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Chai S, Chong Y, Yin D, Qiu Q, Xu S, Yang G. Genomic insights into adaptation to bipedal saltation and desert-like habitats of jerboas. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2516-9. [PMID: 38902451 DOI: 10.1007/s11427-023-2516-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/20/2023] [Indexed: 06/22/2024]
Abstract
Jerboas is a lineage of small rodents displaying atypical mouse-like morphology with elongated strong hindlimbs and short forelimbs. They have evolved obligate bipedal saltation and acute senses, and been well-adapted to vast desert-like habitats. Using a newly sequenced chromosome-scale genome of the Mongolian five-toed jerboa (Orientallactaga sibirica), our comparative genomic analyses and in vitro functional assays showed that the genetic innovations in both protein-coding and non-coding regions played an important role in jerboa morphological and physiological adaptation. Jerboa-specific amino acid substitutions, and segment insertions/deletions (indels) in conserved non-coding elements (CNEs) were found in components of proteoglycan biosynthesis pathway (XYLT1 and CHSY1), which plays an important role in limb development. Meanwhile, we found specific evolutionary changes functionally associated with energy or water metabolism (e.g., specific amino acid substitutions in ND5 and indels in CNEs physically near ROR2) and senses (e.g., expansion of vomeronasal receptors and the FAM136A gene family) in jerboas. Further dual-luciferase reporter assay verified that some of the CNEs with jerboa-specific segment indels exerted a significantly different influence on luciferase activity, suggesting changes in their regulatory function in jerboas. Our results revealed the potential molecular mechanisms underlying jerboa adaptation since the divergence from the Eocene-Oligocene transition, and provided more resources and new insights to enhance our understanding of the molecular basis underlying the phenotypic diversity and the environmental adaptation of mammals.
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Affiliation(s)
- Simin Chai
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Yujie Chong
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Daiqing Yin
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Guang Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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İbiş O, Yesari Selçuk A, Teber S, Baran M, Kaya A, Özcan S, Kefelioğlu H, Tez C. Complete mitogenomes of Turkish tree squirrels, Sciurus anomalus and S. vulgaris, (Sciuridae: Rodentia: Mammalia) and their phylogenetic status within the tribe Sciurini. Gene 2022; 841:146773. [PMID: 35905846 DOI: 10.1016/j.gene.2022.146773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/03/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022]
Abstract
The genus Sciurus, a member of the family Sciuridae, is widely distributed in the Holarctic region. To better understand mitogenomic characteristics and to reveal internal phylogenetic relationships of the genus, 20 complete mitogenomes of Turkish tree squirrels were successfully sequenced for the first time, including 19 for S. anomalus (from 16,505 bp to 16,510 bp) and one for S. vulgaris (16,511 bp). The mitogenomes of two species were AT-biased. All tRNAs for two species displayed a typical clover-leaf structure, except for tRNASer(AGY). The tRNA Serine1 (S1)-GCT structure lacked the dihydrouridine (DHU) loop and stem. Based on mitogenomic dataset for phylogeny of Sciurinae, phylogenetic analyses (Bayesian Inference and Maximum Likelihood) did not support monophyly of Sciurus and proposed that S. anomalus, the most basal taxa in the Sciurini tribe, had at least five mitogenome lineages, which were also supported by network analysis. The dissimilarities among the five linegaes of S. anomalus ranged from 0.0042 (0.42%) to 0.0062 (0.62%) using K2P sequence pairwise distances. In addition to this mitogenomic analysis result, phylogenetic analyses using the CYTB + D-loop dataset proposed the existence of at least nine lineages for S. anomalus, which was different than those of the previous studies. The current study proposed that the use of mitogenomic data for reconstructing the phylogeny of Turkey' Sciurus holds an important value for revealing evolutionary relationships.
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Affiliation(s)
- Osman İbiş
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey; Vectors and Vector-Born Diseases Research and Implementation Center, Erciyes University, Kayseri, Turkey.
| | - Ahmet Yesari Selçuk
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey; Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey.
| | - Saffet Teber
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey.
| | - Mehmet Baran
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey.
| | - Alaettin Kaya
- Department of Basic Sciences, Faculty of Veterinary Medicine, Dicle University, Diyarbakır, Turkey.
| | - Servet Özcan
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey; Department of Biology, Faculty of Sciences, Erciyes University, Kayseri, Turkey.
| | - Haluk Kefelioğlu
- Department of Biology, Faculty of Science and Letters, Ondokuz Mayıs University, Samsun, Turkey.
| | - Coşkun Tez
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey; Department of Biology, Faculty of Sciences, Erciyes University, Kayseri, Turkey.
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ŞEKER PS, SELÇUK AY, SELVİ E, BARAN M, TEBER S, KELEŞ GA, KEFELİOĞLU H, TEZ C, İBİŞ O. Complete mitochondrial genomes of Chionomys roberti and Chionomys nivalis (Mammalia: Rodentia) from Turkey: Insight into their phylogenetic position within Arvicolinae. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00559-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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İbiş O. Whole mitochondrial genome sequence and phylogenetic relationships of Williams's jerboa ( Scarturus williamsi) from Turkey. PeerJ 2020; 8:e9569. [PMID: 32742814 PMCID: PMC7369027 DOI: 10.7717/peerj.9569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/29/2020] [Indexed: 11/29/2022] Open
Abstract
Williams’s jerboa (Scarturus williamsi), a medium-sized jerboa distributed in Anatolia and its adjacent regions, is a member of the four- and five-toed jerboas found mostly in Asia. Disagreements about the taxonomy of this taxon at the genus/species level continue to exist. Here, we report the first effort to sequence and assemble the mitochondrial genome of Williams’s jerboa from Turkey. The mitochondrial genome of S. williamsi was 16,653 bp in total length and contained 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and two non-coding regions (the D-loop and OL region) with intergenic spacer. All of the genes, except ND6 and eight tRNAs, were encoded on the heavy chain strand, similar to the features of mitogenomes of other rodents. When compared with all available rodent mitochondrial genomes, Williams’s jerboa showed (1) a serine deletion at the 3′-end of the ATP8 gene, (2) the ND5 gene terminated with a TAG codon and (3) a tandem repeat cluster (273 bp in length) in the control region. Williams’s jerboa and Siberian jerboa grouped as sister taxa despite the high genetic distance (17.6%) between them, belonging to Allactaginae. This result is consistent with the latest pre-revision, which suggests that Williams’s jerboa and the Siberian jerboa may belong to separate genera, as Scarturus and Orientallactaga, respectively. The present study provides a reference mitochondrial genome for Williams’s jerboa for further molecular studies of other species of Dipodoidea and Rodentia.
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Affiliation(s)
- Osman İbiş
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey.,Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
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