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Duan M, Yang S, Li X, Tang X, Cheng Y, Luo J, Wang J, Song H, Wang Q, Zhu GX. Chromosome-level genome assembly and annotation of the Rhabdophis nuchalis (Hubei keelback). Sci Data 2024; 11:850. [PMID: 39117633 PMCID: PMC11310211 DOI: 10.1038/s41597-024-03708-z] [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: 05/23/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Rhabdophis nuchalis, a snake widely distributed in China, possesses a unique trait: glands beneath the skin on its neck and back, known as nucho-dorsal glands. These features make it a valuable subject for studying genetic diversity and the evolution of complex traits. In this study, we obtained a high-quality chromosome-level reference genome of R. nuchalis using MGI short-read sequencing, PacBio Revio long-read sequencing, and Hi-C sequencing techniques. The final assembly comprised 1.92 Gb of the R. nuchalis genome, anchored to 20 chromosomes (including 9 macrochromosomes and 11 microchromosomes), with a contig N50 of 104.79 Mb, a scaffold N50 of 204.96 Mb, and a BUSCO completeness of 97.50%. Additionally, we annotated a total of 1.09 Gb of repetitive sequences (which constitute 56.51% of the entire genome) and identified 22,057 protein-coding genes. This high-quality reference genome of R. nuchalis furnishes essential genomic data for comprehending the genetic diversity and evolutionary history of the species, as well as for facilitating species conservation efforts and comparative genomics studies.
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Affiliation(s)
- Mingwen Duan
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Shijun Yang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Xiufeng Li
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Xuemei Tang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Yuqi Cheng
- Chengdu Zoo, Chengdu, Sichuan Province, 610081, China
| | - Jingxue Luo
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Ji Wang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Huina Song
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Qin Wang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Guang Xiang Zhu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China.
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Zhu GX, Yang S, Savitzky AH, Zhang L, Cheng Y, Wang J. The Nucho-dorsal Glands of Rhabdophis guangdongensis (Squamata: Colubridae: Natricinae), with Notes on Morphological Variation and Phylogeny Based on Additional Specimens. CURRENT HERPETOLOGY 2020. [DOI: 10.5358/hsj.39.108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Guang-Xiang Zhu
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Shijun Yang
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Alan H. Savitzky
- Department of Biology, Utah State University, Logan, Utah 84322–5305, USA
| | - Liang Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangdong 510260, China
| | - Yuqi Cheng
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Jiajun Wang
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
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Yoshida T, Ujiie R, Savitzky AH, Jono T, Inoue T, Yoshinaga N, Aburaya S, Aoki W, Takeuchi H, Ding L, Chen Q, Cao C, Tsai TS, Silva AD, Mahaulpatha D, Nguyen TT, Tang Y, Mori N, Mori A. Dramatic dietary shift maintains sequestered toxins in chemically defended snakes. Proc Natl Acad Sci U S A 2020; 117:5964-5969. [PMID: 32094167 PMCID: PMC7084117 DOI: 10.1073/pnas.1919065117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unlike other snakes, most species of Rhabdophis possess glands in their dorsal skin, sometimes limited to the neck, known as nucho-dorsal and nuchal glands, respectively. Those glands contain powerful cardiotonic steroids known as bufadienolides, which can be deployed as a defense against predators. Bufadienolides otherwise occur only in toads (Bufonidae) and some fireflies (Lampyrinae), which are known or believed to synthesize the toxins. The ancestral diet of Rhabdophis consists of anuran amphibians, and we have shown previously that the bufadienolide toxins of frog-eating species are sequestered from toads consumed as prey. However, one derived clade, the Rhabdophis nuchalis Group, has shifted its primary diet from frogs to earthworms. Here we confirm that the worm-eating snakes possess bufadienolides in their nucho-dorsal glands, although the worms themselves lack such toxins. In addition, we show that the bufadienolides of R. nuchalis Group species are obtained primarily from fireflies. Although few snakes feed on insects, we document through feeding experiments, chemosensory preference tests, and gut contents that lampyrine firefly larvae are regularly consumed by these snakes. Furthermore, members of the R. nuchalis Group contain compounds that resemble the distinctive bufadienolides of fireflies, but not those of toads, in stereochemistry, glycosylation, acetylation, and molecular weight. Thus, the evolutionary shift in primary prey among members of the R. nuchalis Group has been accompanied by a dramatic shift in the source of the species' sequestered defensive toxins.
