1
|
de Oliveira TD, de Freitas TR. Investigating the evolutionary dynamics of diploid number variation in Ctenomys (Ctenomyidae, Rodentia). Genet Mol Biol 2024; 46:e20230180. [PMID: 38315881 PMCID: PMC10842476 DOI: 10.1590/1678-4685-gmb-2023-0180] [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: 06/07/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024] Open
Abstract
Contrary to predictions from classical hybrid sterility models of chromosomal speciation, some organisms display high rates of karyotype variation. Ctenomys are the current mammals with the greatest interspecific and intraspecific chromosomal variation. A large number of species have been studied cytogenetically. The diploid numbers of chromosomes range from 2n = 10 to 2n = 70. Here, we analyzed karyotype evolution in Ctenomys using comparative phylogenetic methods. We found a strong phylogenetic signal with chromosome number. This refutes the chromosomal megaevolution model, which proposes the independent accumulation of multiple chromosomal rearrangements in each closely related species. We found that Brownian motion (BM) described the observed characteristic changes more thoroughly than the Ornstein-Uhlenbeck and Early-Burst models. This suggests that the evolution of chromosome numbers occurs by a random walk along phylogenetic clades. However, our data indicate that the BM model alone does not fully characterize the chromosomal evolution of Ctenomys.
Collapse
Affiliation(s)
- Thays Duarte de Oliveira
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
| | - Thales R.O. de Freitas
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| |
Collapse
|
2
|
Oliveira da Silva W, Malcher SM, Ferguson-Smith MA, O'Brien PCM, Rossi RV, Geise L, Pieczarka JC, Nagamachi CY. Chromosomal rearrangements played an important role in the speciation of rice rats of genus Cerradomys (Rodentia, Sigmodontinae, Oryzomyini). Sci Rep 2024; 14:545. [PMID: 38177653 PMCID: PMC10766967 DOI: 10.1038/s41598-023-50861-3] [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: 08/24/2023] [Accepted: 12/27/2023] [Indexed: 01/06/2024] Open
Abstract
Rodents of the genus Cerradomys belong to tribe Oryzomyini, one of the most diverse and speciose groups in Sigmodontinae (Rodentia, Cricetidae). The speciation process in Cerradomys is associated with chromosomal rearrangements and biogeographic dynamics in South America during the Pleistocene era. As the morphological, molecular and karyotypic aspects of Myomorpha rodents do not evolve at the same rate, we strategically employed karyotypic characters for the construction of chromosomal phylogeny to investigate whether phylogenetic relationships using chromosomal data corroborate the radiation of Cerradomys taxa recovered by molecular phylogeny. Comparative chromosome painting using Hylaeamys megacephalus (HME) whole chromosome probes in C. langguthi (CLA), Cerradomys scotii (CSC), C. subflavus (CSU) and C. vivoi (CVI) shows that karyotypic variability is due to 16 fusion events, 2 fission events, 10 pericentric inversions and 1 centromeric repositioning, plus amplification of constitutive heterochromatin in the short arms of the X chromosomes of CSC and CLA. The chromosomal phylogeny obtained by Maximum Parsimony analysis retrieved Cerradomys as a monophyletic group with 97% support (bootstrap), with CSC as the sister to the other species, followed by a ramification into two clades (69% of branch support), the first comprising CLA and the other branch including CVI and CSU. We integrated the chromosome painting analysis of Eumuroida rodents investigated by HME and Mus musculus (MMU) probes and identified several syntenic blocks shared among representatives of Cricetidae and Muridae. The Cerradomys genus underwent an extensive karyotypic evolutionary process, with multiple rearrangements that shaped extant karyotypes. The chromosomal phylogeny corroborates the phylogenetic relationships proposed by molecular analysis and indicates that karyotypic diversity is associated with species radiation. Three syntenic blocks were identified as part of the ancestral Eumuroida karyotype (AEK): MMU 7/19 (AEK 1), MMU 14 (AEK 10) and MMU 12 (AEK 11). Besides, MMU 5/10 (HME 18/2/24) and MMU 8/13 (HME 22/5/11) should be considered as signatures for Cricetidae, while MMU 5/9/14, 5/7/19, 5 and 8/17 for Sigmodontinae.
Collapse
Affiliation(s)
- Willam Oliveira da Silva
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Stella Miranda Malcher
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Patricia Caroline Mary O'Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Rogério Vieira Rossi
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal do Mato Grosso (UFMT), Mato Grosso, Brazil
| | - Lena Geise
- Departamento de Zoologia, Laboratório de Mastozoologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil.
| |
Collapse
|
3
|
Romanenko SA, Kliver SF, Serdyukova NA, Perelman PL, Trifonov VA, Seluanov A, Gorbunova V, Azpurua J, Pereira JC, Ferguson-Smith MA, Graphodatsky AS. Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human. Sci Rep 2023; 13:21055. [PMID: 38030702 PMCID: PMC10687270 DOI: 10.1038/s41598-023-46595-x] [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: 06/08/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023] Open
Abstract
Descriptions of karyotypes of many animal species are currently available. In addition, there has been a significant increase in the number of sequenced genomes and an ever-improving quality of genome assembly. To close the gap between genomic and cytogenetic data we applied fluorescent in situ hybridization (FISH) and Hi-C technology to make the first full chromosome-level genome comparison of the guinea pig (Cavia porcellus), naked mole-rat (Heterocephalus glaber), and human. Comparative chromosome maps obtained by FISH with chromosome-specific probes link genomic scaffolds to individual chromosomes and orient them relative to centromeres and heterochromatic blocks. Hi-C assembly made it possible to close all gaps on the comparative maps and to reveal additional rearrangements that distinguish the karyotypes of the three species. As a result, we integrated the bioinformatic and cytogenetic data and adjusted the previous comparative maps and genome assemblies of the guinea pig, naked mole-rat, and human. Syntenic associations in the two hystricomorphs indicate features of their putative ancestral karyotype. We postulate that the two approaches applied in this study complement one another and provide complete information about the organization of these genomes at the chromosome level.
Collapse
Affiliation(s)
- Svetlana A Romanenko
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia.
| | - Sergei F Kliver
- Center for Evolutionary Hologenomics, The Globe Institute, The University of Copenhagen, Copenhagen, Denmark
| | - Natalia A Serdyukova
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Vladimir A Trifonov
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Jorge Azpurua
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA
| | - Jorge C Pereira
- Animal and Veterinary Research Centre, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Malcolm A Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| |
Collapse
|
4
|
Sales-Oliveira V, Altmanová M, Gvoždík V, Kretschmer R, Ezaz T, Liehr T, Padutsch N, Badjedjea G, Utsunomia R, Tanomtong A, Cioffi M. Cross-species chromosome painting and repetitive DNA mapping illuminate the karyotype evolution in true crocodiles (Crocodylidae). Chromosoma 2023; 132:289-303. [PMID: 37493806 DOI: 10.1007/s00412-023-00806-6] [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: 04/17/2023] [Revised: 05/23/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023]
Abstract
Crocodilians have maintained very similar karyotype structures and diploid chromosome numbers for around 100 million years, with only minor variations in collinearity. Why this karyotype structure has largely stayed unaltered for so long is unclear. In this study, we analyzed the karyotypes of six species belonging to the genera Crocodylus and Osteolaemus (Crocodylidae, true crocodiles), among which the Congolian endemic O. osborni was included and investigated. We utilized various techniques (differential staining, fluorescence in situ hybridization with repetitive DNA and rDNA probes, whole chromosome painting, and comparative genomic hybridization) to better understand how crocodile chromosomes evolved. We studied representatives of three of the four main diploid chromosome numbers found in crocodiles (2n = 30/32/38). Our data provided new information about the species studied, including the identification of four major chromosomal rearrangements that occurred during the karyotype diversification process in crocodiles. These changes led to the current diploid chromosome numbers of 2n = 30 (fusion) and 2n = 38 (fissions), derived from the ancestral state of 2n = 32. The conserved cytogenetic tendency in crocodilians, where extant species keep near-ancestral state, contrasts with the more dynamic karyotype evolution seen in other major reptile groups.
Collapse
Affiliation(s)
- Vanessa Sales-Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Marie Altmanová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721, Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, 12844, Prague, Czech Republic
| | - Václav Gvoždík
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Zoology, National Museum of the Czech Republic, Prague, Czech Republic
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Niklas Padutsch
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Gabriel Badjedjea
- Department of Aquatic Ecology, Biodiversity Monitoring Center, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | | | - Alongklod Tanomtong
- Department of Biology Faculty of Science, Khon Kaen University, Muang, Khon Kaen, 40002, Thailand
| | - Marcelo Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil.
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
| |
Collapse
|
5
|
Li X, Li H, Yang Z, Wu Y, Zhang M. Exploring objective feature sets in constructing the evolution relationship of animal genome sequences. BMC Genomics 2023; 24:634. [PMID: 37872534 PMCID: PMC10594854 DOI: 10.1186/s12864-023-09747-x] [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: 08/07/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Exploring evolution regularities of genome sequences and constructing more objective species evolution relationships at the genomic level are high-profile topics. Based on the evolution mechanism of genome sequences proposed in our previous research, we found that only the 8-mers containing CG or TA dinucleotides correlate directly with the evolution of genome sequences, and the relative frequency rather than the actual frequency of these 8-mers is more suitable to characterize the evolution of genome sequences. RESULT Therefore, two types of feature sets were obtained, they are the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers. The evolution relationships of mammals and reptiles were constructed by the relative frequency set of CG1 + CG2 8-mers, and two types of evolution relationships of insects were constructed by the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers respectively. Through comparison and analysis, we found that evolution relationships are consistent with the known conclusions. According to the evolution mechanism, we considered that the evolution relationship constructed by CG1 + CG2 8-mers reflects the evolution state of genome sequences in current time, and the evolution relationship constructed by TA1 + TA2 8-mers reflects the evolution state in the early stage. CONCLUSION Our study provides objective feature sets in constructing evolution relationships at the genomic level.
Collapse
Affiliation(s)
- Xiaolong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Hong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
| | - Zhenhua Yang
- School of Economics and Management, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Yuan Wu
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Mengchuan Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| |
Collapse
|
6
|
Thomas GWC, Hughes JJ, Kumon T, Berv JS, Nordgren CE, Lampson M, Levine M, Searle JB, Good JM. The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555178. [PMID: 37693498 PMCID: PMC10491188 DOI: 10.1101/2023.08.28.555178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is often widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) - a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining new linked-read genome assemblies for seven murine species with eleven published rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.
