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Chernova OF, Kupriyanov VP, Feoktistova NY, Surov AV. Peculiarities of the Structure of the Skin and Its Derivatives in Some Members of the Subfamily Cricetinae (Cricetidae, Rodentia): Why It Is Important to Know. BIOL BULL+ 2022. [DOI: 10.1134/s1062359022080040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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2
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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.
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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.
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3
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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.
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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
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4
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Tourmente M, Sanchez-Rodriguez A, Roldan ERS. Effect of Motility Factors D-Penicillamine, Hypotaurine and Epinephrine on the Performance of Spermatozoa from Five Hamster Species. BIOLOGY 2022; 11:biology11040526. [PMID: 35453725 PMCID: PMC9032960 DOI: 10.3390/biology11040526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/22/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Analysis of sperm performance under in vitro conditions provides a good indication of fertilizing potential. Parameters such as motility, swimming kinetics, acrosome integrity, or ATP content are thus examined in efforts to characterize such potential. Hamster species are a good model to study sperm parameters that are key determinants of fertilizing capacity because these species are at the higher end of the diversity of mammalian sperm morphology and performance. In vitro functional studies demand that sperm remain viable during a long period of time under conditions that resemble those in the female tract. Sperm from certain species require supplementation of the incubation medium with factors that stimulate viability and swimming, or that promote acquisition of fertilizing capacity. Molecules important for sperm performance in hamsters have been identified, namely D-penicillamine, hypotaurine and epinephrine (PHE). In the present study, we investigated the effect of PHE on spermatozoa from five hamster species incubated for up to 4 h. Our results revealed that PHE maintains sperm performance in the golden hamster, whereas it improves sperm quality in the Chinese hamster. In contrast, it does not seem to have any effect on sperm from the Siberian (Djungarian), Roborovski and Campbell’s dwarf hamsters. These results are valuable to understand the different regulatory mechanisms of sperm motility and survival in different species. Abstract Assessments of sperm performance are valuable tools for the analysis of sperm fertilizing potential and to understand determinants of male fertility. Hamster species constitute important animal models because they produce sperm cells in high quantities and of high quality. Sexual selection over evolutionary time in these species seems to have resulted in the largest mammalian spermatozoa, and high swimming and bioenergetic performances. Earlier studies showed that golden hamster sperm requires motility factors such as D-penicillamine, hypotaurine and epinephrine (PHE) to sustain survival over time, but it is unknown how they affect swimming kinetics or ATP levels and if other hamster species also require them. The objective of the present study was to examine the effect of PHE on spermatozoa of five hamster species (Mesocricetus auratus, Cricetulus griseus, Phodopus campbelli, P. sungorus, P. roborovskii). In sperm incubated for up to 4 h without or with PHE, we assessed motility, viability, acrosome integrity, sperm velocity and trajectory, and ATP content. The results showed differences in the effect of PHE among species. They had a significant positive effect on the maintenance of sperm quality in M. auratus and C. griseus, whereas there was no consistent effect on spermatozoa of the Phodopus species. Differences between species may be the result of varying underlying regulatory mechanisms of sperm performance and may be important to understand how they relate to successful fertilization.
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Affiliation(s)
- Maximiliano Tourmente
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Spanish Research Council (CSIC), 28006 Madrid, Spain;
- Centro de Biología Celular y Molecular, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Cordoba X5016GCA, Argentina
- Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Consejo Nacional de Investigaciones Científica y Técnicas (CONICET), Cordoba X5016GCA, Argentina
- Correspondence: (M.T.); (E.R.S.R.)
| | - Ana Sanchez-Rodriguez
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Spanish Research Council (CSIC), 28006 Madrid, Spain;
| | - Eduardo R. S. Roldan
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Spanish Research Council (CSIC), 28006 Madrid, Spain;
- Correspondence: (M.T.); (E.R.S.R.)
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5
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Romanenko SA, Malikov VG, Mahmoudi A, Golenishchev FN, Lemskaya NA, Pereira JC, Trifonov VA, Serdyukova NA, Ferguson-Smith MA, Aliabadian M, Graphodatsky AS. New Data on Comparative Cytogenetics of the Mouse-Like Hamsters ( Calomyscus Thomas, 1905) from Iran and Turkmenistan. Genes (Basel) 2021; 12:genes12070964. [PMID: 34202749 PMCID: PMC8304524 DOI: 10.3390/genes12070964] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
The taxonomy of the genus Calomyscus remains controversial. According to the latest systematics the genus includes eight species with great karyotypic variation. Here, we studied karyotypes of 14 Calomyscus individuals from different regions of Iran and Turkmenistan using a new set of chromosome painting probes from a Calomyscus sp. male (2n = 46, XY; Shahr-e-Kord-Soreshjan-Cheshme Maiak Province). We showed the retention of large syntenic blocks in karyotypes of individuals with identical chromosome numbers. The only rearrangement (fusion 2/21) differentiated Calomyscus elburzensis, Calomyscus mystax mystax, and Calomyscus sp. from Isfahan Province with 2n = 44 from karyotypes of C. bailwardi, Calomyscus sp. from Shahr-e-Kord, Chahar Mahal and Bakhtiari-Aloni, and Khuzestan-Izeh Provinces with 2n = 46. The individuals from Shahdad tunnel, Kerman Province with 2n = 51-52 demonstrated non-centric fissions of chromosomes 4, 5, and 6 of the 46-chromosomal form with the formation of separate small acrocentrics. A heteromorphic pair of chromosomes in a specimen with 2n = 51 resulted from a fusion of two autosomes. C-banding and chromomycin A3-DAPI staining after G-banding showed extensive heterochromatin variation between individuals.
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Affiliation(s)
- Svetlana A. Romanenko
- Institute of Molecular and Cellular Biology (IMCB), Siberian Branch of Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (N.A.L.); (V.A.T.); (N.A.S.); (A.S.G.)
- Correspondence: ; Tel.: +7-383-363-90-63
| | - Vladimir G. Malikov
- Zoological Institute (ZIN), Russian Academy of Sciences (RAS), 199034 Saint-Petersburg, Russia; (V.G.M.); (F.N.G.)
| | - Ahmad Mahmoudi
- Department of Biology, Faculty of Science, Urmia University, Urmia 5756151818, Iran;
| | - Feodor N. Golenishchev
- Zoological Institute (ZIN), Russian Academy of Sciences (RAS), 199034 Saint-Petersburg, Russia; (V.G.M.); (F.N.G.)
| | - Natalya A. Lemskaya
- Institute of Molecular and Cellular Biology (IMCB), Siberian Branch of Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (N.A.L.); (V.A.T.); (N.A.S.); (A.S.G.)
| | - Jorge C. Pereira
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 OES, UK;
| | - Vladimir A. Trifonov
- Institute of Molecular and Cellular Biology (IMCB), Siberian Branch of Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (N.A.L.); (V.A.T.); (N.A.S.); (A.S.G.)
