived than those of the bilateral phase. However, our results suggest that echinoderms may not have experienced much larger modifications to their developmental systems than chordates, at least at the transcriptomic level. In vertebrates, we found that the mid-embryonic and organogenesis stages were generally less derived than the earlier or later stages, indicating that the conserved phylotypic period is also less derived. We also found genes that potentially explain less derivedness, such as Hox genes. Finally, we highlight technical concerns that may influence the measured transcriptomic derivedness, such as read depth and library preparation protocols, for further improvement of our method through future studies. We anticipate that this index will serve as a quantitative guide in the search for constrained developmental phases or processes.
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Affiliation(s)
- Jason Cheok Kuan Leong
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yongxin Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Masahiro Uesaka
- RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Yui Uchida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
| | - Akihito Omori
- Sado Island Center for Ecological Sustainability, Niigata University, Niigata, Japan
| | - Meng Hao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wenting Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yang Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yandong Ren
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Si Zhang
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Tao Zeng
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Fayou Wang
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Luonan Chen
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
| | - Gary Wessel
- Providence Institute of Molecular Oogenesis, Brown University, Providence, RI, United States
| | - Brian T Livingston
- Department of Biological Sciences, California State University, Long Beach, CA, United States
| | - Cynthia Bradham
- Department of Biology, Boston University, Boston, MA, United States
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Naoki Irie
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
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45
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van der Zee JP, Christianen MJA, Bérubé M, Nava M, van der Wal S, Berkel J, Bervoets T, Meijer Zu Schlochtern M, Becking LE, Palsbøll PJ. Demographic changes in Pleistocene sea turtles were driven by past sea level fluctuations affecting feeding habitat availability. Mol Ecol 2021; 31:1044-1056. [PMID: 34861074 PMCID: PMC9299637 DOI: 10.1111/mec.16302] [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: 02/11/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 11/28/2022]
Abstract
Pleistocene environmental changes are generally assumed to have dramatically affected species’ demography via changes in habitat availability, but this is challenging to investigate due to our limited knowledge of how Pleistocene ecosystems changed through time. Here, we tracked changes in shallow marine habitat availability resulting from Pleistocene sea level fluctuations throughout the last glacial cycle (120–14 thousand years ago; kya) and assessed correlations with past changes in genetic diversity inferred from genome‐wide SNPs, obtained via ddRAD sequencing, in Caribbean hawksbill turtles, which feed in coral reefs commonly found in shallow tropical waters. We found sea level regression resulted in an average 75% reduction in shallow marine habitat availability during the last glacial cycle. Changes in shallow marine habitat availability correlated strongly with past changes in hawksbill turtle genetic diversity, which gradually declined to ~1/4th of present‐day levels during the Last Glacial Maximum (LGM; 26–19 kya). Shallow marine habitat availability and genetic diversity rapidly increased after the LGM, signifying a population expansion in response to warming environmental conditions. Our results suggest a positive correlation between Pleistocene environmental changes, habitat availability and species’ demography, and that demographic changes in hawksbill turtles were potentially driven by feeding habitat availability. However, we also identified challenges associated with disentangling the potential environmental drivers of past demographic changes, which highlights the need for integrative approaches. Our conclusions underline the role of habitat availability on species’ demography and biodiversity, and that the consequences of ongoing habitat loss should not be underestimated.