Collapse
Affiliation(s)
- Gregg W. C. Thomas
- Division of Biological Sciences, University of Montana, Missoula, MT, 59801
- Informatics Group, Harvard University, Cambridge, MA, 02138
| | - Jonathan J. Hughes
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, 92521
| | - Tomohiro Kumon
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104
| | - Jacob S. Berv
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109
| | - C. Erik Nordgren
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104
| | - Michael Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104
| | - Mia Levine
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, Missoula, MT, 59801
| |
Collapse
|
7
|
Wang S, Chen J, Zhao Y, Zhang M, Zhang C, He J, Wei L, Xu Z. Paper mulberry leaves as a potential sterilant: evidence from Microtus fortis-a laboratory study. FRONTIERS IN PLANT SCIENCE 2023; 14:1092792. [PMID: 37360716 PMCID: PMC10288988 DOI: 10.3389/fpls.2023.1092792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/25/2023] [Indexed: 06/28/2023]
Abstract
Introduction The Yangtze vole (Microtus fortis) is a small herbivorous rodent that usually causes damage to crops and forests in China. Various measures were used to control their population including chemical rodenticides. However, rodenticides may cause secondary damage to the environment and the ecosystem. Therefore, the development of new rodent sterilants is urgent. Considering that some compounds of paper mulberry leaves have been verified that can inhibit the biosynthesis of sexual hormone, we aimed to explore the antifertility effect of paper mulberry leaves on M. fortis. Methods In this study, voles were divided into three groups including a male group, a female group, and a breeding group, and paper mulberry leaves were added into basal fodder of voles maintained in laboratory, of which the proportion of leaf weight was 50%. In each group, voles were fed with mixed fodder as treatment (BP) and voles were fed with basal fodder as contrast (CK). Results and discussion After feeding for more than 1 month, the results indicated that paper mulberry leaves attracted voles to feed, but inhibited their growth and reproduction. Since the second week, food intakes of BP have been significantly higher than CK (p< 0.05). However, weights of voles in male and female groups were 72.283 ± 7.394 g and 49.717 ± 2.278 g in the fifth week, and both were significantly reduced compared with their original weight (p< 0.05). Meanwhile, testicular volumes of male voles fed with BP were significantly smaller than CK (former: 318.000 ± 44.654 mm3, latter: 459.339 ± 108.755 mm3); the testosterone level, sperm number, and vitality of BP were obviously weaker than CK. Female uteruses and oophoron of BP grew slower, and the organ coefficients of uterus and oophoron fed BP were both significantly lower than CK (p< 0.05). The first reproduction of BP couple voles spent 45 days, while CK spent only 21 days. These results suggest that paper mulberry leaves could be the potential resource to produce sterilants to control rodent populations by delaying their sexual growth and reproduction. If it was practical, the apparent advantages of paper mulberry are that it is an abundant resource and the inhibitory effect could be effective in both male and female individuals. Our conclusion also supports the transformation of rodent management from lethal management to fertility control, which would be more ecologically friendly to agriculture and the ecosystem.
Collapse
Affiliation(s)
- Shuangye Wang
- College of Resources and Environment, Hunan Agricultural University, Changsha, Hunan, China
| | - Junzhi Chen
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
| | - Yunlin Zhao
- College of Resources and Environment, Hunan Agricultural University, Changsha, Hunan, China
| | - Meiwen Zhang
- Dongting Lake Station for Wetland Ecosystem Research, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan, China
| | - Chen Zhang
- Dongting Lake Station for Wetland Ecosystem Research, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan, China
| | - Jianing He
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
- Dongting Lake Station for Wetland Ecosystem Research, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan, China
| | - Lichuan Wei
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
| | - Zhenggang Xu
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
| |
Collapse
|
8
|
Xuan R, Gao J, Lin Q, Yue W, Liu T, Hu S, Song G. Mitochondrial DNA Diversity of Mesocricetus auratus and Other Cricetinae Species among Cricetidae Family. Biochem Genet 2022; 60:1881-1894. [PMID: 35122557 PMCID: PMC8817650 DOI: 10.1007/s10528-022-10195-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 01/25/2022] [Indexed: 11/29/2022]
Abstract
Unique anatomical and physiological features have made hamster species desirable research models. Comparative genomics and phylogenetic analysis of the hamster family members to clarify their evolution and genetic relationship, can provide a genetic basis for the comprehension of the variable research results obtained using different hamster models. The Syrian golden hamster (Mesocricetus auratus) is the most widely used species. In this study, we sequenced the complete mitochondrial genome (mitogenome) of M. auratus, compared it with the mitogenome of other Cricetinae subfamily species, and defined its phylogenetic position in the Cricetidae family. Our results show that the mitogenome organization, gene arrangement, base composition, and genetic analysis of the protein coding genes (PCGs) of M. auratus are similar to those observed in previous reports on Cricetinae species. Nonetheless, our analysis clarifies some striking differences of M. auratus relative to other subfamily members, namely distinct codon usage frequency of TAT (Tyr), AAT (Asn), and GAA (Glu) and the presence of the conserved sequence block 3 (CSB-3) in the control region of M. auratus mitogenome and other hamsters (not found in Arvicolinae). These results suggest the particularity of amino acid codon usage bias of M. auratus and special regulatory signals for the heavy strand replication in Cricetinae. Additionally, Bayesian inference/maximum likelihood (BI/ML) tree shows that Cricetinae and Arvicolinae are sister taxa sharing a common ancestor, and Neotominae split prior to the split between Cricetinae and Arvicolinae. Our results support taxonomy revisions in Cricetulus kamensis and Cricetulus migratorius, and further revision is needed within the other two subfamilies. Among the hamster research models, Cricetulus griseus is the species with highest sequence similarity and closer genetic relationship with M. auratus. Our results show mitochondrial DNA diversity of M. auratus and other Cricetinae species and provide genetic basis for judgement of different hamster models, promoting the development and usage of hamsters with regional characteristics.
Collapse
Affiliation(s)
- Ruijing Xuan
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, 030001, China
| | - Jiping Gao
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, 030001, China
| | - Qiang Lin
- Key Laboratory of Genome Information and Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Wenbin Yue
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu, 030801, China
| | - Tianfu Liu
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, 030001, China
| | - Songnian Hu
- Key Laboratory of Genome Information and Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Guohua Song
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, 030001, China.
| |
Collapse
|
9
|
Kelley DB. Convergent and divergent neural circuit architectures that support acoustic communication. Front Neural Circuits 2022; 16:976789. [PMID: 36466364 PMCID: PMC9712726 DOI: 10.3389/fncir.2022.976789] [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: 06/23/2022] [Accepted: 10/19/2022] [Indexed: 11/18/2022] Open
Abstract
Vocal communication is used across extant vertebrates, is evolutionarily ancient, and been maintained, in many lineages. Here I review the neural circuit architectures that support intraspecific acoustic signaling in representative anuran, mammalian and avian species as well as two invertebrates, fruit flies and Hawaiian crickets. I focus on hindbrain motor control motifs and their ties to respiratory circuits, expression of receptors for gonadal steroids in motor, sensory, and limbic neurons as well as divergent modalities that evoke vocal responses. Hindbrain and limbic participants in acoustic communication are highly conserved, while forebrain participants have diverged between anurans and mammals, as well as songbirds and rodents. I discuss the roles of natural and sexual selection in driving speciation, as well as exaptation of circuit elements with ancestral roles in respiration, for producing sounds and driving rhythmic vocal features. Recent technical advances in whole brain fMRI across species will enable real time imaging of acoustic signaling partners, tying auditory perception to vocal production.
Collapse
|
10
|
Bentz EJ, Ophir AG. Chromosome-scale genome assembly of the African giant pouched rat (Cricetomys ansorgei) and evolutionary analysis reveals evidence of olfactory specialization. Genomics 2022; 114:110521. [PMID: 36351561 DOI: 10.1016/j.ygeno.2022.110521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/07/2022]
Abstract
The Southern giant pouched rat, Cricetomys ansorgei, is a large rodent best known for its ability to detect landmines using its impressive sense of smell. Their powerful chemosensory abilities enable subtle discrimination of chemical social signals, and female pouched rats demonstrate a unique reproductive physiology hypothesized to be mediated by pheromonal mechanisms. Thus, C. ansorgei represents a novel mammalian model for chemosensory physiology, social behavior, and pheromonal control of reproductive physiology. We present the first chromosome-scale genomic sequence of the pouched rat encoding 22,671 protein coding genes, including 1571 olfactory receptors, and provide a glance into the evolutionary history of this species. Functional enrichment analysis reveals genetic expansions specific to the pouched rat are enriched for functions related to olfactory specialization. Overall, this assembly is of reference-quality, and will serve as a useful and informative genomic sequence on which we can confidently base future molecular research involving the pouched rat.
Collapse
Affiliation(s)
- Ehren J Bentz
- Department of Psychology, Cornell University, Ithaca, NY, USA.
| | | |
Collapse
|
11
|
Comprehensive cytogenetic analysis of the most chromosomally variable mammalian genus from South America: Ctenomys (Rodentia: Caviomorpha: Ctenomyidae). Mamm Biol 2022. [DOI: 10.1007/s42991-022-00312-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
12
|
Dudka D, Lampson MA. Centromere drive: model systems and experimental progress. Chromosome Res 2022; 30:187-203. [PMID: 35731424 DOI: 10.1007/s10577-022-09696-3] [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: 01/24/2022] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 11/28/2022]
Abstract
Centromeres connect chromosomes and spindle microtubules to ensure faithful chromosome segregation. Paradoxically, despite this conserved function, centromeric DNA evolves rapidly and centromeric proteins show signatures of positive selection. The centromere drive hypothesis proposes that centromeric DNA can act like a selfish genetic element and drive non-Mendelian segregation during asymmetric female meiosis. Resulting fitness costs lead to genetic conflict with the rest of the genome and impose a selective pressure for centromeric proteins to adapt by suppressing the costs. Here, we describe experimental model systems for centromere drive in yellow monkeyflowers and mice, summarize key findings demonstrating centromere drive, and explain molecular mechanisms. We further discuss efforts to test if centromeric proteins are involved in suppressing drive-associated fitness costs, highlight a model for centromere drive and suppression in mice, and put forth outstanding questions for future research.
Collapse
Affiliation(s)
- Damian Dudka
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael A Lampson
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
13
|
Oliveira da Silva W, Rosa CC, Ferguson-Smith MA, O'Brien PCM, Saldanha J, Rossi RV, Pieczarka JC, Nagamachi CY. The emergence of a new sex-system (XX/XY 1Y 2) suggests a species complex in the "monotypic" rodent Oecomys auyantepui (Rodentia, Sigmodontinae). Sci Rep 2022; 12:8690. [PMID: 35610291 PMCID: PMC9130129 DOI: 10.1038/s41598-022-12706-3] [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: 02/20/2022] [Accepted: 05/11/2022] [Indexed: 11/15/2022] Open
Abstract
X-autosome translocation (XY1Y2) has been reported in distinct groups of vertebrates suggesting that the rise of a multiple sex system within a species may act as a reproductive barrier and lead to speciation. The viability of this system has been linked with repetitive sequences located between sex and autosomal portions of the translocation. Herein, we investigate Oecomys auyantepui, using chromosome banding and Fluorescence In Situ Hybridization with telomeric and Hylaeamys megacephalus whole-chromosome probes, and phylogenetic reconstruction using mtDNA and nuDNA sequences. We describe an amended karyotype for O. auyantepui (2n = 64♀65♂/FNa = 84) and report for the first time a multiple sex system (XX/XY1Y2) in Oryzomyini rodents. Molecular data recovered O. auyantepui as a monophyletic taxon with high support and cytogenetic data indicate that O. auyantepui may exist in two lineages recognized by distinct sex systems. The Neo-X exhibits repetitive sequences located between sex and autosomal portions, which would act as a boundary between these two segments. The G-banding comparisons of the Neo-X chromosomes of other Sigmodontinae taxa revealed a similar banding pattern, suggesting that the autosomal segment in the Neo-X can be shared among the Sigmodontinae lineages with a XY1Y2 sex system.