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Natalia A. Serdyukova
- Institute of Molecular and Cellular Biology (IMCB), Siberian Branch of Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (N.A.L.); (V.A.T.); (N.A.S.); (A.S.G.)
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 OES, UK;
| | - Mansour Aliabadian
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran;
| | - Alexander S. Graphodatsky
- Institute of Molecular and Cellular Biology (IMCB), Siberian Branch of Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (N.A.L.); (V.A.T.); (N.A.S.); (A.S.G.)
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6
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Romanenko SA, Lebedev VS, Bannikova AA, Pavlova SV, Serdyukova NA, Feoktistova NY, Jiapeng Q, Yuehua S, Surov AV, Graphodatsky AS. Karyotypic and molecular evidence supports the endemic Tibetan hamsters as a separate divergent lineage of Cricetinae. Sci Rep 2021; 11:10557. [PMID: 34006914 PMCID: PMC8131748 DOI: 10.1038/s41598-021-89890-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/30/2021] [Indexed: 11/21/2022] Open
Abstract
The genus status of Urocricetus was defined recently based on morphological and molecular data. Even though the amount of evidence for a separate phylogenetic position of this genus among Cricetinae continues to increase, there is still no consensus on its relationship to other groups. Here we give the first comprehensive description of the U. kamensis karyotype (2n = 30, NFa = 50) including results of comparative cytogenetic analysis and detailed examination of its phylogenetic position by means of numerous molecular markers. The molecular data strongly indicated that Urocricetus is a distant sister group to Phodopus. Comparative cytogenetic data showed significant reorganization of the U. kamensis karyotype compared to karyotypes of all other hamsters investigated earlier. The totality of findings undoubtedly means that Urocricetus belongs to a separate divergent lineage of Cricetinae.
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Affiliation(s)
- Svetlana A Romanenko
- Institute of Molecular and Cellular Biology (IMCB), Siberian Branch of Russian Academy of Sciences (SB RAS), 8/2 Lavrentjev Ave., 630090, Novosibirsk, Russia.
| | | | - Anna A Bannikova
- Lomonosov Moscow State University, Vorobievy Gory, 119991, Moscow, Russia
| | - Svetlana V Pavlova
- A.N. Severtsov Institute of Ecology and Evolution, RAS, 119071, Moscow, Russia
| | - Natalia A Serdyukova
- Institute of Molecular and Cellular Biology (IMCB), Siberian Branch of Russian Academy of Sciences (SB RAS), 8/2 Lavrentjev Ave., 630090, Novosibirsk, Russia
| | | | - Qu Jiapeng
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, Qinghai Province, People's Republic of China
| | - Sun Yuehua
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Alexey V Surov
- A.N. Severtsov Institute of Ecology and Evolution, RAS, 119071, Moscow, Russia
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology (IMCB), Siberian Branch of Russian Academy of Sciences (SB RAS), 8/2 Lavrentjev Ave., 630090, Novosibirsk, Russia
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7
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Brekke TD, Moore EC, Campbell-Staton SC, Callahan CM, Cheviron ZA, Good JM. X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters. Genetics 2021; 218:6168998. [PMID: 33710276 DOI: 10.1093/genetics/iyab043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/16/2021] [Indexed: 11/14/2022] Open
Abstract
Embryonic development in mammals is highly sensitive to changes in gene expression within the placenta. The placenta is also highly enriched for genes showing parent-of-origin or imprinted expression, which is predicted to evolve rapidly in response to parental conflict. However, little is known about the evolution of placental gene expression, or if divergence of placental gene expression plays an important role in mammalian speciation. We used crosses between two species of dwarf hamsters (Phodopus sungorus and Phodopus campbelli) to examine the genetic and regulatory underpinnings of severe placental overgrowth in their hybrids. Using quantitative genetic mapping and mitochondrial substitution lines, we show that overgrowth of hybrid placentas was primarily caused by genetic differences on the maternally inherited P. sungorus X chromosome. Mitochondrial interactions did not contribute to abnormal hybrid placental development, and there was only weak correspondence between placental disruption and embryonic growth. Genome-wide analyses of placental transcriptomes from the parental species and first- and second-generation hybrids revealed a central group of co-expressed X-linked and autosomal genes that were highly enriched for maternally biased expression. Expression of this gene network was strongly correlated with placental size and showed widespread misexpression dependent on epistatic interactions with X-linked hybrid incompatibilities. Collectively, our results indicate that the X chromosome is likely to play a prominent role in the evolution of placental gene expression and the accumulation of hybrid developmental barriers between mammalian species.
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Affiliation(s)
- Thomas D Brekke
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA.,School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Emily C Moore
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Shane C Campbell-Staton
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA.,Department of Ecology and Evolutionary Biology; Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Colin M Callahan
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Zachary A Cheviron
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Jeffrey M Good
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
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8
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Ivanova NG, Ostromyshenskii D, Podgornaya O. Tandem Repeat-Based Probes Support the Loop Model of Pericentromere Packing. Cytogenet Genome Res 2021; 161:93-102. [PMID: 33601374 DOI: 10.1159/000513228] [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: 06/15/2020] [Accepted: 08/18/2020] [Indexed: 11/19/2022] Open
Abstract
Constitutive heterochromatin is the most mysterious part of the eukaryotic genome. It forms vital chromosome regions such as the centromeric and the pericentromeric ones. The main component of heterochromatic regions are tandem repeats (TR), and their specific organization complicates assembly, annotation, and mapping of these regions. Unannotated and unmapped TR arrays are still present in database contigs. In this study, we used a set of TR in the genomes of the pig (Sus scrofa) and the Chinese hamster (Cricetulus griseus) identified with the help of bioinformatics techniques and determined the specificity of the designed probes. The signal of the 4 pig TR probes in spermatogenic cells was often ring-shaped, especially in primary spermatocytes. The rings were located in the regions relatively weakly stained with DAPI. The unique assembly of the centromeric region was traced using the hamster meiotic chromosomes. The probe specific to chromosome 5 was used. Two signals, arranged as rings, were seen at the pachytene stage, similar to those in the pig spermatogenic cells. In the spermatogenic cells of both pig and hamster, the rings appeared on the chromosomes with pericentromeric TR probes. Our observations support the loop model of the centromeric region, the size of the loops being about 50 kb.
