icacgm18th International Colloquim of Animal Cytogenetics and Gene Mapping 2008

Session IV - Karyotype Evolution and Comparative Genomics


Phylogenomics, ancestral karyotypes and the effects of lineage sorting in constructing chromosomal phylogenies: contributions from chromosome painting and genome sequence assemblies

T.J. Robinson (1) and A.Ruiz-Herrera (2)

1. Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch (South Africa);
2. Laboratorio di Biologia Cellulare e Molecolare, Dipartimento di Genetica e Microbiologia, Universita’ degli Studi di Pavia, via Ferrata 1, Pavia (Italy)

The need to distinguish between chromosomal characters that are symplesiomorphic and those that define monophyletic groups has placed significant constraints on resolving the deeper nodes of the eutherian tree (specifically Afrotheria and Xenarthra) since cross-species chromosome painting (Zoo-Flourescence in situ hybridization, Zoo-FISH) to marsupials, the appropriate outgroup, is not possible. However, with the advent of complete genome assemblies for several vertebrates including the opossum and chicken, it is now possible to view the chromosomal characters that have been proposed as defining basal karyotypes in the context of their presence in an outgroup. We have screened genomic assemblies of the two eutherian outgroup species, the opossum and chicken, for the presence/absence of the conserved chromosomes and syntenic associations hypothesized to be present in the eutherian ancestral karyotype as well as in Afrotheria and Xenarthra. We show among others, that many of the primitive chromosomal states defining the eutherian ancestral karyotype are symplesiomorphies whereas only synapomorphic similarity is indicative of monophyly within an organismal phylogeny. For example, in terms of chromosomal characters thought to underpin Afrotheria, which is often basal in phylogenetic analysis of large nuclear gene data sets, we show that the HSA 1/19p synteny is currently ambiguous, but that the junction, likely 1(p)/19p, is probably a shared synteny for Atlantogenata (Afrotheria + Xenarthra). In addition, the HSA 3p/21 synteny was present in the amniote ancestor (i.e., common to turtles, lepidosaurs, crocodilians, birds and mammals) and its expansion to include HSA 5 validates the HSA 3/21/5 synteny that defines the monophyly of Afrotheria. Its fission into two segments (HSA 3p/21 + HSA 5/21) is probably shared by all Paenungulata.


Chromosome Evolution in Bovids as revealed by comparative banding and FISH-mapping techniques

Leopoldo Iannuzzi

National Research Council (CNR), Institute of Animal Production Systems in Mediterranean Environments (ISPAAM), Laboratory of Animal Cytogenetics and Gene Mapping, Naples (Italy)

Chromosomes are widely considered very important biological material to study the evolution of species. Indeed, the most important mutations which have differentiated species during their evolution have been accumulated at chromosomal level. The Bovidae (order Cetartiodactyla, sub-order Ruminantia) are a very interesting family for studying the karyotype evolution of species. The family includes 123 species and 45 extant genera grouped into nine subfamilies: Bovinae, Caprinae, Hippotraginae, Reduncinae, Alcelaphinae, Antilopinae, Cephalophinae, Aepycerotinae and Peleinae. The chromosomal changes that have occurred in this family can be grouped into four levels of differentiation: autosomes, gonosomes, nucleolus organizer chromosomes (NOCs) and heterochromatin. Comparative studies using conventional stained preparations and later applying both chromosome banding and FISH-mapping techniques have reached the following conclusions: (a) while the diploid number varies between 30 to 60, the fundamental number (FN) most often varies between 58 to 62, with the exception of 3 species (Tetracerus quadricornis, Rhyncotragus kirki, Gazella thomsoni); (b) the reduction in diploid number has been accompanied by the formation of biarmed autosomes originating from centric fusion translocations (CFs) followed by loss of constitutive heterochromatin (and specific Satellite-DNA); (c) acrocentric autosomes (or chromosome arms) are conserved among all species; (d) "bovine" and "caprine" chromosomes 9 and 14 differ in a pericentromeric region translocated from "bovine" chromosome 9 to "caprine" chromosome 14 by a simple translocation event, thus differentiating both chromosomes in the two subfamilies; (e) sex chromosomes have undergone complex evolution that has resulted in changes of morphology (due to the centromere position), size (due to heterochromatin variation) and gene order (due to chromosome transposition or inversions); (f) NORs are often present at the telomeres of different (non-homologous) chromosomes in many species, although NO-chromosomes are generally homologous among species belonging to the same genus; (g) sex chromosomes are fused with autosomes in some species; (h) the Bovinae sub-family appears ancestral to the remaining sub-families; indeed, X-bovine type and bovine chromosomes 9 and 14 are only present in this subfamily, while X-caprine type and caprine chromosomes 9 and 14 are present in the remaining subfamilies. This has also been confirmed by comparison with species of other families (Cervidae) and with humans (same conserved syntenies between bovine chromosome 9 and HSA6q).