Collapse
Affiliation(s)
- Willam Oliveira da Silva
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Celina Coelho Rosa
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, UK
| | - Patricia Caroline Mary O'Brien
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, UK
| | - Juliane Saldanha
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal do Mato Grosso (UFMT), Cuiabá, Mato Grosso, Brazil
| | - Rogério Vieira Rossi
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal do Mato Grosso (UFMT), Cuiabá, Mato Grosso, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil.
| |
Collapse
|
14
|
3D chromatin remodelling in the germ line modulates genome evolutionary plasticity. Nat Commun 2022; 13:2608. [PMID: 35546158 PMCID: PMC9095871 DOI: 10.1038/s41467-022-30296-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/21/2022] [Indexed: 11/09/2022] Open
Abstract
Chromosome folding has profound impacts on gene regulation, whose evolutionary consequences are far from being understood. Here we explore the relationship between 3D chromatin remodelling in mouse germ cells and evolutionary changes in genome structure. Using a comprehensive integrative computational analysis, we (i) reconstruct seven ancestral rodent genomes analysing whole-genome sequences of 14 species representatives of the major phylogroups, (ii) detect lineage-specific chromosome rearrangements and (iii) identify the dynamics of the structural and epigenetic properties of evolutionary breakpoint regions (EBRs) throughout mouse spermatogenesis. Our results show that EBRs are devoid of programmed meiotic DNA double-strand breaks (DSBs) and meiotic cohesins in primary spermatocytes, but are associated in post-meiotic cells with sites of DNA damage and functional long-range interaction regions that recapitulate ancestral chromosomal configurations. Overall, we propose a model that integrates evolutionary genome reshuffling with DNA damage response mechanisms and the dynamic spatial genome organisation of germ cells. The role of genome folding in the heritability and evolvability of structural variations is not well understood. Here the authors investigate the impact of the three-dimensional genome topology of germ cells in the formation and transmission of gross structural genomic changes detected from comparing whole-genome sequences of 14 rodent species.
Collapse
|
15
|
Ivanova NG, Kartavtseva IV, Stefanova VN, Ostromyshenskii DI, Podgornaya OI. Tandem Repeat Diversity in Two Closely Related Hamster Species—The Chinese Hamster (Cricetulus griseus) and Striped Hamster (Cricetulus barabensis). Biomedicines 2022; 10:biomedicines10040925. [PMID: 35453675 PMCID: PMC9025346 DOI: 10.3390/biomedicines10040925] [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: 03/02/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 11/16/2022] Open
Abstract
The Chinese hamster (Cricetulus griseus) and striped hamster (Cricetulus barabensis) are very closely related species with similar karyotypes. The karyotypes differ from each other by one Robertsonian rearrangement and X-chromosome morphology. The level of the tandem repeat (TR) sequences’ evolutional variability is high. The aim of the current work was to trace the TR distribution on the chromosomes of two very closely related species. The striped hamster genome has not yet been sequenced. We classified the Chinese hamster TR in the assemblies available and then compared the mode of the TR distribution in closely related species. Chinese and striped hamsters are separate species due to the relative species specificity of Chinese hamster TR and prominent differences in the TR distribution in both species. The TR variation observed within homologous striped hamster chromosomes is caused by a lack of inbreeding in natural populations. The set of TR tested could be used to examine the CHO lines’ instability that has been observed in heterochromatic regions.
Collapse
Affiliation(s)
- Nadezhda G. Ivanova
- Laboratory of Noncoding DNA, Institute of Cytology RAS, Saint Petersburg 194064, Russia; (V.N.S.); (D.I.O.); (O.I.P.)
- Correspondence:
| | - Irina V. Kartavtseva
- Laboratory of Evolutionary Zoology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Vladivostok 690022, Russia;
| | - Vera N. Stefanova
- Laboratory of Noncoding DNA, Institute of Cytology RAS, Saint Petersburg 194064, Russia; (V.N.S.); (D.I.O.); (O.I.P.)
| | - Dmitrii I. Ostromyshenskii
- Laboratory of Noncoding DNA, Institute of Cytology RAS, Saint Petersburg 194064, Russia; (V.N.S.); (D.I.O.); (O.I.P.)
| | - Olga I. Podgornaya
- Laboratory of Noncoding DNA, Institute of Cytology RAS, Saint Petersburg 194064, Russia; (V.N.S.); (D.I.O.); (O.I.P.)
- Department of Cytology and Histology, Faculty of Biology, St. Petersburg State University, Saint Petersburg 199034, Russia
| |
Collapse
|
16
|
Bakloushinskaya I. Chromosome Changes in Soma and Germ Line: Heritability and Evolutionary Outcome. Genes (Basel) 2022; 13:genes13040602. [PMID: 35456408 PMCID: PMC9029507 DOI: 10.3390/genes13040602] [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: 02/22/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 12/13/2022] Open
Abstract
The origin and inheritance of chromosome changes provide the essential foundation for natural selection and evolution. The evolutionary fate of chromosome changes depends on the place and time of their emergence and is controlled by checkpoints in mitosis and meiosis. Estimating whether the altered genome can be passed to subsequent generations should be central when we consider a particular genome rearrangement. Through comparative analysis of chromosome rearrangements in soma and germ line, the potential impact of macromutations such as chromothripsis or chromoplexy appears to be fascinating. What happens with chromosomes during the early development, and which alterations lead to mosaicism are other poorly studied but undoubtedly essential issues. The evolutionary impact can be gained most effectively through chromosome rearrangements arising in male meiosis I and in female meiosis II, which are the last divisions following fertilization. The diversity of genome organization has unique features in distinct animals; the chromosome changes, their internal relations, and some factors safeguarding genome maintenance in generations under natural selection were considered for mammals.
Collapse
Affiliation(s)
- Irina Bakloushinskaya
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| |
Collapse
|
17
|
|
18
|
Haugg E, Borner J, Diedrich V, Herwig A. Comparative transcriptomics of the Djungarian hamster hypothalamus during short photoperiod acclimation and spontaneous torpor. FEBS Open Bio 2022; 12:443-459. [PMID: 34894101 PMCID: PMC8804604 DOI: 10.1002/2211-5463.13350] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/30/2021] [Accepted: 12/10/2021] [Indexed: 12/03/2022] Open
Abstract
The energy-saving strategy of Djungarian hamsters (Phodopus sungorus, Cricetidae) to overcome harsh environmental conditions comprises of behavioral, morphological, and physiological adjustments, including spontaneous daily torpor, a metabolic downstate. These acclimatizations are triggered by short photoperiod and orchestrated by the hypothalamus. Key mechanisms of long-term photoperiodic acclimatizations have partly been described, but specific mechanisms that acutely control torpor remain incomplete. Here, we performed comparative transcriptome analysis on hypothalamus of normometabolic hamsters in their summer- and winter-like state to enable us to identify changes in gene expression during photoperiodic acclimations. Comparing nontorpid and torpid hamsters may also be able to pin down mechanisms relevant for torpor control. A de novo assembled transcriptome of the hypothalamus was generated from hamsters acclimated to long photoperiod or to short photoperiod. The hamsters were sampled either during long photoperiod normothermia, short photoperiod normothermia, or short photoperiod-induced spontaneous torpor with a body temperature of 24.6 ± 1.0 °C, or. The mRNA-seq analysis revealed that 32 and 759 genes were differentially expressed during photoperiod or torpor, respectively. Biological processes were not enriched during photoperiodic acclimatization but were during torpor, where transcriptional and metabolic processes were reinforced. Most extremely regulated genes (those genes with |log2(FC)| > 2.0 and padj < 0.05 of a pairwise group comparison) underpinned the role of known key players in photoperiodic comparison, but these genes exhibit adaptive and protective adjustments during torpor. Targeted analyses of genes from potentially involved hypothalamic systems identified gene regulation of previously described torpor-relevant systems and a potential involvement of glucose transport.
Collapse
Affiliation(s)
- Elena Haugg
- Institute of NeurobiologyUlm UniversityGermany
| | - Janus Borner
- Institute of Evolutionary Ecology and Conservation GenomicsUlm UniversityGermany
- Sackler Institute for Comparative GenomicsAmerican Museum of Natural HistoryNew YorkNYUSA
| | | | | |
Collapse
|
19
|
Rezazadeh E, Aliabadian M, Ahmadzadeh F. Genetic variation and cytological diversity in the Urar Brush-tailed Mouse, Calomyscus urartensis Vorontsov & Kartavseva, 1979 (Mammalia: Rodentia) in Lesser Caucasia. ZOOLOGY IN THE MIDDLE EAST 2022. [DOI: 10.1080/09397140.2021.2021659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Elham Rezazadeh
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mansour Aliabadian
- Institute of Applied Zoology, Faculty of Science, Zoological Innovations Research Department, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| |
Collapse
|
20
|
Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer. Nat Commun 2021; 12:6858. [PMID: 34824214 PMCID: PMC8617201 DOI: 10.1038/s41467-021-27091-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 10/25/2021] [Indexed: 01/23/2023] Open
Abstract
Muntjac deer have experienced drastic karyotype changes during their speciation, making it an ideal model for studying mechanisms and functional consequences of mammalian chromosome evolution. Here we generated chromosome-level genomes for Hydropotes inermis (2n = 70), Muntiacus reevesi (2n = 46), female and male M. crinifrons (2n = 8/9) and a contig-level genome for M. gongshanensis (2n = 8/9). These high-quality genomes combined with Hi-C data allowed us to reveal the evolution of 3D chromatin architectures during mammalian chromosome evolution. We find that the chromosome fusion events of muntjac species did not alter the A/B compartment structure and topologically associated domains near the fusion sites, but new chromatin interactions were gradually established across the fusion sites. The recently borne neo-Y chromosome of M. crinifrons, which underwent male-specific inversions, has dramatically restructured chromatin compartments, recapitulating the early evolution of canonical mammalian Y chromosomes. We also reveal that a complex structure containing unique centromeric satellite, truncated telomeric and palindrome repeats might have mediated muntjacs' recurrent chromosome fusions. These results provide insights into the recurrent chromosome tandem fusion in muntjacs, early evolution of mammalian sex chromosomes, and reveal how chromosome rearrangements can reshape the 3D chromatin regulatory conformations during species evolution.
Collapse
|
21
|
Saunders PA, Veyrunes F. Unusual Mammalian Sex Determination Systems: A Cabinet of Curiosities. Genes (Basel) 2021; 12:1770. [PMID: 34828376 PMCID: PMC8617835 DOI: 10.3390/genes12111770] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/29/2021] [Accepted: 11/05/2021] [Indexed: 11/21/2022] Open
Abstract
Therian mammals have among the oldest and most conserved sex-determining systems known to date. Any deviation from the standard XX/XY mammalian sex chromosome constitution usually leads to sterility or poor fertility, due to the high differentiation and specialization of the X and Y chromosomes. Nevertheless, a handful of rodents harbor so-called unusual sex-determining systems. While in some species, fertile XY females are found, some others have completely lost their Y chromosome. These atypical species have fascinated researchers for over 60 years, and constitute unique natural models for the study of fundamental processes involved in sex determination in mammals and vertebrates. In this article, we review current knowledge of these species, discuss their similarities and differences, and attempt to expose how the study of their exceptional sex-determining systems can further our understanding of general processes involved in sex chromosome and sex determination evolution.