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Affiliation(s)
- Nadezhda G Ivanova
- Laboratory of Non-coding DNA, Institute of Cytology RAS, St. Petersburg, Russian Federation,
| | | | - Olga Podgornaya
- Laboratory of Non-coding DNA, Institute of Cytology RAS, St. Petersburg, Russian Federation.,Department of Cytology and Histology, St. Petersburg State University, St. Petersburg, Russian Federation
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9
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Bikchurina TI, Tishakova KV, Kizilova EA, Romanenko SA, Serdyukova NA, Torgasheva AA, Borodin PM. Chromosome Synapsis and Recombination in Male-Sterile and Female-Fertile Interspecies Hybrids of the Dwarf Hamsters ( Phodopus, Cricetidae). Genes (Basel) 2018; 9:genes9050227. [PMID: 29693587 PMCID: PMC5977167 DOI: 10.3390/genes9050227] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/09/2018] [Accepted: 04/18/2018] [Indexed: 02/06/2023] Open
Abstract
Hybrid sterility is an important step in the speciation process. Hybrids between dwarf hamsters Phodopus sungorus and P.campbelli provide a good model for studies in cytological and genetic mechanisms of hybrid sterility. Previous studies in hybrids detected multiple abnormalities of spermatogenesis and a high frequency of dissociation between the X and Y chromosomes at the meiotic prophase. In this study, we found that the autosomes of the hybrid males and females underwent paring and recombination as normally as their parental forms did. The male hybrids showed a significantly higher frequency of asynapsis and recombination failure between the heterochromatic arms of the X and Y chromosomes than the males of the parental species. Female hybrids as well as the females of the parental species demonstrated a high incidence of centromere misalignment at the XX bivalent and partial asynapsis of the ends of its heterochromatic arms. In all three karyotypes, recombination was completely suppressed in the heterochromatic arm of the X chromosome, where the pseudoautosomal region is located. We propose that this recombination pattern speeds up divergence of the X- and Y-linked pseudoautosomal regions between the parental species and results in their incompatibility in the male hybrids.
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Affiliation(s)
- Tatiana I Bikchurina
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Katerina V Tishakova
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Elena A Kizilova
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Svetlana A Romanenko
- Novosibirsk State University, Novosibirsk 630090, Russia.
- Institute of Cell and Molecular Biology, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
| | - Natalya A Serdyukova
- Institute of Cell and Molecular Biology, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
| | - Anna A Torgasheva
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Pavel M Borodin
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
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10
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Vieira-da-Silva A, Adega F, Guedes-Pinto H, Chaves R. LINE-1 distribution in six rodent genomes follow a species-specific pattern. J Genet 2016; 95:21-33. [PMID: 27019429 DOI: 10.1007/s12041-015-0595-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
L1 distribution in mammal's genomes is yet a huge riddle. However, these repetitive sequences were already found in all chromosomic regions, and in general, they seem to be nonrandomly distributed in the genome. It also seems that after insertion and when they are not deleterious, they are always involved in dynamic processes occurring on that particular chromosomic region. Furthermore, it seems that large-scale genome rearrangements and L1 activity and accumulation are somehow interconnected. In the present study, we analysed L1 genomic distribution in Tatera gambiana (Muridae, Gerbillinae), Acomys sp. (Muridae, Deomyinae), Cricetomys sp. (Nesomyidae, Cricetomyinae), Microtus arvalis (Cricetidae, Arvicolinae), Phodopus roborovskii and P. sungorus (Cricetidae, Cricetinae). All the species studied here seems to exhibit a species-specific pattern.Possible mechanisms, and processes involved in L1 distribution and preferential accumulation in certain regions are di scussed.
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Affiliation(s)
- A Vieira-da-Silva
- Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trάs-os-Montes and Alto Douro (UTAD), 5001, 801 Vila Real,
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11
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Ishishita S, Matsuda Y. Interspecific hybrids of dwarf hamsters and Phasianidae birds as animal models for studying the genetic and developmental basis of hybrid incompatibility. Genes Genet Syst 2016; 91:63-75. [PMID: 27628130 DOI: 10.1266/ggs.16-00022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Hybrid incompatibility is important in speciation as it prevents gene flow between closely related populations. Reduced fitness from hybrid incompatibility may also reinforce prezygotic reproductive isolation between sympatric populations. However, the genetic and developmental basis of hybrid incompatibility in higher vertebrates remains poorly understood. Mammals and birds, both amniotes, have similar developmental processes, but marked differences in development such as the XY/ZW sex determination systems and the presence or absence of genomic imprinting. Here, we review the sterile phenotype of hybrids between the Phodopus dwarf hamsters P. campbelli and P. sungorus, and the inviable phenotype of hybrids between two birds of the family Phasianidae, chicken (Gallus gallus domesticus) and Japanese quail (Coturnix japonica). We propose hypotheses for developmental defects that are associated with these hybrid incompatibilities. In addition, we discuss the genetic and developmental basis for these defects in conjunction with recent findings from mouse and avian models of genetics, reproductive biology and genomics. We suggest that these hybrids are ideal animal models for studying the genetic and developmental basis of hybrid incompatibility in amniotes.
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Affiliation(s)
- Satoshi Ishishita
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University
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Paço A, Adega F, Meštrović N, Plohl M, Chaves R. The puzzling character of repetitive DNA in Phodopus genomes (Cricetidae, Rodentia). Chromosome Res 2016; 23:427-40. [PMID: 26281779 DOI: 10.1007/s10577-015-9481-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Three novel repetitive DNA sequences are described, presenting a similar heterochromatic chromosomal location in two hamster species: Phodopus roborovskii and Phodopus sungorus (Cricetidae, Rodentia). Namely, two species-specific repetitive sequences (PROsat from P. roborovskii and PSUchr1sat from P. sungorus) surrounding a third one (PsatDNA), that is shared by both hamster genomes. Fiber-FISH analyses revealed that PROsat intermingles with PsatDNA in P. roborovskii and PSUchr1sat intermingles with PsatDNA in P. sungorus. A model explaining the evolution of this intricate chromosomal distribution is proposed, which can explain better the evolution of these very derivative genomes (in comparison to the ancestral Muroidea). The most plausible evolutionary scenario seems to be the expansion of a number of repeats into other's domain, most probably resulting in its intermingling, followed by the subsequent spread of these complex repeats from a single chromosomal location to other chromosomes. Evidences of an association between repetitive sequences and the chromosome evolution process were observed, namely for PROsat. Most probably, the evolutionary breakpoints that shaped PRO and PSU chromosomes (pericentric inversions and fusions) occurred within the boundaries of PROsat blocks in the ancestor. The repeats high diversity at the heterochromatic regions of Phodopus chromosomes, together with its complex organization, suggests that these species are important models for evolutionary studies, namely in the investigation of a possible relationship between repetitive sequences and the occurrence of chromosomal rearrangements and consequently, in genome evolution.