A cytogenetic investigation on the yak (Bos grunniens) reared in central Italy

Davide Nicodemo (1), Alfredo Pauciullo (1), Alberto Castello (2), Gianfranco Cosenza (1) , Vincenzo Peretti (3), Angela Perucatti (4), Giulia Pia Di Meo (4) , Ficco G (5), Luigi Ramunno (1), Leopoldo Iannuzzi (4) , Jiri Rubes (6), Dino Di Berardino (1)

1. Department of Soil, Plant, Environment and Animal Production Sciences, University of Naples "Federico II", Portici (Italy);
2. Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Cientificas, Madrid, (Espana);
3. Department of Animal Science and Food Inspection,University of Naples "Federico II", Naples, (Italy);
4. Research National Council (CNR), ISPAAM, Laboratory of Animal Cytogenetics and Gene mapping, Naples (Italy);
5. CRA-PCM, Research Center for the production of meat and Genetic improvement, Monterotondo (Italy);
6. Veterinary Research Institute, Brno (Czech Republic).

The domestic yak (Bos grunniens) is an important Bovidae species which in Asia plays a remarkable role for the economy of the Tibetan high lands (over the 4.000 m.a.s.). Despite its strategical and economical importance, this species has been nearly neglected, in so far, from a cytogenetic point of view, as demonstrated by the few papers present in the literature. To fill this gap, we undertook a cytogenetic investigation by using blood samples of eight yak bulls recently imported in central Italy. C- G- R-banding , silver staining and FISH-techniques were applied. The preliminary results were as follows: (a) the chromosomal make-up of the yak was 2n=60,XY, (b) the animals investigated showed normal karyotype,(c) the frequency of chromosome/chromatid breaks was similar to that of cattle (3.7 vs 3.0 %, respectively), (d) the mean rate of SCE/cell at 10 µg/ml (f.c.) was significantly (P<0,001) lower compared to that of cattle (5,2 vs 8,3, respectively), (e) the GTG-RBA-RBG banding patterns -at the 400 bands level of resolution- did not reveal structural differences compared to cattle, (f) the CBA-banding pattern was also similar to cattle, i.e. no C-bands on the subcentromeric X , while the Y- chromosome showed heterochromatic tips in the short arms. Zoo-FISH with bovine painting probes derived from microdissected chromosomes 5-X-Xcen and Y- upon yak metaphase chromosomes showed complete hybridization, thus confirming the close homology between the two species. In addition, FISH-mapping with bovine BAC-clones containing ZFY and SRY genes to the yak Y-chromosome also revealed the same localization as reported in cattle (Yp12.2 and Yq23dist, respectively). However, the fact that Bos taurus x Bos grunniens F1 male hybrids are sterile, while the females are normally fertile, suggests that the main difference between yak and cattle might be in the X-Y pseudoautosomal (PAR) region of the two species. Further investigation, therefore, is necessary with more effective cytogenetic techniques, such as high resolution banding, fine gene mapping analysis and DNA sequencing.


Molecular cytogenetic maps of turkey, duck and zebra finch and their implications for genome evolution

K. E. Fowler (1), B. M. Skinner (1), L. B. W. Robertson (2), H. G. Tempest (3), M. Völker (1), D. K. Griffin (1)

1. Department of Biosciences, University of Kent, Canterbury, Kent, (UK)
2. Bridge Genoma, London Bioscience Innovation Centre, London, (UK)
3. Department of Medical Genetics, University of Calgary, Calgary, (Canada)

Comparative genomics allows the transfer of genomic information from a well characterised genome to one that is less well understood. In birds, most comparative genomics to date has been with reference to the chicken, an important model organism and the only bird with a published genome sequence. Comparative chromosome painting studies have demonstrated that inter-chromosomal rearrangements in birds are rare. Higher resolution studies involving the hybridisation of chicken BAC clones have allowed comparative physical maps to be created. These provide information on the intra-chromosomal rearrangements through evolution. Here, we report the current state of the art in comparative physical mapping in birds and the insights it provides on genome evolution. Comparative maps have been generated for the turkey (Meleagris gallopavo) and for duck (Anas platyrhynchos). We have also successfully mapped chicken clones to the Zebra Finch (Taeniopygia guttata) as a prelude to the generation of a comparative map. Breakpoint mapping using FISH and microarrays suggests that, in birds, fusions and fissions (but not inversions) have occurred at ancestral centromeres.