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Affiliation(s)
- Tatsuya Yoshida
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University, Sakyo, 606-8502 Kyoto, Japan
| | - Rinako Ujiie
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University, Sakyo, 606-8502 Kyoto, Japan
| | - Alan H Savitzky
- Department of Biology, Utah State University, Logan, UT 84322-5305
| | - Teppei Jono
- Laboratory of Ryukyu Island Biogeography, Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, 903-0213 Okinawa, Japan
| | - Takato Inoue
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University, Sakyo, 606-8502 Kyoto, Japan;
| | - Naoko Yoshinaga
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University, Sakyo, 606-8502 Kyoto, Japan
| | - Shunsuke Aburaya
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University, Sakyo, 606-8502 Kyoto, Japan
| | - Wataru Aoki
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University, Sakyo, 606-8502 Kyoto, Japan
| | - Hirohiko Takeuchi
- Laboratory of Biology, College of Bioresource Science, Nihon University, Fujisawa, 252-0880 Kanagawa, Japan
| | - Li Ding
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan, China
| | - Qin Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan, China
| | - Chengquan Cao
- College of Life Sciences, Leshan Normal University, Leshan, 614000 Sichuan, China
| | - Tein-Shun Tsai
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Neipu Township, 91201 Pingtung, Taiwan
| | | | - Dharshani Mahaulpatha
- Department of Zoology, Faculty of Applied Biological Sciences, University of Sri Jayewardenepura, 10250 Nugegoda, Sri Lanka
| | - Tao Thien Nguyen
- Department of Nature Conservation, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Cau Giay, Hanoi 100000, Vietnam
| | - Yezhong Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan, China
| | - Naoki Mori
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University, Sakyo, 606-8502 Kyoto, Japan
| | - Akira Mori
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, 606-8502 Kyoto, Japan
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Takeuchi H, Savitzky AH, Ding L, de Silva A, Das I, Nguyen TT, Tsai T, Jono T, Zhu G, Mahaulpatha D, Tang Y, Mori A. Evolution of nuchal glands, unusual defensive organs of Asian natricine snakes (Serpentes: Colubridae), inferred from a molecular phylogeny. Ecol Evol 2018; 8:10219-10232. [PMID: 30397460 PMCID: PMC6206205 DOI: 10.1002/ece3.4497] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 06/22/2018] [Accepted: 07/24/2018] [Indexed: 01/25/2023] Open
Abstract
A large body of evidence indicates that evolutionary innovations of novel organs have facilitated the subsequent diversification of species. Investigation of the evolutionary history of such organs should provide important clues for understanding the basis for species diversification. An Asian natricine snake, Rhabdophis tigrinus, possesses a series of unusual organs, called nuchal glands, which contain cardiotonic steroid toxins known as bufadienolides. Rhabdophis tigrinus sequesters bufadienolides from its toad prey and stores them in the nuchal glands as a defensive mechanism. Among more than 3,500 species of snakes, only 17 Asian natricine species are known to possess nuchal glands or their homologues. These 17 species belong to three nominal genera, Balanophis, Macropisthodon, and Rhabdophis. In Macropisthodon and Rhabdophis, however, species without nuchal glands also exist. To infer the evolutionary history of the nuchal glands, we investigated the molecular phylogenetic relationships among Asian natricine species with and without nuchal glands, based on variations in partial sequences of Mt-CYB, Cmos, and RAG1 (total 2,767 bp). Results show that all species with nuchal glands belong to a single clade (NGC). Therefore, we infer that the common ancestor of this clade possessed nuchal glands with no independent origins of the glands within the members. Our results also imply that some species have secondarily lost the glands. Given the estimated divergence time of related species, the ancestor of the nuchal gland clade emerged 19.18 mya. Our study shows that nuchal glands are fruitful subjects for exploring the evolution of novel organs. In addition, our analysis indicates that reevaluation of the taxonomic status of the genera Balanophis and Macropisthodon is required. We propose to assign all species belonging to the NGC to the genus Rhabdophis, pending further study.
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Affiliation(s)
- Hirohiko Takeuchi
- Seto Marine Biological LaboratoryField Science Education and Research CenterKyoto UniversityShirahamaJapan
- Present address:
College of Bioresource ScienceNihon UniversityFujisawaKanagawaJapan
| | | | - Li Ding
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
| | | | - Indraneil Das
- Institute of Biodiversity and Environmental ConservationUniversity Malaysia SarawakSarawakMalaysia
| | - Tao Thien Nguyen
- Vietnam National Museum of NatureVietnam Academy of Science and TechnologyHanoiVietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and TechnologyHanoiVietnam
| | - Tein‐Shun Tsai
- Department of Biological Science and TechnologyNational Pingtung University of Science and TechnologyNeipu TownshipTaiwan
| | - Teppei Jono
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
- Present address:
Tropical Biosphere Research CenterUniversity of the RyukyusNishiharaOkinawaJapan
| | - Guang‐Xiang Zhu
- College of Life ScienceSichuan Agricultural UniversityYa'anChina
| | | | - Yezhong Tang
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
| | - Akira Mori
- Department of ZoologyGraduate School of ScienceKyoto UniversityKyotoJapan
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