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Affiliation(s)
- Ana Paço
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Vila Real, Portugal
| | - Filomena Adega
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Vila Real, Portugal.,University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
| | - Nevenka Meštrović
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, HR-10002, Zagreb, Croatia
| | - Miroslav Plohl
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, HR-10002, Zagreb, Croatia
| | - Raquel Chaves
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Vila Real, Portugal. .,University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal.
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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.
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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:
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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.
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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: ;
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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.
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Affiliation(s)
- Ana Vieira-da-Silva
- Center of Agricultural and Genomics Biotechnology (CGBA), University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
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16
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Ishishita S, Tsuboi K, Ohishi N, Tsuchiya K, Matsuda Y. Abnormal pairing of X and Y sex chromosomes during meiosis I in interspecific hybrids of Phodopus campbelli and P. sungorus. Sci Rep 2015; 5:9435. [PMID: 25801302 PMCID: PMC4371188 DOI: 10.1038/srep09435] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/27/2015] [Indexed: 11/09/2022] Open
Abstract
Hybrid sterility plays an important role in the maintenance of species identity and promotion of speciation. Male interspecific hybrids from crosses between Campbell's dwarf hamster (Phodopus campbelli) and the Djungarian hamster (P. sungorus) exhibit sterility with abnormal spermatogenesis. However, the meiotic phenotype of these hybrids has not been well described. In the present work, we observed the accumulation of spermatocytes and apoptosis of spermatocyte-like cells in the testes of hybrids between P. campbelli females and P. sungorus males. In hybrid spermatocytes, a high frequency of asynapsis of X and Y chromosomes during the pachytene-like stage and dissociation of these chromosomes during metaphase I (MI) was observed. No autosomal univalency was observed during pachytene-like and MI stages in the hybrids; however, a low frequency of synapsis between autosomes and X or Y chromosomes, interlocking and partial synapsis between autosomal pairs, and γ-H2AFX staining in autosomal chromatin was observed during the pachytene-like stage. Degenerated MI-like nuclei were frequently observed in the hybrids. Most of the spermatozoa in hybrid epididymides exhibited head malformation. These results indicate that the pairing of X and Y chromosomes is more adversely affected than that of autosomes in Phodopus hybrids.
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Affiliation(s)
- Satoshi Ishishita
- Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Kazuma Tsuboi
- Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Namiko Ohishi
- Laboratory of Animal Cytogenetics, Graduate School of Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | | | - Yoichi Matsuda
- Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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17
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Hilger C, Dubey VP, Lentz D, Davril C, Revets D, Muller CP, Diederich C, De La Barrière H, Codreanu-Morel F, Morisset M, Lehners C, De PK, Hentges F. Male-specific submaxillary gland protein, a lipocalin allergen of the golden hamster, differs from the lipocalin allergens of Siberian and Roborovski dwarf hamsters. Int Arch Allergy Immunol 2015; 166:30-40. [PMID: 25765367 DOI: 10.1159/000371420] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/05/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND An increasing number of asthma cases upon exposure to hamsters and anaphylactic reactions following hamster bites are being reported, but the allergens responsible are still poorly characterized. In the Golden hamster, male-specific submaxillary gland protein (MSP), a lipocalin expressed in a sex- and tissue-specific manner in the submaxillary and lacrimal glands, is secreted in the saliva, tears and urine. The purpose of this study was to determine if MSP is an allergen, to identify IgE-reactive proteins of different hamster species and to analyse potential cross-reactivities. METHODS Fur extracts were prepared from four hamster species. Hamster-allergic patients were selected based on a history of positive IgE-test to hamster epithelium. The IgE-reactivity of patients' sera was investigated by means of immunoblot and ELISA. IgE-reactive proteins in fur extracts and the submaxillary gland were identified using anti-MSP antibodies, Edman sequencing or mass spectrometry. MSP was purified from Golden hamster and recombinant MSP was expressed in E. coli. RESULTS Four patients had IgE-antibodies against 20.5-kDa and 24-kDa proteins of Golden hamster fur extract, which were identified as MSP. IgE-reactive MSP-like proteins were detected in European hamster fur extract. Three patient sera showed IgE-reactive bands at 17-21 kDa in Siberian and Roborovski hamster fur extracts. These proteins were identified as two closely related lipocalins. Immunoblot inhibition experiments showed that they are cross-reactive and are different from MSP. CONCLUSION MSP lipocalin of the Golden hamster was identified as an allergen, and it is different from the cross-reactive lipocalin allergens of Siberian and Roborovski hamsters. Our findings highlight the need for specific tools for the in vitro and in vivo diagnosis of allergy to different hamster species.
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Affiliation(s)
- Christiane Hilger
- Departments of Infection and Immunity, Luxembourg Institute of Health, Luxembourg, Luxembourg
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18
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Tchitchek N, Safronetz D, Rasmussen AL, Martens C, Virtaneva K, Porcella SF, Feldmann H, Ebihara H, Katze MG. Sequencing, annotation and analysis of the Syrian hamster (Mesocricetus auratus) transcriptome. PLoS One 2014; 9:e112617. [PMID: 25398096 PMCID: PMC4232415 DOI: 10.1371/journal.pone.0112617] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 10/06/2014] [Indexed: 11/18/2022] Open
Abstract
Background The Syrian hamster (golden hamster, Mesocricetus auratus) is gaining importance as a new experimental animal model for multiple pathogens, including emerging zoonotic diseases such as Ebola. Nevertheless there are currently no publicly available transcriptome reference sequences or genome for this species. Results A cDNA library derived from mRNA and snRNA isolated and pooled from the brains, lungs, spleens, kidneys, livers, and hearts of three adult female Syrian hamsters was sequenced. Sequence reads were assembled into 62,482 contigs and 111,796 reads remained unassembled (singletons). This combined contig/singleton dataset, designated as the Syrian hamster transcriptome, represents a total of 60,117,204 nucleotides. Our Mesocricetus auratus Syrian hamster transcriptome mapped to 11,648 mouse transcripts representing 9,562 distinct genes, and mapped to a similar number of transcripts and genes in the rat. We identified 214 quasi-complete transcripts based on mouse annotations. Canonical pathways involved in a broad spectrum of fundamental biological processes were significantly represented in the library. The Syrian hamster transcriptome was aligned to the current release of the Chinese hamster ovary (CHO) cell transcriptome and genome to improve the genomic annotation of this species. Finally, our Syrian hamster transcriptome was aligned against 14 other rodents, primate and laurasiatheria species to gain insights about the genetic relatedness and placement of this species. Conclusions This Syrian hamster transcriptome dataset significantly improves our knowledge of the Syrian hamster's transcriptome, especially towards its future use in infectious disease research. Moreover, this library is an important resource for the wider scientific community to help improve genome annotation of the Syrian hamster and other closely related species. Furthermore, these data provide the basis for development of expression microarrays that can be used in functional genomics studies.