Collapse
Affiliation(s)
- Paul A. Saunders
- Institut des Sciences de l’Evolution de Montpellier, ISEM UMR 5554 (CNRS/Université Montpellier/IRD/EPHE), 34090 Montpellier, France;
- School of Natural Sciences, University of Tasmania, Sandy Bay, TAS 7000, Australia
| | - Frédéric Veyrunes
- Institut des Sciences de l’Evolution de Montpellier, ISEM UMR 5554 (CNRS/Université Montpellier/IRD/EPHE), 34090 Montpellier, France;
| |
Collapse
|
22
|
Paixão VDS, Suárez P, Oliveira da Silva W, Geise L, Ferguson-Smith MA, O’Brien PCM, Mendes-Oliveira AC, Rossi RV, Pieczarka JC, Nagamachi CY. Comparative genomic mapping reveals mechanisms of chromosome diversification in Rhipidomys species (Rodentia, Thomasomyini) and syntenic relationship between species of Sigmodontinae. PLoS One 2021; 16:e0258474. [PMID: 34634084 PMCID: PMC8504764 DOI: 10.1371/journal.pone.0258474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
Rhipidomys (Sigmodontinae, Thomasomyini) has 25 recognized species, with a wide distribution ranging from eastern Panama to northern Argentina. Cytogenetic data has been described for 13 species with 12 of them having 2n = 44 with a high level of autosomal fundamental number (FN) variation, ranging from 46 to 80, assigned to pericentric inversions. The species are grouped in groups with low FN (46-52) and high FN (72-80). In this work the karyotypes of Rhipidomys emiliae (2n = 44, FN = 50) and Rhipidomys mastacalis (2n = 44, FN = 74), were studied by classical cytogenetics and by fluorescence in situ hybridization using telomeric and whole chromosome probes (chromosome painting) of Hylaeamys megacephalus (HME). Chromosome painting revealed homology between 36 segments of REM and 37 of RMA. We tested the hypothesis that pericentric inversions are the predominant chromosomal rearrangements responsible for karyotypic divergence between these species, as proposed in literature. Our results show that the genomic diversification between the karyotypes of the two species resulted from translocations, centromeric repositioning and pericentric inversions. The chromosomal evolution in Rhipidomys was associated with karyotypical orthoselection. The HME probes revealed that seven syntenic probably ancestral blocks for Sigmodontinae are present in Rhipidomys. An additional syntenic block described here is suggested as part of the subfamily ancestral karyotype. We also define five synapomorphies that can be used as chromosomal signatures for Rhipidomys.
Collapse
Affiliation(s)
- Vergiana dos Santos Paixão
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Pablo Suárez
- Instituto de Biologia Subtropical (CONICET-UNAM), Puerto Iguazú, Misiones, Argentina
| | - Willam Oliveira da Silva
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Lena Geise
- Laboratório de Mastozoologia, Departamento de Zoologia, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Patricia Caroline Mary O’Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ana Cristina Mendes-Oliveira
- Laboratório de Zoologia e Ecologia de Vertebrados, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Rogério Vieira Rossi
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal do Mato Grosso (UFMT), Cuiabá, Mato Grosso, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| |
Collapse
|
23
|
Convergent evolution of a genomic rearrangement may explain cancer resistance in hystrico- and sciuromorpha rodents. NPJ Aging Mech Dis 2021; 7:20. [PMID: 34471123 PMCID: PMC8410860 DOI: 10.1038/s41514-021-00072-9] [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: 10/22/2020] [Accepted: 06/21/2021] [Indexed: 11/09/2022] Open
Abstract
The rodents of hystricomorpha and sciuromorpha suborders exhibit remarkably lower incidence of cancer. The underlying genetic basis remains obscure. We report a convergent evolutionary split of human 3p21.31, a locus hosting a large number of tumour-suppressor genes (TSGs) and frequently deleted in several tumour types, in hystrico- and sciuromorphs. Analysis of 34 vertebrate genomes revealed that the synteny of 3p21.31 cluster is functionally and evolutionarily constrained in most placental mammals, but exhibit large genomic interruptions independently in hystricomorphs and sciuromorphs, owing to relaxation of underlying constraints. Hystrico- and sciuromorphs, therefore, escape from pro-tumorigenic co-deletion of several TSGs in cis. The split 3p21.31 sub-clusters gained proximity to proto-oncogene clusters from elsewhere, which might further nullify pro-tumorigenic impact of copy number variations due to co-deletion or co-amplification of genes with opposing effects. The split of 3p21.31 locus coincided with the accelerated rate of its gene expression and the body mass evolution of ancestral hystrico- and sciuromorphs. The genes near breakpoints were associated with the traits specific to hystrico- and sciuromorphs, implying adaptive significance. We conclude that the convergently evolved chromosomal interruptions of evolutionarily constrained 3p21.31 cluster might have impacted evolution of cancer resistance, body mass variation and ecological adaptations in hystrico- and sciuromorphs.
Collapse
|
24
|
Zhou X, Dou Q, Fan G, Zhang Q, Sanderford M, Kaya A, Johnson J, Karlsson EK, Tian X, Mikhalchenko A, Kumar S, Seluanov A, Zhang ZD, Gorbunova V, Liu X, Gladyshev VN. Beaver and Naked Mole Rat Genomes Reveal Common Paths to Longevity. Cell Rep 2021; 32:107949. [PMID: 32726638 DOI: 10.1016/j.celrep.2020.107949] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 02/20/2020] [Accepted: 07/02/2020] [Indexed: 11/29/2022] Open
Abstract
Long-lived rodents have become an attractive model for the studies on aging. To understand evolutionary paths to long life, we prepare chromosome-level genome assemblies of the two longest-lived rodents, Canadian beaver (Castor canadensis) and naked mole rat (NMR, Heterocephalus glaber), which were scaffolded with in vitro proximity ligation and chromosome conformation capture data and complemented with long-read sequencing. Our comparative genomic analyses reveal that amino acid substitutions at "disease-causing" sites are widespread in the rodent genomes and that identical substitutions in long-lived rodents are associated with common adaptive phenotypes, e.g., enhanced resistance to DNA damage and cellular stress. By employing a newly developed substitution model and likelihood ratio test, we find that energy and fatty acid metabolism pathways are enriched for signals of positive selection in both long-lived rodents. Thus, the high-quality genome resource of long-lived rodents can assist in the discovery of genetic factors that control longevity and adaptive evolution.
Collapse
Affiliation(s)
- Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, Massachusetts, MA 02142, USA
| | - Qianhui Dou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Quanwei Zhang
- Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Maxwell Sanderford
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
| | - Alaattin Kaya
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, Massachusetts, MA 02142, USA; Department of Biology, Virginia Commonwealth University, Richmond, VA 23284 USA
| | - Jeremy Johnson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, MA 02142, USA
| | - Elinor K Karlsson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, MA 02142, USA; University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Xiao Tian
- Department of Biology, University of Rochester, Rochester, NY 14627, USA; Department of Medicine, University of Rochester, Rochester, NY 14627, USA
| | - Aleksei Mikhalchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA; Department of Medicine, University of Rochester, Rochester, NY 14627, USA
| | | | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA; Department of Medicine, University of Rochester, Rochester, NY 14627, USA
| | - Xin Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, Massachusetts, MA 02142, USA.
| |
Collapse
|
25
|
Ishino K, Hasuwa H, Yoshimura J, Iwasaki YW, Nishihara H, Seki NM, Hirano T, Tsuchiya M, Ishizaki H, Masuda H, Kuramoto T, Saito K, Sakakibara Y, Toyoda A, Itoh T, Siomi MC, Morishita S, Siomi H. Hamster PIWI proteins bind to piRNAs with stage-specific size variations during oocyte maturation. Nucleic Acids Res 2021; 49:2700-2720. [PMID: 33590099 PMCID: PMC7969018 DOI: 10.1093/nar/gkab059] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/18/2021] [Accepted: 01/23/2021] [Indexed: 12/27/2022] Open
Abstract
In animal gonads, transposable elements are actively repressed to preserve genome integrity through the PIWI-interacting RNA (piRNA) pathway. In mice, piRNAs are abundantly expressed in male germ cells, and form effector complexes with three distinct PIWIs. The depletion of individual Piwi genes causes male-specific sterility with no discernible phenotype in female mice. Unlike mice, most other mammals have four PIWI genes, some of which are expressed in the ovary. Here, purification of PIWI complexes from oocytes of the golden hamster revealed that the size of the PIWIL1-associated piRNAs changed during oocyte maturation. In contrast, PIWIL3, an ovary-specific PIWI in most mammals, associates with short piRNAs only in metaphase II oocytes, which coincides with intense phosphorylation of the protein. An improved high-quality genome assembly and annotation revealed that PIWIL1- and PIWIL3-associated piRNAs appear to share the 5'-ends of common piRNA precursors and are mostly derived from unannotated sequences with a diminished contribution from TE-derived sequences, most of which correspond to endogenous retroviruses. Our findings show the complex and dynamic nature of biogenesis of piRNAs in hamster oocytes, and together with the new genome sequence generated, serve as the foundation for developing useful models to study the piRNA pathway in mammalian oocytes.
Collapse
Affiliation(s)
- Kyoko Ishino
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hidetoshi Hasuwa
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Yuka W Iwasaki
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Saitama, Japan
| | - Hidenori Nishihara
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa 226-8501, Japan
| | - Naomi M Seki
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
- Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Takamasa Hirano
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
- National Institute of Genetics, Mishima 411-8540, Japan
| | - Marie Tsuchiya
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | | | - Harumi Masuda
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Tae Kuramoto
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa 226-8501, Japan
| | - Kuniaki Saito
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
- National Institute of Genetics, Mishima 411-8540, Japan
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan
| | | | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa 226-8501, Japan
| | - Mikiko C Siomi
- Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| |
Collapse
|
26
|
Oliveira da Silva W, Rosa CC, Pieczarka JC, Ferguson-Smith MA, O’Brien PCM, Mendes-Oliveira AC, Rossi RV, Nagamachi CY. Karyotypic divergence reveals that diversity in the Oecomys paricola complex (Rodentia, Sigmodontinae) from eastern Amazonia is higher than previously thought. PLoS One 2020; 15:e0241495. [PMID: 33119689 PMCID: PMC7595413 DOI: 10.1371/journal.pone.0241495] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/15/2020] [Indexed: 11/26/2022] Open
Abstract
The genus Oecomys (Rodentia, Sigmodontinae) is distributed from southern Central America to southeastern Brazil in South America. It currently comprises 18 species, but multidisciplinary approaches such as karyotypic, morphological and molecular studies have shown that there is a greater diversity within some lineages than others. In particular, it has been proposed that O. paricola constitutes a species complex with three evolutionary units, which have been called the northern, eastern and western clades. Aiming to clarify the taxonomic status of O. paricola and determine the relevant chromosomal rearrangements, we investigated the karyotypes of samples from eastern Amazonia by chromosomal banding and FISH with Hylaeamys megacephalus (HME) whole-chromosome probes. We detected three cytotypes for O. paricola: A (OPA-A; 2n = 72, FN = 75), B (OPA-B; 2n = 70, FN = 75) and C (OPA-C; 2n = 70, FN = 72). Comparative chromosome painting showed that fusions/fissions, translocations and pericentric inversions or centromeric repositioning were responsible for the karyotypic divergence. We also detected exclusive chromosomal signatures that can be used as phylogenetic markers. Our analysis of karyotypic and distribution information indicates that OPA-A, OPA-B and OPA-C are three distinct species that belong to the eastern clade, with sympatry occurring between two of them, and that the “paricola group” is more diverse than was previously thought.