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Affiliation(s)
- Jurjan P van der Zee
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, AG Groningen, the Netherlands.,Wageningen Marine Research, Den Helder, the Netherlands
| | - Marjolijn J A Christianen
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, AG Groningen, the Netherlands.,Aquatic Ecology and Water Quality Management Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Martine Bérubé
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, AG Groningen, the Netherlands.,Center for Coastal Studies, Provincetown, Massachusetts, USA
| | - Mabel Nava
- Sea Turtle Conservation Bonaire, Kralendijk, Bonaire, Caribbean Netherlands
| | | | - Jessica Berkel
- Sint Eustatius National Parks Foundation, Sint Eustatius, Caribbean Netherlands
| | - Tadzio Bervoets
- Sint Maarten Nature Foundation, Cole Bay, Sint Maarten.,Dutch Caribbean Nature Alliance, Kralendijk, Bonaire, Caribbean Netherlands
| | | | - Leontine E Becking
- Wageningen Marine Research, Den Helder, the Netherlands.,Marine Animal Ecology Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Per J Palsbøll
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, AG Groningen, the Netherlands.,Center for Coastal Studies, Provincetown, Massachusetts, USA
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46
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The population genomic structure of green turtles (Chelonia mydas) suggests a warm-water corridor for tropical marine fauna between the Atlantic and Indian oceans during the last interglacial. Heredity (Edinb) 2021; 127:510-521. [PMID: 34635850 PMCID: PMC8626443 DOI: 10.1038/s41437-021-00475-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 01/01/2023] Open
Abstract
The occasional westward transport of warm water of the Agulhas Current, "Agulhas leakage", around southern Africa has been suggested to facilitate tropical marine connectivity between the Atlantic and Indian oceans, but the "Agulhas leakage" hypothesis does not explain the signatures of eastward gene flow observed in many tropical marine fauna. We investigated an alternative hypothesis: the establishment of a warm-water corridor during comparatively warm interglacial periods. The "warm-water corridor" hypothesis was investigated by studying the population genomic structure of Atlantic and Southwest Indian Ocean green turtles (N = 27) using 12,035 genome-wide single nucleotide polymorphisms (SNPs) obtained via ddRAD sequencing. Model-based and multivariate clustering suggested a hierarchical population structure with two main Atlantic and Southwest Indian Ocean clusters, and a Caribbean and East Atlantic sub-cluster nested within the Atlantic cluster. Coalescent-based model selection supported a model where Southwest Indian Ocean and Caribbean populations diverged from the East Atlantic population during the transition from the last interglacial period (130-115 thousand years ago; kya) to the last glacial period (115-90 kya). The onset of the last glaciation appeared to isolate Atlantic and Southwest Indian Ocean green turtles into three refugia, which subsequently came into secondary contact in the Caribbean and Southwest Indian Ocean when global temperatures increased after the Last Glacial Maximum. Our findings support the establishment of a warm-water corridor facilitating tropical marine connectivity between the Atlantic and Southwest Indian Ocean during warm interglacials.
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47
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Vilaça ST, Piccinno R, Rota‐Stabelli O, Gabrielli M, Benazzo A, Matschiner M, Soares LS, Bolten AB, Bjorndal KA, Bertorelle G. Divergence and hybridization in sea turtles: Inferences from genome data show evidence of ancient gene flow between species. Mol Ecol 2021; 30:6178-6192. [PMID: 34390061 PMCID: PMC9292604 DOI: 10.1111/mec.16113] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/26/2021] [Indexed: 11/30/2022]
Abstract
Reconstructing past events of hybridization and population size changes are required to understand speciation mechanisms and current patterns of genetic diversity, and ultimately contribute to species' conservation. Sea turtles are ancient species currently facing anthropogenic threats including climate change, fisheries, and illegal hunting. Five of the seven extant sea turtle species are known to currently hybridize, especially along the Brazilian coast where some populations can have ~32%-42% of hybrids. Although frequently observed today, it is not clear what role hybridization plays in the evolutionary diversification of this group of reptiles. In this study, we generated whole genome resequencing data of the five globally distributed sea turtle species to estimate a calibrated phylogeny and the population size dynamics, and to understand the role of hybridization in shaping the genomes of these ancient species. Our results reveal discordant species divergence dates between mitochondrial and nuclear genomes, with a high frequency of conflicting trees throughout the nuclear genome suggesting that some sea turtle species frequently hybridized in the past. The reconstruction of the species' demography showed a general decline in effective population sizes with no signs of recovery, except for the leatherback sea turtle. Furthermore, we discuss the influence of reference bias in our estimates. We show long-lasting ancestral gene flow events within Chelonioidea that continued for millions of years after initial divergence. Speciation with gene flow is a common pattern in marine species, and it raises questions whether current hybridization events should be considered as a part of these species' evolutionary history or a conservation issue.