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Affiliation(s)
- Nicolas Tchitchek
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - David Safronetz
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Angela L Rasmussen
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Craig Martens
- Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Kimmo Virtaneva
- Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Hideki Ebihara
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Michael G Katze
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America; Washington National Primate Research Center, University of Washington, Seattle, Washington, United States of America
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Paço A, Adega F, Meštrović N, Plohl M, Chaves R. Evolutionary story of a satellite DNA from Phodopus sungorus (Rodentia, Cricetidae). Genome Biol Evol 2014; 6:2944-55. [PMID: 25336681 PMCID: PMC4224359 DOI: 10.1093/gbe/evu233] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2014] [Indexed: 12/23/2022] Open
Abstract
With the goal to contribute for the understanding of satellite DNA evolution and its genomic involvement, in this work it was isolated and characterized the first satellite DNA (PSUcentSat) from Phodopus sungorus (Cricetidae). Physical mapping of this sequence in P. sungorus showed large PSUcentSat arrays located at the heterochromatic (peri)centromeric region of five autosomal pairs and Y-chromosome. The presence of orthologous PSUcentSat sequences in the genomes of other Cricetidae and Muridae rodents was also verified, presenting however, an interspersed chromosomal distribution. This distribution pattern suggests a PSUcentSat-scattered location in an ancestor of Muridae/Cricetidae families, that assumed afterwards, in the descendant genome of P. sungorus a restricted localization to few chromosomes in the (peri)centromeric region. We believe that after the divergence of the studied species, PSUcentSat was most probably highly amplified in the (peri)centromeric region of some chromosome pairs of this hamster by recombinational mechanisms. The bouquet chromosome configuration (prophase I) possibly displays an important role in this selective amplification, providing physical proximity of centromeric regions between chromosomes with similar size and/or morphology. This seems particularly evident for the acrocentric chromosomes of P. sungorus (including the Y-chromosome), all presenting large PSUcentSat arrays at the (peri)centromeric region. The conservation of this sequence in the studied genomes and its (peri)centromeric amplification in P. sungorus strongly suggests functional significance, possibly displaying this satellite family different functions in the different genomes. The verification of PSUcentSat transcriptional activity in normal proliferative cells suggests that its transcription is not stage-limited, as described for some other satellites.
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Affiliation(s)
- Ana Paço
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro (IBB/CGBUTAD), Vila Real, Portugal
| | - Filomena Adega
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro (IBB/CGBUTAD), Vila Real, Portugal Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Nevenka Meštrović
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Miroslav Plohl
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Raquel Chaves
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro (IBB/CGBUTAD), Vila Real, Portugal Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
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Arslan A, Zima J. Karyotypes of the mammals of Turkey and neighbouring regions: a review. FOLIA ZOOLOGICA 2014. [DOI: 10.25225/fozo.v63.i1.a1.2014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Atilla Arslan
- Department of Biology, Faculty of Science, Selçuk University, 42031 Konya, Turkey
| | - Jan Zima
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Květná 8, 603 65 Brno, Czech Republic
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Jayapal KP, Goudar CT. Transcriptomics as a tool for assessing the scalability of mammalian cell perfusion systems. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 139:227-43. [PMID: 23949697 DOI: 10.1007/10_2013_239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
DNA microarray-based transcriptomics have been used to determine the time course of laboratory and manufacturing-scale perfusion bioreactors in an attempt to characterize cell physiological state at these two bioreactor scales. Given the limited availability of genomic data for baby hamster kidney (BHK) cells, a Chinese hamster ovary (CHO)-based microarray was used following a feasibility assessment of cross-species hybridization. A heat shock experiment was performed using both BHK and CHO cells and resulting DNA microarray data were analyzed using a filtering criteria of perfect match (PM)/single base mismatch (MM) > 1.5 and PM-MM > 50 to exclude probes with low specificity or sensitivity for cross-species hybridizations. For BHK cells, 8910 probe sets (39 %) passed the cutoff criteria, whereas 12,961 probe sets (56 %) passed the cutoff criteria for CHO cells. Yet, the data from BHK cells allowed distinct clustering of heat shock and control samples as well as identification of biologically relevant genes as being differentially expressed, indicating the utility of cross-species hybridization. Subsequently, DNA microarray analysis was performed on time course samples from laboratory- and manufacturing-scale perfusion bioreactors that were operated under the same conditions. A majority of the variability (37 %) was associated with the first principal component (PC-1). Although PC-1 changed monotonically with culture duration, the trends were very similar in both the laboratory and manufacturing-scale bioreactors. Therefore, despite time-related changes to the cell physiological state, transcriptomic fingerprints were similar across the two bioreactor scales at any given instance in culture. Multiple genes were identified with time-course expression profiles that were very highly correlated (> 0.9) with bioprocess variables of interest. Although the current incomplete annotation limits the biological interpretation of these observations, their full potential may be realized in due course when richer genomic data become available. By taking a pragmatic approach of transcriptome fingerprinting, we have demonstrated the utility of systems biology to support the comparability of laboratory and manufacturing-scale perfusion systems. Scale-down model qualification is the first step in process characterization and hence is an integral component of robust regulatory filings. Augmenting the current paradigm, which relies primarily on cell culture and product quality information, with gene expression data can help make a substantially stronger case for similarity. With continued advances in systems biology approaches, we expect them to be seamlessly integrated into bioprocess development, which can translate into more robust and high yielding processes that can ultimately reduce cost of care for patients.