Karyotypic relationships among Asiatic asses (kulan and kiang) and domestic horse defined using horse chromosome arm-specific probes

P. Musilova (1), S. Kubickova (1), P. Horin (2), R. Vodicka (3), J. Rubes (1)

1. Veterinary Research Institute, Brno (Czech Republic);
2. Faculty of Veterinary Medicine, Brno (Czech Republic);
3. The Prague Zoological Garden, Prague (Czech Republic)

The set of horse chromosome arm-specific probes were hybridized onto chromosomes of Equus hemionus kulan (2n=54) and E. kiang (2n=52) in order to establish a genome-wide chromosomal correspondence among Asiatic asses and horse. Our results and results of comparative mapping in E. h. onager (2n=56) demonstrate that karyotype of kulan differs from that of onager only by a centric fission of chromosome homologous to horse chromosome (ECA) 2q/3q. This fusion/fission causes chromosome number polymorphism in several Equids including kulan and onager. Furthermore, results of comparative painting provide evidence for a very close karyotypic relationship between kulan and kiang. In fact, only four kiang chromosomes differ from kulan chromosomes. These four kiang chromosomes can be rearranged from five kulan chromosomes through one centric fission (ECA 2q/3q) and two fusions (ECA 8q/15 and ECA 7/25). The other twenty-one autosomes are entirely homologous in these two species. Comparative chromosome painting in kiang completed efforts to establish chromosomal homologies in family Equidae.


Multispecies comparative immunogenomics: TRG loci as markers in reconstructing the evolutionary pathway from ancestral to modern mammal genomes

S Massari (2) , G Vaccarelli (3), MC Miccoli (3), MP Lefranc (1), R Antonacci (3), S Ciccarese (3)

1. IMGT®, LIGM, Montpellier Cedex 5 (France);
2. DISTEBA, University of Salento, Lecce (Italy);
3. DIGEMI, University of Bari (Italy)

The paradigm of γδ high (artiodactyls and chickens) and γδ low (human and mice) species is still unresolved. Previous comparative analyses defined the peculiarity of the organization of ovine and bovine T cell receptor gamma (TRG1 and TRG2) loci in cassettes, each containing the basic recombinational unit. The two TRG loci in cattle and sheep as compared to the single human locus revealead that Bovidae and human loci, although not correlated in general structure, share extensive colinearity in the regulatory and intergenic as well as in the coding regions. On the other hand the phylogenetic conservation of the nine enhancer-like elements found in ovine and bovine compared with the single copy present in the human indicates that they play a key role in the functional organization of the Bovidae TRG loci. In this context the distribution of the "similarity peaks" through the mVISTA program by comparing variable (TRGV), joining (TRGJ) and constant (TRGC) genes as shared markers is applied to human, mouse, cattle, sheep and dog comparative maps to impute the ancestral mammalian immuno-subgenome. Distances between species dominated by duplications, deletions and inversions are presented in a first multispecies attempt, using ordered mapping data to reconstruct the evolutionary exchanges that preceded modern mammal organization of TRG regions.


Centric fusion/fission polymorphisms in non-domestic bovidae

J. Rubes (1), E. Pagacova (1), S. Kubickova (1), H. Cernohorska (1), J. Vahala (2)

1. Veterinary Research Institute, Brno (Czech Republic);
2. ZOO Dvur Kralove, Dvur Kralove/ L. (Czech Republic)

Centric fusion/fission polymorphism has been described repeatedly in various families. We studied the chromosomes of 150 captive-born specimens of family Bovidae subfamilies Bovinae (genus Syncerus), Reduncinae (genera Kobus, Redunca), Alcelaphinae (genera Damaliscus, Connochaetes), Hippotraginae (genera Hippotragus, Oryx), Antylopinae (genera Antidorcas, Gazella) and Aepycerotinae. The highest rate of chromosome polymorphism was detected in subfamilies Reduncinae and Aepycerotinae. Two new types of polymorphism were revealed. The defassa waterbuck (Kobus ellipsiprymnus defassa) was polymorphic for a 7;29 centric fusion and African buffalo (Syncerus caffer caffer) for 1;13 centric fission. The formerly described polymorphism in impala (Aepyceros melampus) was determined in our study as 14;20 centric fusion. The findings were confirmed by cross-species fluorescence in situ hybridization (FISH) with bovine (Bos taurus L.) chromosome painting probes. The study demonstrates the relevance of cytogenetic screening in captive animals from zoological gardens.