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Affiliation(s)
| | - Riccardo Piccinno
- Department of Sustainable Agro‐ecosystems and BioresourcesFondazione Edmund MachTrentoItaly
| | - Omar Rota‐Stabelli
- Department of Sustainable Agro‐ecosystems and BioresourcesFondazione Edmund MachTrentoItaly
| | - Maëva Gabrielli
- Department of Life Sciences and BiotechnologyUniversity of FerraraFerraraItaly
| | - Andrea Benazzo
- Department of Life Sciences and BiotechnologyUniversity of FerraraFerraraItaly
| | | | - Luciano S. Soares
- Archie Carr Center for Sea Turtle Research and Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | - Alan B. Bolten
- Archie Carr Center for Sea Turtle Research and Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | - Karen A. Bjorndal
- Archie Carr Center for Sea Turtle Research and Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | - Giorgio Bertorelle
- Department of Life Sciences and BiotechnologyUniversity of FerraraFerraraItaly
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48
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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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49
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Sex Chromosomes and Master Sex-Determining Genes in Turtles and Other Reptiles. Genes (Basel) 2021; 12:genes12111822. [PMID: 34828428 PMCID: PMC8622242 DOI: 10.3390/genes12111822] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022] Open
Abstract
Among tetrapods, the well differentiated heteromorphic sex chromosomes of birds and mammals have been highly investigated and their master sex-determining (MSD) gene, Dmrt1 and SRY, respectively, have been identified. The homomorphic sex chromosomes of reptiles have been the least studied, but the gap with birds and mammals has begun to fill. This review describes our current knowledge of reptilian sex chromosomes at the cytogenetic and molecular level. Most of it arose recently from various studies comparing male to female gene content. This includes restriction site-associated DNA sequencing (RAD-Seq) experiments in several male and female samples, RNA sequencing and identification of Z- or X-linked genes by male/female comparative transcriptome coverage, and male/female transcriptomic or transcriptome/genome substraction approaches allowing the identification of Y- or W-linked transcripts. A few putative master sex-determining (MSD) genes have been proposed, but none has been demonstrated yet. Lastly, future directions in the field of reptilian sex chromosomes and their MSD gene studies are considered.
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50
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Global Analysis of Transcriptome and Translatome Revealed That Coordinated WNT and FGF Regulate the Carapacial Ridge Development of Chinese Soft-Shell Turtle. Int J Mol Sci 2021; 22:ijms222212441. [PMID: 34830331 PMCID: PMC8621500 DOI: 10.3390/ijms222212441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 12/16/2022] Open
Abstract
The turtle carapace is composed of severely deformed fused dorsal vertebrae, ribs, and bone plates. In particular, the lateral growth in the superficial layer of turtle ribs in the dorsal trunk causes an encapsulation of the scapula and pelvis. The recent study suggested that the carapacial ridge (CR) is a new model of epithelial–mesenchymal transition which is essential for the arrangement of the ribs. Therefore, it is necessary to explore the regulatory mechanism of carapacial ridge development to analyze the formation of the turtle shell. However, the current understanding of the regulatory network underlying turtle carapacial ridge development is poor due to the lack of both systematic gene screening at different carapacial ridge development stages and gene function verification studies. In this study, we obtained genome-wide gene transcription and gene translation profiles using RNA sequencing and ribosome nascent-chain complex mRNA sequencing from carapacial ridge tissues of Chinese soft-shell turtle at different development stages. A correlation analysis of the transcriptome and translatome revealed that there were 129, 670, and 135 codifferentially expressed genes, including homodirection and opposite-direction differentially expressed genes, among three comparison groups, respectively. The pathway enrichment analysis of codifferentially expressed genes from the Kyoto Encyclopedia of Genes and Genomes showed dynamic changes in signaling pathways involved in carapacial ridge development. Especially, the results revealed that the Wnt signaling pathway and MAPK signaling pathway may play important roles in turtle carapacial ridge development. In addition, Wnt and Fgf were expressed during the carapacial ridge development. Furthermore, we discovered that Wnt5a regulated carapacial ridge development through the Wnt5a/JNK pathway. Therefore, our studies uncover that the morphogenesis of the turtle carapace might function through the co-operation between conserved WNT and FGF signaling pathways. Consequently, our findings revealed the dynamic signaling pathways acting on the carapacial ridge development of Chinese soft-shell turtle and provided new insights into uncover the molecular mechanism underlying turtle shell morphogenesis.
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