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Affiliation(s)
- Karthik P Jayapal
- Cell Culture Development, Global Biological Development Bayer HealthCare, 800 Dwight Way, Berkeley, CA, 94710, USA
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22
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Romanenko SA, Lebedev VS, Serdukova NA, Feoktistova NY, Surov AV, Graphodatsky AS. Comparative cytogenetics of hamsters of the genus Allocricetulus argyropulo 1932 (Cricetidae, Rodentia). Cytogenet Genome Res 2013; 139:258-66. [PMID: 23328385 DOI: 10.1159/000346194] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2012] [Indexed: 11/19/2022] Open
Abstract
Chromosome painting and G-banding analyses were used to delimit homologous chromosomal segments among 4 taxa of the hamsters genus Allocricetulus Argyropulo 1932 (Cricetidae, Murоidea, Rodentia)--A. curtatus (2n = 20), A. eversmanni eversmanni, A. eversmanni pseudocurtatus, and the hybrid A. eversmanni beljaevi × A. eversmanni pseudocurtatus (all 2n = 26). Comparative maps between the 4 karyotypes were established based on chromosome painting of chromosome-specific probes from the Syrian hamster (Mesocricetus auratus, 2n = 44). A putative ancestral karyotype for the genus Allocricetulus (AAK) was proposed and contains 12-13 ancestral autosomal elements. Integrated maps demonstrate extended conservation of syntenies within this rodent genus and show the predominant role of Robertsonian rearrangements in the karyotype evolution of the genus Allocricetulus. At the cytogenetic level, we clearly demonstrate karyological differences between karyotypes of species (A. curtatus vs. A. eversmanni) and subspecies A. e. eversmanni and A. e. beljaevi versus A. e. pseudocurtatus, but the karyotypes of A. e. eversmanni and A. e. beljaevi are identical at this level of resolution.
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Affiliation(s)
- S A Romanenko
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia.
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Solovjeva LV, Demin SJ, Pleskach NM, Kuznetsova MO, Svetlova MP. Characterization of telomeric repeats in metaphase chromosomes and interphase nuclei of Syrian Hamster Fibroblasts. Mol Cytogenet 2012; 5:37. [PMID: 22938505 PMCID: PMC3488537 DOI: 10.1186/1755-8166-5-37] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 06/29/2012] [Indexed: 11/10/2022] Open
Abstract
Background Rodents have been reported to contain large arrays of interstitial telomeric sequences (TTAGGG)n (ITS) located in pericentromeric heterochromatin. The relative sizes of telomeric sequences at the ends of chromosomes (TS) and ITS in Syrian hamster (Mesocricetus auratus) cells have not been evaluated yet, as well as their structural organization in interphase nuclei. Results FISH signal distribution analysis was performed on DAPI-banded metaphase chromosomes of Syrian hamster fibroblasts, and relative lengths of telomere signals were estimated. Besides well-distinguished FISH signals from ITS located on chromosomes ##2, 4, 14, 20 and X that we reported earlier, low-intensity FISH signals were visualized with different frequency of detection on all other metacentric chromosomes excluding chromosome #21. The analysis of 3D-distribution of TS in interphase nuclei demonstrated that some TS foci formed clearly distinguished associations (2–3 foci in a cluster) in the nuclei of cells subjected to FISH or transfected with the plasmid expressing telomeric protein TRF1 fused with GFP. In G0 and G1/early S-phase, the average total number of GFP-TRF1 foci per nucleus was less than that of PNA FISH foci in the corresponding cell cycle phases suggesting that TRF1 overexpression might contribute to the fusion of neighboring telomeres. The mean total number of GFP-TRF1 and FISH foci per nucleus was increased during the transition from G0 to G1/early S-phase that might be the consequence of duplication of some TS. Conclusions The relative lengths of TS in Syrian hamster cells were found to be moderately variable. All but one metacentric chromosomes contain ITS in pericentromeric heterochromatin indicating that significant rearrangements of ancestral genome occurred in evolution. Visualization of GFP-TRF1 fibrils that formed bridges between distinct telomeric foci allowed suggesting that telomere associations observed in interphase cells are reversible. The data obtained in the study provide the further insight in the structure and dynamics of telomeric sequences in somatic mammalian cells.
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Chaves R, Louzada S, Meles S, Wienberg J, Adega F. Praomys tullbergi (Muridae, Rodentia) genome architecture decoded by comparative chromosome painting with Mus and Rattus. Chromosome Res 2012; 20:673-83. [PMID: 22847644 DOI: 10.1007/s10577-012-9304-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/28/2012] [Accepted: 06/29/2012] [Indexed: 11/25/2022]
Abstract
The order Rodentia and in particular the Muridae are characterised by extremely high rates of chromosome evolution and remarkable chromosome diversity. The Praomys group (Murinae, Muridae and Rodentia) constitutes a diverse and abundant group divided into two complexes, the jacksoni complex and the tullbergi complex which includes the species Praomys tullbergi. Comparative chromosome painting using the two index genomes, Mus musculus and Rattus norvegicus, was performed resulting in a high resolution chromosome map for P. tullbergi. The combined use of rat and mouse probes and the assistance of the assembly of all the available sequencing data from Ensembl genome browser allowed a great dissection of P. tullbergi genome, the detection of inversion events and ultimately the refinement of P. tullbergi comparative map. A key achievement was the reconstruction of a high precision Muroidea ancestral karyotype (Muridae/Cricetidae and Murine) based in a broad species analysis combining previous reported comparative maps together with the presented data. This permitted the reconstruction of the evolutionary history of chromosome changes since the ancestral Muroidea genome and enlightened the phylogenetic relationships with the related species mouse and rat. The analysis of constitutive heterochromatin and its co-localisation with the identified evolutionary breakpoints regions was performed suggesting the involvement of repetitive sequences in the chromosome rearrangements that originated the present P. tullbergi genome architecture.
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Affiliation(s)
- Raquel Chaves
- Centre of Genomics and Biotechnology, Institute for Biotechnology and Bioengineering, University of Trás-os-Montes and Alto Douro (IBB/CGB-UTAD), Vila Real, Portugal.