Collapse
Affiliation(s)
- Willam Oliveira da Silva
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Celina Coelho Rosa
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Department of Veterinary Medicine, University of Cambridge, Cambridge Resource Centre for Comparative Genomics, Cambridge, United Kingdom
| | - Patricia Caroline Mary O’Brien
- Department of Veterinary Medicine, University of Cambridge, Cambridge Resource Centre for Comparative Genomics, Cambridge, United Kingdom
| | - Ana Cristina Mendes-Oliveira
- Laboratório de Ecologia e Zoologia de Vertebrados, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Rogério Vieira Rossi
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal do Mato Grosso (UFMT), Mato Grosso, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
- * E-mail:
| |
Collapse
|
27
|
Chromosomal Signatures Corroborate the Phylogenetic Relationships within Akodontini (Rodentia, Sigmodontinae). Int J Mol Sci 2020; 21:ijms21072415. [PMID: 32244440 PMCID: PMC7177754 DOI: 10.3390/ijms21072415] [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: 03/02/2020] [Revised: 03/28/2020] [Accepted: 03/28/2020] [Indexed: 12/30/2022] Open
Abstract
Comparative chromosome-painting analysis among highly rearranged karyotypes of Sigmodontinae rodents (Rodentia, Cricetidae) detects conserved syntenic blocks, which are proposed as chromosomal signatures and can be used as phylogenetic markers. In the Akodontini tribe, the molecular topology (Cytb and/or IRBP) shows five low-supported clades (divisions: “Akodon”, “Bibimys”, “Blarinomys”, “Oxymycterus”, and “Scapteromys”) within two high-supported major clades (clade A: “Akodon”, “Bibimys”, and “Oxymycterus”; clade B: “Blarinomys” and “Scapteromys”). Here, we examine the chromosomal signatures of the Akodontini tribe by using Hylaeamysmegacephalus (HME) probes to study the karyotypes of Oxymycterus amazonicus (2n = 54, FN = 64) and Blarinomys breviceps (2n = 28, FN = 50), and compare these data with those from other taxa investigated using the same set of probes. We strategically employ the chromosomal signatures to elucidate phylogenetic relationships among the Akodontini. When we follow the evolution of chromosomal signature states, we find that the cytogenetic data corroborate the current molecular relationships in clade A nodes. We discuss the distinct events that caused karyotypic variability in the Oxymycterus and Blarinomys genera. In addition, we propose that Blarinomys may constitute a species complex, and that the taxonomy should be revised to better delimit the geographical boundaries and their taxonomic status.
Collapse
|
28
|
Li J, Shang S, Fang N, Zhu Y, Zhang J, Irwin DM, Zhang S, Wang Z. Accelerated Evolution of Limb-Related Gene Hoxd11 in the Common Ancestor of Cetaceans and Ruminants (Cetruminantia). G3 (BETHESDA, MD.) 2020; 10:515-524. [PMID: 31792005 PMCID: PMC7003097 DOI: 10.1534/g3.119.400512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/24/2019] [Indexed: 11/18/2022]
Abstract
Reduced numbers of carpal and tarsal bones (wrist and ankle joints) are extensively observed in the clade of Cetacea and Ruminantia (Cetruminantia). Homebox D11 (Hoxd11) is one of the important genes required for limb development in mammals. Mutations in Hoxd11 can lead to defects in particular bones of limbs, including carpus and tarsus. To test whether evolutionary changes in Hoxd11 underlie the loss of these bones in Cetruminantia, we sequenced and analyzed Hoxd11 coding sequences and compared them with other 5' HoxA and HoxD genes in a taxonomic coverage of Cetacea, Ruminantia and other mammalian relatives. Statistical tests on the Hoxd11 sequences found an accelerated evolution in the common ancestor of cetaceans and ruminants, which coincided with the reduction of carpal and tarsal bones in this clade. Five amino acid substitutions (G222S, G227A, G229S, A240T and G261V) and one amino acid deletion (G254Del) occurred in this lineage. In contrast, other 5' HoxA and HoxD genes do not show this same evolutionary pattern, but instead display a highly conserved pattern of evolution in this lineage. Accelerated evolution of Hoxd11, but not other 5' HoxA and HoxD genes, is probably related to the reduction of the carpal and tarsal bones in Cetruminantia. Moreover, we found two amino acid substitutions (G110S and D223N) in Hoxd11 that are unique to the lineage of Cetacea, which coincided with hindlimb loss in the common ancestor of cetaceans. Our results give molecular evidence of Hoxd11 adaptive evolution in cetaceans and ruminants, which could be correlated with limb morphological adaptation.
Collapse
Affiliation(s)
- Jun Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Songyang Shang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Na Fang
- State Key Laboratory of Estuarine and Coastal Research, Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China, and
| | - Yubo Zhu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Junpeng Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhe Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China,
| |
Collapse
|
29
|
Oliveira da Silva W, Pieczarka JC, Rodrigues da Costa MJ, Ferguson-Smith MA, O'Brien PCM, Mendes-Oliveira AC, Rossi RV, Nagamachi CY. Chromosomal phylogeny and comparative chromosome painting among Neacomys species (Rodentia, Sigmodontinae) from eastern Amazonia. BMC Evol Biol 2019; 19:184. [PMID: 31601183 PMCID: PMC6785907 DOI: 10.1186/s12862-019-1515-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 09/16/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Neacomys genus is predominantly found in the Amazon region, and belongs to the most diverse tribe of the Sigmodontinae subfamily (Rodentia, Cricetidae, Oryzomyini). The systematics of this genus and questions about its diversity and range have been investigated by morphological, molecular (Cytb and COI sequences) and karyotype analysis (classic cytogenetics and chromosome painting), which have revealed candidate species and new distribution areas. Here we analyzed four species of Neacomys by chromosome painting with Hylaeamys megacephalus (HME) whole-chromosome probes, and compared the results with two previously studied Neacomys species and with other taxa from Oryzomyini and Akodontini tribes that have been hybridized with HME probes. Maximum Parsimony (MP) analyses were performed with the PAUP and T.N.T. software packages, using a non-additive (unordered) multi-state character matrix, based on chromosomal morphology, number and syntenic blocks. We also compared the chromosomal phylogeny obtained in this study with molecular topologies (Cytb and COI) that included eastern Amazonian species of Neacomys, to define the phylogenetic relationships of these taxa. RESULTS The comparative chromosome painting analysis of the seven karyotypes of the six species of Neacomys shows that their diversity is due to 17 fusion/fission events and one translocation, pericentric inversions in four syntenic blocks, and constitutive heterochromatin (CH) amplification/deletion of six syntenic autosomal blocks plus the X chromosome. The chromosomal phylogeny is consistent with the molecular relationships of species of Neacomys. We describe new karyotypes and expand the distribution area for species from eastern Amazonia and detect complex rearrangements by chromosome painting among the karyotypes. CONCLUSIONS Our phylogeny reflects the molecular relationships of the Akodontini and Oryzomyini taxa and supports the monophyly of Neacomys. This work presents new insights about the chromosomal evolution of this group, and we conclude that the karyotypic divergence is in accord with phylogenetic relationships.
Collapse
Affiliation(s)
- Willam Oliveira da Silva
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Julio Cesar Pieczarka
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Marlyson Jeremias Rodrigues da Costa
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Patricia Caroline Mary O'Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Rogério Vieira Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso (UFMT), Cuiabá, Mato Grosso, Brazil
| | - Cleusa Yoshiko Nagamachi
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil.
| |
Collapse
|
30
|
Smalec BM, Heider TN, Flynn BL, O'Neill RJ. A centromere satellite concomitant with extensive karyotypic diversity across the Peromyscus genus defies predictions of molecular drive. Chromosome Res 2019; 27:237-252. [PMID: 30771198 PMCID: PMC6733818 DOI: 10.1007/s10577-019-09605-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/26/2019] [Accepted: 01/29/2019] [Indexed: 12/17/2022]
Abstract
A common feature of eukaryotic centromeres is the presence of large tracts of tandemly arranged repeats, known as satellite DNA. However, these centromeric repeats appear to experience rapid evolution under forces such as molecular drive and centromere drive, seemingly without consequence to the integrity of the centromere. Moreover, blocks of heterochromatin within the karyotype, including the centromere, are hotspots for chromosome rearrangements that may drive speciation events by contributing to reproductive isolation. However, the relationship between the evolution of heterochromatic sequences and the karyotypic dynamics of these regions remains largely unknown. Here, we show that a single conserved satellite DNA sequence in the order Rodentia of the genus Peromyscus localizes to recurrent sites of chromosome rearrangements and heterochromatic amplifications. Peromyscine species display several unique features of chromosome evolution compared to other Rodentia, including stable maintenance of a strict chromosome number of 48 among all known species in the absence of any detectable interchromosomal rearrangements. Rather, the diverse karyotypes of Peromyscine species are due to intrachromosomal variation in blocks of repeated DNA content. Despite wide variation in the copy number and location of repeat blocks among different species, we find that a single satellite monomer maintains a conserved sequence and homogenized tandem repeat structure, defying predictions of molecular drive. The conservation of this satellite monomer results in common, abundant, and large blocks of chromatin that are homologous among chromosomes within one species and among diverged species. Thus, such a conserved repeat may have facilitated the retention of polymorphic chromosome variants within individuals and intrachromosomal rearrangements between species-both factors that have previously been hypothesized to contribute towards the extremely wide range of ecological adaptations that this genus exhibits.
Collapse
Affiliation(s)
- Brendan M Smalec
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, 67 North Eagleville Road, Unit 3127, Storrs, CT, 06269, USA
| | - Thomas N Heider
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, 67 North Eagleville Road, Unit 3127, Storrs, CT, 06269, USA
| | - Brianna L Flynn
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, 67 North Eagleville Road, Unit 3127, Storrs, CT, 06269, USA
| | - Rachel J O'Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, 67 North Eagleville Road, Unit 3127, Storrs, CT, 06269, USA.
| |
Collapse
|
31
|
Kartavtseva IV, Vasilieva TV, Sheremetyeva IN, Lemskaya NA, Moroldoev IV, Golenishchev FN. Genetic Variability of Three Isolated Populations of the Muya Valley Vole Alexandromys mujanensis Orlov et Kovalskaja, 1978 (Rodentia, Arvicolinae). RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419080076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
32
|
Milioto V, Vlah S, Mazzoleni S, Rovatsos M, Dumas F. Chromosomal Localization of 18S-28S rDNA and (TTAGGG)n Sequences in Two South African Dormice of the Genus Graphiurus (Rodentia: Gliridae). Cytogenet Genome Res 2019; 158:145-151. [PMID: 31234172 DOI: 10.1159/000500985] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2019] [Indexed: 11/19/2022] Open
Abstract
Classical cytogenetics and mapping of 18S-28S rDNA and (TTAGGG)n sequences by fluorescence in situ hybridization (FISH) was performed on Graphiurus platyops (GPL) and Graphiurus ocularis (GOC) metaphases with the aim to characterize the genomes. In both species, inverted DAPI karyotypes showed the same diploid number, 2n = 46, and hybridization of the (TTAGGG)n probe revealed interstitial telomeric sequences (ITSs) at the centromeres of almost all bi-armed chromosomes. FISH with the rDNA probe localized nucleolus organizer regions (NORs), at the terminal ends of the p arms of the subtelocentric pairs 16 and 17 in both species and detected additional signals on GPL8 and GOC18, 19, and 22. The species have similar karyotypes, but their chromosome pairs 18-22 differ in morphology; these are acrocentric in G. platyops, as also confirmed by C-banding, and subtelocentric in G. ocularis. These differences in pairs 18-22 were also highlighted by hybridization of the telomeric probe (TTAGGG)n, which showed the small p arms in G. ocularis enriched with ITSs. FISH of rDNA probes detected multiple NOR loci in G. ocularis, underlining the intense evolutionary dynamics related to these genes. Although the Graphiurus species analyzed have similar karyotypes, the results on the repetitive sequences indicate a complex pattern of genomic reorganization and evolution occurring in these phylogenetically close species.