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Romanenko SA, Perelman PL, Trifonov VA, Graphodatsky AS. Chromosomal evolution in Rodentia. Heredity (Edinb) 2012; 108:4-16. [PMID: 22086076 PMCID: PMC3238120 DOI: 10.1038/hdy.2011.110] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 10/06/2011] [Accepted: 10/07/2011] [Indexed: 11/08/2022] Open
Abstract
Rodentia is the most species-rich mammalian order and includes several important laboratory model species. The amount of new information on karyotypic and phylogenetic relations within and among rodent taxa is rapidly increasing, but a synthesis of these data is currently lacking. Here, we have integrated information drawn from conventional banding studies, recent comparative painting investigations and molecular phylogenetic reconstructions of different rodent taxa. This permitted a revision of several ancestral karyotypic reconstructions, and a more accurate depiction of rodent chromosomal evolution.
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Affiliation(s)
- S A Romanenko
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia.
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Graphodatsky AS, Trifonov VA, Stanyon R. The genome diversity and karyotype evolution of mammals. Mol Cytogenet 2011; 4:22. [PMID: 21992653 PMCID: PMC3204295 DOI: 10.1186/1755-8166-4-22] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 10/12/2011] [Indexed: 01/30/2023] Open
Abstract
The past decade has witnessed an explosion of genome sequencing and mapping in evolutionary diverse species. While full genome sequencing of mammals is rapidly progressing, the ability to assemble and align orthologous whole chromosome regions from more than a few species is still not possible. The intense focus on building of comparative maps for companion (dog and cat), laboratory (mice and rat) and agricultural (cattle, pig, and horse) animals has traditionally been used as a means to understand the underlying basis of disease-related or economically important phenotypes. However, these maps also provide an unprecedented opportunity to use multispecies analysis as a tool for inferring karyotype evolution. Comparative chromosome painting and related techniques are now considered to be the most powerful approaches in comparative genome studies. Homologies can be identified with high accuracy using molecularly defined DNA probes for fluorescence in situ hybridization (FISH) on chromosomes of different species. Chromosome painting data are now available for members of nearly all mammalian orders. In most orders, there are species with rates of chromosome evolution that can be considered as 'default' rates. The number of rearrangements that have become fixed in evolutionary history seems comparatively low, bearing in mind the 180 million years of the mammalian radiation. Comparative chromosome maps record the history of karyotype changes that have occurred during evolution. The aim of this review is to provide an overview of these recent advances in our endeavor to decipher the karyotype evolution of mammals by integrating the published results together with some of our latest unpublished results.
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Beklemisheva VR, Romanenko SA, Biltueva LS, Trifonov VA, Vorobieva NV, Serdukova NA, Rubtsova NV, Brandler OV, O'Brien PCM, Yang F, Stanyon R, Ferguson-Smith MA, Graphodatsky AS. Reconstruction of karyotype evolution in core Glires. I. The genome homology revealed by comparative chromosome painting. Chromosome Res 2011; 19:549-65. [PMID: 21559983 DOI: 10.1007/s10577-011-9210-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 04/20/2011] [Accepted: 04/25/2011] [Indexed: 11/25/2022]
Abstract
Glires represent a eutherian clade consisting of rodents and lagomorphs (hares, rabbits, and pikas). Chromosome evolution of Glires is known to have variable rates in different groups: from slowly evolving lagomorphs and squirrels to extremely rapidly evolving muroids. Previous interordinal homology maps between slowly evolving Glires were based on comparison with humans. Here, we used sets of chromosome-specific probes from Tamias sibiricus (Sciuridae), Castor fiber (Castoridae) and humans to study karyotypes of six ground squirrels (genera Marmota and Spermophilus) and one tree squirrel (genus Sciurus), mountain hare (genus Lepus), and rabbit (genus Oryctolagus). These data supplemented with GTG banding comparisons allowed us to build comparative chromosome maps. Our data showed the absence of previously found squirrel associations HSA 1/8 and 2/17 in the Eurasian ground squirrels--sousliks and woodchucks, and disruptions of squirrel HSA 10/13 and HSA 8/4/8/12/22 syntenies in the four Spermophilus species studied here. We found that the karyotypes of Sciuridae and Leporidae are highly conserved and close to the Rodentia ancestral karyotype, while Castoridae chromosomes underwent many more changes. We suggest that Lagomorpha and Sciuridae (in contrast to all other rodent families) should be considered as core Glires lineages, characterized by cytogenetically conserved karyotypes which contain chromosomal elements inherent to karyotype of common Glires ancestor. Our data allowed us to further refine the putative ancestral karyotypes of Rodentia. We also describe here the putative ancestral karyotypes of Glires and lagomorphs.
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Affiliation(s)
- Violetta R Beklemisheva
- Department of Molecular and Cellular Biology of the Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, 630090, Russia
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Trifonov VA, Kosyakova N, Romanenko SA, Stanyon R, Graphodatsky AS, Liehr T. New insights into the karyotypic evolution in muroid rodents revealed by multicolor banding applying murine probes. Chromosome Res 2010; 18:265-75. [PMID: 20127166 DOI: 10.1007/s10577-010-9110-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Accepted: 01/05/2010] [Indexed: 01/13/2023]
Abstract
Muroid rodents are composed of a wide range of species characterized by extensive karyotypic evolution. Even if this group includes such important laboratory animal models as domestic mouse (Mus musculus), Norway rat (Rattus norvegicus), Chinese hamster (Cricetulus griseus), and golden hamster (Mesocricetus auratus), comparative cytogenetic studies between rodents are difficult due to the characteristic rapid karyotypic evolution. Molecular cytogenetic methods can help resolve problems of comparing muroid chromosomes. Here, we used cross-species comparative multicolour banding with probes obtained from mouse chromosomes 3, 6, 18, and 19 to study the karyotypes of nine muroid species from the three subfamilies Murinae, Cricetinae, and Arvicolinae. Results from multicolour banding with these murine probes (mcb) allowed us to improve the comparative homology maps between these species and to obtain new insights into their karyotypic evolution. We identified evolutionary conserved chromosomal breakpoints and revealed four previously unrecognized homologous segments, four inversions, and 14 evolutionary new centromeres in the nine muroid species studied. We found Mus apomorphic rearrangements, not seen in other muroids, and defined several subfamily specific chromosome breaks, characteristic for Arvicolinae and Cricetinae. We show that mcb libraries are an effective tool both for the cytogenetic characterisation of important laboratory models such as the rat and hamster as well as elucidating the complex phylogenomics relationships of muroids.
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Affiliation(s)
- Vladimir A Trifonov
- Molecular and Cellular Biology Department, Institute of Chemical Biology and Fundamental Medicine, Scapital VE, Cyrillic RAS, Novosibirsk, Russia.