Collapse
|
33
|
Lang D, Lim BK, Gao Y, Wang X. Adaptive evolutionary expansion of the ribonuclease 6 in Rodentia. Integr Zool 2019; 14:306-317. [PMID: 30688011 DOI: 10.1111/1749-4877.12382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Ribonuclease 6 (RNase6 or RNase K6) is a protein that belongs to a superfamily thought to be the sole verte-brate-specific enzyme known for a wide range of physiological functions, including digestion, cytotoxicity, angiogenesis, male reproduction and host defense. In our study, 51 functional genes and 11 pseudogenes were identified from 27 Rodentia species. Intriguingly, in the 3 main lineages of rodents there were multiple RNase6s identified in all species of Ctenohystrica, whereas only a single RNase6 was observed in other Rodentia species examined except for 2 species in the mouse-related clade. The evolutionary scenario of "birth (gene duplication) and death (gene deactivation)" and gene sorting have been demonstrated in Ctenohystrica. In addition, bursts of positive selection, diversification of isoelectric point and positive net charge have been identified in Ctenohystrica, especially at two key sites that are involved in antimicrobial function. Site Trp30 has undergone positive selection and Ile45 has changed into other residues in Group B and Group C of the Ctenohystrica. Our results demonstrated a complex and intriguing evolutionary pattern of rodent RNase6, and indicated that functional modification may have occurred, which establishes an important theoretical foundation for future functional assays in rodent RNase6.
Collapse
Affiliation(s)
- Datian Lang
- Agronomy and Life Science Department, Zhaotong University, Zhaotong, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, China
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, China
| | - Xiaoping Wang
- School of Life Sciences, Yunnan University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, China.,Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, Yunnan University, Kunming, China
| |
Collapse
|
34
|
Romanenko SA, Serdyukova NA, Perelman PL, Trifonov VA, Golenishchev FN, Bulatova NS, Stanyon R, Graphodatsky AS. Multiple intrasyntenic rearrangements and rapid speciation in voles. Sci Rep 2018; 8:14980. [PMID: 30297915 PMCID: PMC6175948 DOI: 10.1038/s41598-018-33300-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 09/26/2018] [Indexed: 11/09/2022] Open
Abstract
Remarkably stable genomic chromosome elements (evolutionary conserved segments or syntenies) are the basis of large-scale chromosome architecture in vertebrate species. However, these syntenic elements harbour evolutionary important changes through intrachromosomal rearrangements such as inversions and centromere repositioning. Here, using FISH with a set of 20 region-specific probes on a wide array of 28 species, we analyzed evolution of three conserved syntenic regions of the Arvicolinae ancestral karyotype. Inside these syntenies we uncovered multiple, previously cryptic intrachromosomal rearrangements. Although in each of the three conserved blocks we found inversions and centromere repositions, the blocks experienced different types of rearrangements. In two syntenies centromere repositioning predominated, while in the third region, paracentric inversions were more frequent, whereas pericentric inversions were not detected. We found that some of the intrachromosomal rearrangements, mainly paracentric inversions, were synapomorphic for whole arvicoline genera or tribes: genera Alexandromys and Microtus, tribes Ellobini and Myodini. We hypothesize that intrachromosomal rearrangements within conserved syntenic blocks are a major evolutionary force modulating genome architecture in species-rich and rapidly-evolving rodent taxa. Inversions and centromere repositioning may impact speciation and provide a potential link between genome evolution, speciation, and biogeography.
Collapse
Affiliation(s)
- Svetlana A Romanenko
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
| | | | - Polina L Perelman
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Vladimir A Trifonov
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | - Nina Sh Bulatova
- A.N. Severtsov Institute of Ecology and Evolution, RAS, Moscow, Russia
| | - Roscoe Stanyon
- Department of Biology, Anthropology Laboratories, University of Florence, Florence, Italy
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| |
Collapse
|
35
|
Lipka A, Paukszto L, Majewska M, Jastrzebski JP, Myszczynski K, Panasiewicz G, Szafranska B. Identification of differentially expressed placental transcripts during multiple gestations in the Eurasian beaver (Castor fiber L.). Reprod Fertil Dev 2018; 29:2073-2084. [PMID: 28193317 DOI: 10.1071/rd16186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 12/22/2016] [Indexed: 12/26/2022] Open
Abstract
The Eurasian beaver is one of the largest rodents that, despite its high impact on the environment, is a non-model species that lacks a reference genome. Characterising genes critical for pregnancy outcome can serve as a basis for identifying mechanisms underlying effective reproduction, which is required for the success of endangered species conservation programs. In the present study, high-throughput RNA sequencing (RNA-seq) was used to analyse global changes in the Castor fiber subplacenta transcriptome during multiple pregnancy. De novo reconstruction of the C. fiber subplacenta transcriptome was used to identify genes that were differentially expressed in placentas (n=5) from two females (in advanced twin and triple pregnancy). Analyses of the expression values revealed 124 contigs with significantly different expression; of these, 55 genes were identified using MegaBLAST. Within this group of differentially expressed genes (DEGs), 18 were upregulated and 37 were downregulated in twins. Most DEGs were associated with the following gene ontology terms: cellular process, single organism process, response to stimulus, metabolic process and biological regulation. Some genes were also assigned to the developmental process, the reproductive process or reproduction. Among this group, four genes (namely keratin 19 (Krt19) and wingless-type MMTV integration site family - member 2 (Wnt2), which were downregulated in twins, and Nik-related kinase (Nrk) and gap junction protein β2 (Gjb2), which were upregulated in twins) were assigned to placental development and nine (Krt19, Wnt2 and integrin α7 (Itga7), downregulated in twins, and Nrk, gap junction protein β6 (Gjb6), GATA binding protein 6 (Gata6), apolipoprotein A-I (ApoA1), apolipoprotein B (ApoB) and haemoglobin subunit α1 (HbA1), upregulated in twins) were assigned to embryo development. The results of the present study indicate that the number of fetuses affects the expression profile in the C. fiber subplacental transcriptome. Enhancement of transcriptomic resources for C. fiber will improve understanding of the pathways relevant to proper placental development and successful reproduction.
Collapse
Affiliation(s)
- A Lipka
- Department of Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Str 1A, 10-719 Olsztyn-Kortowo, Poland
| | - L Paukszto
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Str 1A, 10-719 Olsztyn-Kortowo, Poland
| | - M Majewska
- Department of Human Physiology, Faculty of Medical Sciences, University of Warmia and Mazury in Olsztyn, Warszawska Str 30, 10-082 Olsztyn, Poland
| | - J P Jastrzebski
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Str 1A, 10-719 Olsztyn-Kortowo, Poland
| | - K Myszczynski
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Str 1A, 10-719 Olsztyn-Kortowo, Poland
| | - G Panasiewicz
- Department of Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Str 1A, 10-719 Olsztyn-Kortowo, Poland
| | - B Szafranska
- Department of Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Str 1A, 10-719 Olsztyn-Kortowo, Poland
| |
Collapse
|
36
|
Capilla L, Sánchez-Guillén RA, Farré M, Paytuví-Gallart A, Malinverni R, Ventura J, Larkin DM, Ruiz-Herrera A. Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia. Genome Biol Evol 2018; 8:3703-3717. [PMID: 28175287 PMCID: PMC5521730 DOI: 10.1093/gbe/evw276] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2016] [Indexed: 12/16/2022] Open
Abstract
Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints.
Collapse
Affiliation(s)
- Laia Capilla
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Rosa Ana Sánchez-Guillén
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Marta Farré
- Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Andreu Paytuví-Gallart
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, London, UK.,Sequentia Biotech S.L. Calle Comte d'Urgell, Barcelona, Spain
| | - Roberto Malinverni
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Jacint Ventura
- Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Denis M Larkin
- Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Aurora Ruiz-Herrera
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Sequentia Biotech S.L. Calle Comte d'Urgell, Barcelona, Spain
| |
Collapse
|
37
|
Suárez-Villota EY, Carmignotto AP, Brandão MV, Percequillo AR, Silva MJDJ. Systematics of the genus Oecomys (Sigmodontinae: Oryzomyini): molecular phylogenetic, cytogenetic and morphological approaches reveal cryptic species. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx095] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Elkin Y Suárez-Villota
- Laboratório de Ecologia e Evolução, Instituto Butantan, Av. Vital Brazil, São Paulo, Brazil
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Edificio Emilio Pugín, campus Isla Teja, Valdivia, Chile
| | - Ana Paula Carmignotto
- Laboratório de Diversidade Animal, Departamento de Biologia, Universidade Federal de São Carlos, campus Sorocaba, Rodovia João Leme dos Santos, Sorocaba, São Paulo, Brazil
| | - Marcus Vinícius Brandão
- Laboratório de Diversidade Animal, Departamento de Biologia, Universidade Federal de São Carlos, campus Sorocaba, Rodovia João Leme dos Santos, Sorocaba, São Paulo, Brazil
| | - Alexandre Reis Percequillo
- Departamento de Ciências Biolόgicas, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, Av. Pádua Dias, Piracicaba, São Paulo, Brazil
| | - Maria José de J Silva
- Laboratório de Ecologia e Evolução, Instituto Butantan, Av. Vital Brazil, São Paulo, Brazil
| |
Collapse
|
38
|
Savić I, Ćirović D, Bugarski-Stanojević V. Exceptional Chromosomal Evolution and Cryptic Speciation of Blind Mole Rats Nannospalax leucodon (Spalacinae, Rodentia) from South-Eastern Europe. Genes (Basel) 2017; 8:E292. [PMID: 29068425 PMCID: PMC5704205 DOI: 10.3390/genes8110292] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/12/2017] [Accepted: 10/17/2017] [Indexed: 01/13/2023] Open
Abstract
Mole rats are exclusively subterranean and highly specialized rodents. Their long lifespans, remarkable anti-cancer mechanisms, and various distinctive adaptive features make them a useful research model. Moreover, opposing convergence of morphological traits, they have developed extremely high karyotype variability. Thus, 74 chromosomal forms have been described so far and new ones are being revealed continuously. These evolved during the process of rapid radiation and occur in different biogeographical regions. During research into their reproductive biology we have already provided substantial evidence for species-level separation of these taxa. Here, we review diverse chromosomal forms of the lesser blind mole rat, Mediterranean Nannospalax leucodon, distributed in South-eastern Europe, their karyotype records, biogeography, origin, and phylogeny from our extensive research. In the light of new data from molecular genetic studies, we question some former valuations and propose a cryptospecies rank for seven reproductively isolated chromosomal forms with sympatric and parapatric distribution and clear ecogeographical discrepances in their habitats, as well as new experimental and theoretical methods for understanding the courses of speciation of these unique fossorial mammals.
Collapse
Affiliation(s)
- Ivo Savić
- Biological Faculty, University of Belgrade, 11000 Belgrade, Serbia.
| | - Duško Ćirović
- Biological Faculty, University of Belgrade, 11000 Belgrade, Serbia.
| | - Vanja Bugarski-Stanojević
- Institute for Biological Research "Siniša Stanković", University of Belgrade, 11060 Belgrade, Serbia.
| |
Collapse
|
39
|
Lang DT, Wang XP, Wang L, Yu L. Molecular evolution of pancreatic ribonuclease gene ( RNase1 ) in Rodentia. J Genet Genomics 2017; 44:219-222. [DOI: 10.1016/j.jgg.2017.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 02/15/2017] [Accepted: 03/06/2017] [Indexed: 01/26/2023]
|
40
|
Ding L, Li W, Liao J. Mitochondrial genome of Cricetulus migratorius (Rodentia: Cricetidae): Insights into the characteristics of the mitochondrial genome and the phylogenetic relationships of Cricetulus species. Gene 2016; 595:121-129. [DOI: 10.1016/j.gene.2016.10.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/16/2016] [Accepted: 10/02/2016] [Indexed: 11/29/2022]
|
41
|
Iturbe-Morgado JC, Falcón-Ordaz J, Lira-Guerrero G, Fernández JA, Acosta R. Nematofauna of Rodents of the Families Heteromyidae and Cricetidae from the Mexican Plateau. J Parasitol 2016; 103:127-131. [PMID: 27788020 DOI: 10.1645/16-105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
As a part of an ongoing project to inventory the helminth parasites of rodents in Mexico, 85 specimens of 2 families of rodents were collected from the Mexican Plateau: Cricetidae ( Neotoma sp., Neotoma leucodon , Onychomys arenicola , Peromyscus sp., Peromyscus eremicus , and Reithrodontomys sp.) and Heteromyidae ( Chaetodipus sp., Chaetodipus eremicus , Chaetodipus hispidus , Dipodomys merriami , Dipodomys ordii , Dipodomys ornatus, Dipodomys spectabilis , Liomys irroratus , Perognathus sp., and Perognathus flavus ). A total of 13 taxa of helminths were found: Heteromyoxyuris longejector, Heteromyoxyuris otomii, Heteromyoxyuris sp., Onchocercidae gen. sp. 1 and sp. 2, Physalopteridae gen. sp., Protospirura dipodomis, Pterygodermatites dipodomis, Subulura sp., Syphacia sp., Trichuris dipodomis, Vexillata liomyos, and Vexillata armande. The highest species richness was recorded in D. merriami (7 taxa). This study is the first report of nematodes from O. arenicola (Physalopteridae gen. sp.) and C. eremicus (H. longejector) and for V. liomyos from D. merriami . All reports of these species of nematodes represent new collection localities in Mexico.
Collapse
Affiliation(s)
- José Carlos Iturbe-Morgado
- Laboratorio de Morfología Animal, Universidad Autónoma del Estado de Hidalgo, Ciudad Universitaria, Carretera Pachuca Tulancingo s/n Km. 4.5, 42184 Mineral de la Reforma, Hidalgo, México
| | - Jorge Falcón-Ordaz
- Laboratorio de Morfología Animal, Universidad Autónoma del Estado de Hidalgo, Ciudad Universitaria, Carretera Pachuca Tulancingo s/n Km. 4.5, 42184 Mineral de la Reforma, Hidalgo, México
| | - Georgina Lira-Guerrero
- Laboratorio de Morfología Animal, Universidad Autónoma del Estado de Hidalgo, Ciudad Universitaria, Carretera Pachuca Tulancingo s/n Km. 4.5, 42184 Mineral de la Reforma, Hidalgo, México
| | - Jesús A Fernández
- Laboratorio de Morfología Animal, Universidad Autónoma del Estado de Hidalgo, Ciudad Universitaria, Carretera Pachuca Tulancingo s/n Km. 4.5, 42184 Mineral de la Reforma, Hidalgo, México
| | - Roxana Acosta
- Laboratorio de Morfología Animal, Universidad Autónoma del Estado de Hidalgo, Ciudad Universitaria, Carretera Pachuca Tulancingo s/n Km. 4.5, 42184 Mineral de la Reforma, Hidalgo, México
| |
Collapse
|
42
|
Gomes Júnior RG, Schneider CH, de Lira T, Carvalho NDM, Feldberg E, da Silva MNF, Gross MC. Intense genomic reorganization in the genus Oecomys (Rodentia, Sigmodontinae): comparison between DNA barcoding and mapping of repetitive elements in three species of the Brazilian Amazon. COMPARATIVE CYTOGENETICS 2016; 10:401-426. [PMID: 27830049 PMCID: PMC5088352 DOI: 10.3897/compcytogen.v10i3.8306] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/29/2016] [Indexed: 05/31/2023]
Abstract
Oecomys Thomas, 1906 is one of the most diverse and widely distributed genera within the tribe Oryzomyini. At least sixteen species in this genus have been described to date, but it is believed this genus contains undescribed species. Morphological, molecular and cytogenetic study has revealed an uncertain taxonomic status for several Oecomys species, suggesting the presence of a complex of species. The present work had the goal of contributing to the genetic characterization of the genus Oecomys in the Brazilian Amazon. Thirty specimens were collected from four locations in the Brazilian Amazon and three nominal species recognized: Oecomys auyantepui (Tate, 1939), Oecomys bicolor (Tomes, 1860) and Oecomys rutilus (Anthony, 1921). COI sequence analysis grouped Oecomys auyantepui, Oecomys bicolor and Oecomys rutilus specimens into one, three and two clades, respectively, which is consistent with their geographic distribution. Cytogenetic data for Oecomys auyantepui revealed the sympatric occurrence of two different diploid numbers, 2n=64/NFa=110 and 2n=66/NFa=114, suggesting polymorphism while Oecomys bicolor exhibited 2n=80/NFa=142 and Oecomys rutilus 2n=54/NFa=90. The distribution of constitutive heterochromatin followed a species-specific pattern. Interspecific variation was evident in the chromosomal location and number of 18S rDNA loci. However, not all loci showed signs of activity. All three species displayed a similar pattern for 5S rDNA, with only one pair carrying this locus. Interstitial telomeric sites were found only in Oecomys auyantepui. The data presented in this work reinforce intra- and interspecific variations observed in the diploid number of Oecomys species and indicate that chromosomal rearrangements have led to the appearance of different diploid numbers and karyotypic formulas.
Collapse
Affiliation(s)
- Renan Gabriel Gomes Júnior
- Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Departamento de Genética, Laboratório de Citogenômica Animal, Av. General Rodrigo Otávio, 3000, Japiim, Zip code 69077-000 Manaus, AM, Brazil
| | - Carlos Henrique Schneider
- Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Departamento de Genética, Laboratório de Citogenômica Animal, Av. General Rodrigo Otávio, 3000, Japiim, Zip code 69077-000 Manaus, AM, Brazil
| | - Thatianna de Lira
- Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936 Zip Code 69077-000, Manaus, AM, Brazil
| | - Natália Dayane Moura Carvalho
- Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Departamento de Genética, Laboratório de Citogenômica Animal, Av. General Rodrigo Otávio, 3000, Japiim, Zip code 69077-000 Manaus, AM, Brazil
| | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936 Zip Code 69077-000, Manaus, AM, Brazil
| | | | - Maria Claudia Gross
- Universidade Federal da Integração Latino Americana, Laboratório de Genética, Av. Tarquínio Joslin dos Santos, 1000, Jardim Universitário, Zip code 85857-190, Foz do Iguaçu, PR, Brazil
| |
Collapse
|
43
|
Chromosomal variability and evolution in the tribe Phyllotini (Rodentia, Cricetidae, Sigmodontinae). MAMMAL RES 2016. [DOI: 10.1007/s13364-016-0286-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
44
|
Pereira AL, Malcher SM, Nagamachi CY, O’Brien PCM, Ferguson-Smith MA, Mendes-Oliveira AC, Pieczarka JC. Extensive Chromosomal Reorganization in the Evolution of New World Muroid Rodents (Cricetidae, Sigmodontinae): Searching for Ancestral Phylogenetic Traits. PLoS One 2016; 11:e0146179. [PMID: 26800516 PMCID: PMC4723050 DOI: 10.1371/journal.pone.0146179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 12/13/2015] [Indexed: 12/05/2022] Open
Abstract
Sigmodontinae rodents show great diversity and complexity in morphology and ecology. This diversity is accompanied by extensive chromosome variation challenging attempts to reconstruct their ancestral genome. The species Hylaeamys megacephalus–HME (Oryzomyini, 2n = 54), Necromys lasiurus—NLA (Akodontini, 2n = 34) and Akodon sp.–ASP (Akodontini, 2n = 10) have extreme diploid numbers that make it difficult to understand the rearrangements that are responsible for such differences. In this study we analyzed these changes using whole chromosome probes of HME in cross-species painting of NLA and ASP to construct chromosome homology maps that reveal the rearrangements between species. We include data from the literature for other Sigmodontinae previously studied with probes from HME and Mus musculus (MMU) probes. We also use the HME probes on MMU chromosomes for the comparative analysis of NLA with other species already mapped by MMU probes. Our results show that NLA and ASP have highly rearranged karyotypes when compared to HME. Eleven HME syntenic blocks are shared among the species studied here. Four syntenies may be ancestral to Akodontini (HME2/18, 3/25, 18/25 and 4/11/16) and eight to Sigmodontinae (HME26, 1/12, 6/21, 7/9, 5/17, 11/16, 20/13 and 19/14/19). Using MMU data we identified six associations shared among rodents from seven subfamilies, where MMU3/18 and MMU8/13 are phylogenetic signatures of Sigmodontinae. We suggest that the associations MMU2entire, MMU6proximal/12entire, MMU3/18, MMU8/13, MMU1/17, MMU10/17, MMU12/17, MMU5/16, MMU5/6 and MMU7/19 are part of the ancestral Sigmodontinae genome.
Collapse
Affiliation(s)
- Adenilson Leão Pereira
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, Belém, Pará, Brasil
| | - Stella Miranda Malcher
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, Belém, Pará, Brasil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, Belém, Pará, Brasil
- CNPq Researcher, Brasília, Brasil
| | - Patricia Caroline Mary O’Brien
- Cambridge Resource Center for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Center for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, Belém, Pará, Brasil
- CNPq Researcher, Brasília, Brasil
- * E-mail:
| |
Collapse
|
45
|
Suárez P, Nagamachi CY, Lanzone C, Malleret MM, O’Brien PCM, Ferguson-Smith MA, Pieczarka JC. Clues on Syntenic Relationship among Some Species of Oryzomyini and Akodontini Tribes (Rodentia: Sigmodontinae). PLoS One 2015; 10:e0143482. [PMID: 26642204 PMCID: PMC4671618 DOI: 10.1371/journal.pone.0143482] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 11/05/2015] [Indexed: 11/18/2022] Open
Abstract
Sigmodontinae rodents represent one of the most diverse and complex components of the mammalian fauna of South America. Among them most species belongs to Oryzomyini and Akodontini tribes. The highly specific diversification observed in both tribes is characterized by diploid complements, which vary from 2n = 10 to 86. Given this diversity, a consistent hypothesis about the origin and evolution of chromosomes depends on the correct establishment of synteny analyzed in a suitable phylogenetic framework. The chromosome painting technique has been particularly useful for identifying chromosomal synteny. In order to extend our knowledge of the homeological relationships between Akodontini and Oryzomyini species, we analyzed the species Akodon montensis (2n = 24) and Thaptomys nigrita (2n = 52) both from the tribe Akodontini, with chromosome probes of Hylaeamys megacephalus (2n = 54) of the tribe Oryzomyini. The results indicate that at least 12 of the 26 autosomes of H. megacephalus show conserved synteny in A. montensis and 14 in T. nigrita. The karyotype of Akodon montensis, as well as some species of the Akodon cursor species group, results from many chromosomal fusions and therefore the syntenic associations observed probably represent synapomorphies. Our finding of a set of such associations revealed by H. megacephalus chromosome probes (6/21; 3/25; 11/16/17; and, 14/19) provides phylogenetic information for both tribes. An extension of these observations to other members of Akodontini and Oryzomyini tribes should improve our knowledge about chromosome evolution in both these groups.