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Divergent patterns of breakpoint reuse in Muroid rodents. Mamm Genome 2009; 21:77-87. [PMID: 20033182 DOI: 10.1007/s00335-009-9242-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 11/09/2009] [Indexed: 01/09/2023]
Abstract
Multiple Genome Rearrangement (MGR) analysis was used to define the trajectory and pattern of chromosome rearrangement within muroid rodents. MGR was applied using 107 chromosome homologies between Mus, Rattus, Peromyscus, the muroid sister taxon Cricetulus griseus, and Sciurus carolinensis as a non-Muroidea outgroup, with specific attention paid to breakpoint reuse and centromere evolution. This analysis revealed a high level of chromosome breakpoint conservation between Rattus and Peromyscus and indicated that the chromosomes of Mus are highly derived. This analysis identified several conserved evolutionary breakpoints that have been reused multiple times during karyotypic evolution in rodents. Our data demonstrate a high level of reuse of breakpoints among muroid rodents, further supporting the "Fragile Breakage Model" of chromosome evolution. We provide the first analysis of rodent centromeres with respect to evolutionary breakpoints. By analyzing closely related rodent species we were able to clarify muroid rodent karyotypic evolution. We were also able to derive several high-resolution ancestral karyotypes and identify rearrangements specific to various stages of Muroidea evolution. These data were useful in further characterizing lineage-specific modes of chromosome evolution.
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Abstract
The evolution of karyotypes has been the subject of intensive study since the middle of the 20th century. This was motivated by the observation that the karyotypes of related species showed remarkable conservation. The recent emergence of whole-genome sequencing projects gives the opportunity to complement the cytogenetic approaches by addressing the conservation of karyotypes using chromosome sequence comparison. In this short review we present a description of recent advances in computational biology methods dedicated to the study of chromosome evolution and more specifically ancestral karyotype reconstruction in an attempt to provide an integrated overview of both cytogenetic and computational approaches.
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Chromosomal phylogeny of four Akodontini species (Rodentia, Cricetidae) from southern Brazil established by Zoo-FISH using Mus musculus (Muridae) painting probes. Chromosome Res 2008; 16:75-88. [PMID: 18293106 DOI: 10.1007/s10577-007-1211-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We established chromosome homology maps between Mus musculus (MMU) and five species of the Akodontini tribe, Akodon cursor (2n = 14, 15 and 16), A. montensis (2n = 24), A. paranaensis (2n = 44), A. serrensis (2n = 46) and Oligoryzomys flavescens (2n = 66) by Zoo-FISH (fluorescence in situ hybridization) using mouse chromosome-specific probes. The aims of this study were (1) to detect the chromosomal rearrangements responsible for the karyotype variation in this tribe and (2) to reconstruct the phylogenetic relationships among these species. We observed four common syntenic associations of homologous chromosome segments, of which the MMU 7/19 has been described previously in other rodents from Africa, Asia and Europe, and might represent a phylogenetic link between the Old World and Neotropical rodents. The remaining three associations (3/18, 6/12 and 8/13) have been observed exclusively in Neotropical rodents so far, which at present can be considered synapomorphic traits of this group. Five further mouse chromosomes (MMU 4, 9, 14, 18 and 19) were each found evolutionarily conserved as a separate syntenic unit. Our phylogenetic analysis using parsimony and heuristic search detected one consistent group, separating the Akodontini from other rodents.
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Williams GA, Jacobs GH. Absence of functional short-wavelength sensitive cone pigments in hamsters (Mesocricetus). J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2008; 194:429-39. [PMID: 18259758 DOI: 10.1007/s00359-008-0316-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 01/17/2008] [Accepted: 01/19/2008] [Indexed: 11/28/2022]
Abstract
Studies of Syrian golden hamsters (Mesocricetus auratus) have yielded contradictory evidence as to whether the retina of this species supports a population of cones containing short-wavelength sensitive pigments. We undertook a re-examination of this issue by (a) measuring lens transmission, (b) determining complete spectral sensitivity functions using electroretinogram (ERG) flicker photometry, (c) employing a sensitive chromatic-adaptation paradigm in conjunction with ERG measurements to conduct a specific search for the presence of a short-wavelength sensitive mechanism, and (d) assaying for the presence of retinal mRNA using real-time, reverse transcription polymerase chain reactions (RT-PCR). Parallel measurements were made on Turkish hamster (Mesocricetus brandtii) and control measurements were derived from recordings made on a rodent whose retina is known to contain a population of short-wavelength sensitive cones (the rat, Rattus norvegicus). Although UV opsin transcripts can be detected in the retina of the Syrian hamster, the electrophysiological measurements imply that these are not translated. Syrian hamsters thus lack a functional short-wavelength sensitive pigment, and that seems also true for the Turkish hamster. Members of this genus belong to a disparate group of mammals that have lost function of their short-wavelength sensitive cone pigments through ancestral opsin gene mutations.
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Affiliation(s)
- Gary A Williams
- Neuroscience Research Institute and Department of Psychology, University of California, Santa Barbara, CA 93106, USA
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Sitnikova NA, Romanenko SA, O'Brien PCM, Perelman PL, Fu B, Rubtsova NV, Serdukova NA, Golenishchev FN, Trifonov VA, Ferguson-Smith MA, Yang F, Graphodatsky AS. Chromosomal evolution of Arvicolinae (Cricetidae, Rodentia). I. The genome homology of tundra vole, field vole, mouse and golden hamster revealed by comparative chromosome painting. Chromosome Res 2007; 15:447-56. [PMID: 17497247 DOI: 10.1007/s10577-007-1137-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Revised: 03/28/2007] [Accepted: 03/28/2007] [Indexed: 10/23/2022]
Abstract
Cross-species chromosome painting has become the mainstay of comparative cytogenetic and chromosome evolution studies. Here we have made a set of chromosomal painting probes for the field vole (Microtus agrestis) by DOP-PCR amplification of flow-sorted chromosomes. Together with painting probes of golden hamster (Mesocricetus auratus) and mouse (Mus musculus), the field vole probes have been hybridized onto the metaphases of the tundra vole (Microtus oeconomus). A comparative chromosome map between these two voles, golden hamster and mouse has been established based on the results of cross-species chromosome painting and G-banding comparisons. The sets of paints from the field vole, golden hamster and mouse identified a total of 27, 40 and 47 homologous autosomal regions, respectively, in the genome of tundra vole; 16, 41 and 51 fusion/fission rearrangements differentiate the karyotype of the tundra vole from the karyotypes of the field vole, golden hamster and mouse, respectively.
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