Collapse
Affiliation(s)
- Pablo Suárez
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, UFPa, Belém, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, UFPa, Belém, Pará, Brazil
- CNPq Researchers, Brasilia, Brazil
| | - Cecilia Lanzone
- Laboratorio de Genética Evolutiva, IBS, FCEQyN, CONICET-UNaM, Posadas, Misiones, Argentina
| | | | - Patricia Caroline Mary O’Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, UFPa, Belém, Pará, Brazil
- CNPq Researchers, Brasilia, Brazil
- * E-mail: ;
| |
Collapse
|
46
|
Romanenko SA, Lemskaya NA, Trifonov VA, Serdyukova NA, O'Brien PCM, Bulatova NS, Golenishchev FN, Ferguson-Smith MA, Yang F, Graphodatsky AS. Genome-wide comparative chromosome maps of Arvicola amphibius, Dicrostonyx torquatus, and Myodes rutilus. Chromosome Res 2015; 24:145-59. [PMID: 26611440 DOI: 10.1007/s10577-015-9504-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/05/2015] [Accepted: 11/09/2015] [Indexed: 11/25/2022]
Abstract
The subfamily Arvicolinae consists of a great number of species with highly diversified karyotypes. In spite of the wide use of arvicolines in biological and medicine studies, the data on their karyotype structures are limited. Here, we made a set of painting probes from flow-sorted chromosomes of a male Palearctic collared lemming (Dicrostonyx torquatus, DTO). Together with the sets of painting probes made previously from the field vole (Microtus agrestis, MAG) and golden hamster (Mesocricetus auratus, MAU), we carried out a reciprocal chromosome painting between these three species. The three sets of probes were further hybridized onto the chromosomes of the Eurasian water vole (Arvicola amphibius) and northern red-backed vole (Myodes rutilus). We defined the diploid chromosome number in D. torquatus karyotype as 2n = 45 + Bs and showed that the system of sex chromosomes is X1X2Y1. The probes developed here provide a genomic tool-kit, which will help to investigate the evolutionary biology of the Arvicolinae rodents. Our results show that the syntenic association MAG1/17 is present not only in Arvicolinae but also in some species of Cricetinae; and thus, should not be considered as a cytogenetic signature for Arvicolinae. Although cytogenetic signature markers for the genera have not yet been found, our data provides insight into the likely ancestral karyotype of Arvicolinae. We conclude that the karyotypes of modern voles could have evolved from a common ancestral arvicoline karyotype (AAK) with 2n = 56 mainly by centric fusions and fissions.
Collapse
Affiliation(s)
- Svetlana A Romanenko
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia.
| | - Natalya A Lemskaya
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090, Russia
| | - Vladimir A Trifonov
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Natalya A Serdyukova
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090, Russia
| | - Patricia C M O'Brien
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Madingley Road, Cambridge, CB3 OES, UK
| | - Nina Sh Bulatova
- A. N. Severtsov Institute of Ecology and Evolution, Moscow, 119071, Russia
| | | | - Malcolm A Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Madingley Road, Cambridge, CB3 OES, UK
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | | |
Collapse
|
47
|
Sergina S, Antonova E, Ilyukha V, Łapiński S, Lis M, Niedbała P, Unzhakov A, Belkin V. Biochemical adaptations to dive-derived hypoxia/reoxygenation in semiaquatic rodents. Comp Biochem Physiol B Biochem Mol Biol 2015; 190:37-45. [PMID: 26341791 DOI: 10.1016/j.cbpb.2015.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 08/20/2015] [Accepted: 08/25/2015] [Indexed: 11/15/2022]
Abstract
To meet the challenges presented by dive-derived hypoxia/reoxygenation transition, the aquatic mammals possess multi-level adaptations. However, the adjustments of the semiaquatic animals as modern analogs of evolutionary intermediates between ancestral terrestrial mammals and their fully aquatic descendants are still not fully elucidated. The aim of this study was to analyze the total lactate dehydrogenase (LDH) activity (in the lactate to pyruvate direction), the LDH patterns and the antioxidant defense in the tissues (heart, kidney, liver, lung, muscle, spleen) of semiaquatic rodents such as Eurasian beaver (Castor fiber), muskrat (Ondatra zibethicus) and nutria (Myocastor coypus). Samples from Wistar rat were used for comparison. Semiaquatic rodents had higher catalase activity compared to rats. The superoxide dismutase activity was higher and the catalase activity was lower in almost all tissues of muskrat than of both beaver and nutria. Comparing beaver and nutria, no significant differences in the antioxidant enzyme activities were found for the heart, kidney and liver. In beaver, most of the examined tissues (heart, kidney, lung and spleen) use lactate as preference to glucose as a substrate but in muskrat the heart, liver and skeletal muscle showed the increased LDH activity. Nutria had the unusual LDH properties that are needed to be further investigated. Our results suggest that beaver, nutria and muskrat have distinct mechanisms of adaptation to diving hypoxia/reoxygenation and support the hypothesis that semiaquatic mammals are the intermediate animals that help to define which potential selection factors and mechanical constraints may have directed the evolution of the aquatic forms.
Collapse
Affiliation(s)
- Svetlana Sergina
- Institute of Biology, Karelian Research Centre, Russian Academy of Sciences, Petrozavodsk, Russia.
| | - Ekaterina Antonova
- Institute of Biology, Karelian Research Centre, Russian Academy of Sciences, Petrozavodsk, Russia
| | - Viktor Ilyukha
- Institute of Biology, Karelian Research Centre, Russian Academy of Sciences, Petrozavodsk, Russia
| | - Stanisław Łapiński
- Institute of Animal Sciences, University of Agriculture in Krakow, Krakow, Poland
| | - Marcin Lis
- Institute of Veterinary Sciences, University of Agriculture in Krakow, Krakow, Poland
| | - Piotr Niedbała
- Institute of Animal Sciences, University of Agriculture in Krakow, Krakow, Poland
| | - Alexey Unzhakov
- Institute of Biology, Karelian Research Centre, Russian Academy of Sciences, Petrozavodsk, Russia
| | - Vladimir Belkin
- Institute of Biology, Karelian Research Centre, Russian Academy of Sciences, Petrozavodsk, Russia
| |
Collapse
|
48
|
Romanenko SA, Perelman PL, Trifonov VA, Serdyukova NA, Li T, Fu B, O’Brien PCM, Ng BL, Nie W, Liehr T, Stanyon R, Graphodatsky AS, Yang F. A First Generation Comparative Chromosome Map between Guinea Pig (Cavia porcellus) and Humans. PLoS One 2015; 10:e0127937. [PMID: 26010445 PMCID: PMC4444286 DOI: 10.1371/journal.pone.0127937] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 04/21/2015] [Indexed: 11/19/2022] Open
Abstract
The domesticated guinea pig, Cavia porcellus (Hystricomorpha, Rodentia), is an important laboratory species and a model for a number of human diseases. Nevertheless, genomic tools for this species are lacking; even its karyotype is poorly characterized. The guinea pig belongs to Hystricomorpha, a widespread and important group of rodents; so far the chromosomes of guinea pigs have not been compared with that of other hystricomorph species or with any other mammals. We generated full sets of chromosome-specific painting probes for the guinea pig by flow sorting and microdissection, and for the first time, mapped the chromosomal homologies between guinea pig and human by reciprocal chromosome painting. Our data demonstrate that the guinea pig karyotype has undergone extensive rearrangements: 78 synteny-conserved human autosomal segments were delimited in the guinea pig genome. The high rate of genome evolution in the guinea pig may explain why the HSA7/16 and HSA16/19 associations presumed ancestral for eutherians and the three syntenic associations (HSA1/10, 3/19, and 9/11) considered ancestral for rodents were not found in C. porcellus. The comparative chromosome map presented here is a starting point for further development of physical and genetic maps of the guinea pig as well as an aid for genome assembly assignment to specific chromosomes. Furthermore, the comparative mapping will allow a transfer of gene map data from other species. The probes developed here provide a genomic toolkit, which will make the guinea pig a key species to unravel the evolutionary biology of the Hystricomorph rodents.
Collapse
Affiliation(s)
- Svetlana A. Romanenko
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- * E-mail: (SAR); (FY)
| | - Polina L. Perelman
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Vladimir A. Trifonov
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | - Tangliang Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
| | - Beiyuan Fu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Patricia C. M. O’Brien
- Centre for Veterinary Science, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Bee L. Ng
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Wenhui Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
| | - Thomas Liehr
- Jena University Hospital, Institute of Human Genetics and Anthropology, Jena, Germany
| | - Roscoe Stanyon
- Department of Biology, University of Florence, Florence, Italy
| | - Alexander S. Graphodatsky
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
- * E-mail: (SAR); (FY)
| |
Collapse
|
49
|
Vieira-da-Silva A, Louzada S, Adega F, Chaves R. A High-Resolution Comparative Chromosome Map of Cricetus cricetus and Peromyscus eremicus Reveals the Involvement of Constitutive Heterochromatin in Breakpoint Regions. Cytogenet Genome Res 2015; 145:59-67. [PMID: 25999143 DOI: 10.1159/000381840] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2015] [Indexed: 11/19/2022] Open
Abstract
Compared to humans and other mammals, rodent genomes, specifically Muroidea species, underwent intense chromosome reshuffling in which many complex structural rearrangements occurred. This fact makes them preferential animal models for studying the process of karyotype evolution. Here, we present the first combined chromosome comparative maps between 2 Cricetidae species, Cricetus cricetus and Peromyscus eremicus, and the index species Mus musculus and Rattus norvegicus. Comparative chromosome painting was done using mouse and rat paint probes together with in silico analysis from the Ensembl genome browser database. Hereby, evolutionary events (inter- and intrachromosomal rearrangements) that occurred in C. cricetus and P. eremicus since the putative ancestral Muroidea genome could be inferred, and evolutionary breakpoint regions could be detected. A colocalization of constitutive heterochromatin and evolutionary breakpoint regions in each genome was observed. Our results suggest the involvement of constitutive heterochromatin in karyotype restructuring of these species, despite the different levels of conservation of the C. cricetus (derivative) and P. eremicus (conserved) genomes.
Collapse
Affiliation(s)
- Ana Vieira-da-Silva
- Center of Agricultural and Genomics Biotechnology (CGBA), University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | | | | | | |
Collapse
|
50
|
Weise A, Kosyakova N, Voigt M, Aust N, Mrasek K, Löhmer S, Rubtsov N, Karamysheva TV, Trifonov VA, Hardekopf D, Jančušková T, Pekova S, Wilhelm K, Liehr T, Fan X. Comprehensive Analyses of White-Handed Gibbon Chromosomes Enables Access to 92 Evolutionary Conserved Breakpoints Compared to the Human Genome. Cytogenet Genome Res 2015; 145:42-9. [PMID: 25926034 DOI: 10.1159/000381764] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2015] [Indexed: 11/19/2022] Open
Abstract
Gibbon species (Hylobatidae) impress with an unusually high number of numerical and structural chromosomal changes within the family itself as well as compared to other Hominoidea including humans. In former studies applying molecular cytogenetic methods, 86 evolutionary conserved breakpoints (ECBs) were reported in the white-handed gibbon (Hylobates lar, HLA) with respect to the human genome. To analyze those ECBs in more detail and also to achieve a better understanding of the fast karyotype evolution in Hylobatidae, molecular data for these regions are indispensably necessary. In the present study, we obtained whole chromosome-specific probes by microdissection of all 21 HLA autosomes and prepared them for aCGH. Locus-specific DNA probes were also used for further molecular cytogenetic characterization of selected regions. Thus, we could map 6 yet unreported ECBs in HLA with respect to the human genome. Additionally, in 26 of the 86 previously reported ECBs, the present approach enabled a more precise breakpoint mapping. Interestingly, a preferred localization of ECBs within segmental duplications, copy number variant regions, and fragile sites was observed.
Collapse
Affiliation(s)
- Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|