The freewill of evolution in the structuring of Rodentia genomes

F. Adega (1), S. Louzada (1), A. Vieira-da-Silva (1), H. Guedes-Pinto (1), A. Kofler (2), J. Wienberg (3), R. Chaves (1)

1. Institute for Biotechnology and Bioengineering, Centre of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (CGB-UTAD/IBB), 1013, 5001-801 Vila Real (Portugal);
2. Chrombios GmbH, Muhlenstr.1, D-83064 Raubling (Germany);
3. Department of Biology II, University of Munich, Großhaderner Strasse 2, 82152 Planegg-Martinsried (Germany)

Two rodent species, the common hamster Cricetus cricetus, and the cactus mouse Peromyscus eremicus (Rodentia: Cricetidae), displaying diploid chromosome numbers of 22 and 48 chromosomes, respectively, were studied. C. cricetus encloses a nearly meta/submetacentric karyotype, whose constitutive heterochromatin (CH) seems to be greatly found at the (peri)centromeric regions, exhibiting the majority of the chromosomes two very large blocks at this location. P. eremicus exhibits a very distinct karyotype organization, solely constituted by submetacentric chromosomes. This karyotype also displays great amounts of CH, being the p-arms of the majority of the chromosomes almost entirely heterochromatic. The index genome Rattus rattus allowed deciphering the different genomic architecture of these two genomes. Comparative Chromosome Painting illuminated the evolutionary pathways that created these two genomes of species belonging to the same family. As more Rodentia species are thoroughly analyzed, more complex seems to have been the evolutionary events in this order.

This work was supported by the project POCI/BIA-BCM/ 58541/2004 and the PosDoc and PhD grants SFRH/BPD/32661/2006, SFRH/BD/25813/2005 and SFRH/BD/41942/2007 of Portugal FCT. We are deeply grateful to Dr. Vitaly Volobouev for providing the Rodentia cell cultures.


A high-resolution comparative FISH and radiation hybrid map of sheep chromosome X

T. Goldammer (1), R.M. Brunner (1), C.H. Wu (2), K. Nomura (3), T. Hadfield (2), C. Gill (4), B.P. Dalrymple (5), N.E. Cockett (2)

1. Forschungsbereich Molekularbiologie, Forschungsinstitut fur die Biologie landwirtschaftlicher Nutztiere (FBN), D-18196 Dummerstorf, Wilhelm-Stahl-Allee 2 (Germany);
2. Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT 84322-4700 (USA);
3. Tokyo University of Agriculture, Department of Animal Science, Laboratory of Animal Genetics and Breeding, 1737 Funako Atsugi-shi, Kanagawa 243-0034, Tokyo (Japan);
4. Department of Animal Science, Texas A&M University, College Station, TX 77843 (USA);
5. CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, QLD 4067 (Australia).

A preliminary high-resolution cytogenetic and radiation hybrid (RH) map containing nearly 170 loci on the sheep X chromosome (Ovis aries; OARX) was constructed based on a comparative mapping approach. We selected DNA sequences for mapping using the Virtual Sheep Genome Browser v1.1 combining data from human, cattle, dog, and sheep genomes. Performed genotyping of DNA sequences in the USUoRH5000 ovine whole-genome radiation hybrid panel followed by RH map construction using the Carthagene 1.1R software package revealed RH loci order on OARX. The RH map consists of three linkage groups with an average loci density of 1.3 megabases. Whereas loci of 80 BAC end sequences (BES) determine the backbone of the RH map, assignments of 30 identified and verified gene loci within mapped BACs and loci for further 30 gene loci on the map allow good comparison of OARX with X chromosomes of evolutionary related species. Loci for 14 microsatellite markers on the RH map of OARX anchor available linkage maps physically to the chromosome. The cytogenetic map based on fluorescence in situ hybridization (FISH) of 22 BAC clones of the CHORI sheep BAC library CH243. FISH loci represent cytogenetic anchors and support loci order within the constructed RH map. Except for some little rearrangements, the map is concordant with the virtual OARX map. A developed comparative map between sheep, cattle, and human X chromosomes identifies conserved synteny and likewise chromosome rearrangements between the three species.


Large Y chromosome in the nine-spined stickleback - another piece in the puzzle called stickleback’s sex chromosome evolution

K., Ocalewicz, P., Woznicki, M., Jankun

Department of Ichthyology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 5, 10-957 Olsztyn, (Poland)

Sticklebacks (Gasterosteidae) seem to be very interesting models for investigating the evolution of sex chromosomes. Species from this family exhibit female or male heterogamety with cytologically distinguishable sex chromosomes, or show Y- and X-linked DNA sequences with out any visible sex chromosomes. In the present paper we provide cytological information about the sex chromosomes in the nine-spined stickleback (Pungitius pungitius L.). Specimens analyzed from two freshwater populations of P. pungitius from Poland showed sex-related chromosomal polymorphism. A heteromorphic pair of chromosomes was noticed in the male diploid cells only. The Y chromosome was the largest chromosome in the nine-spined stickleback karyotype. Karyological analysis performed with Giemsa staining, C- , DAPI- and CMA3 banding techniques provided cytogenetic characterisation of the sex chromosomes in the nine-spined sticklebacks from the studied populations. A multichromosomal location of 5S rRNA genes was observed using PRINS technique however, none of the hybridization spots derived from the sex chromosomes. The origin of the exceptionally large Y chromosome is discussed.


Evolutionary chromosome repositioning of orthologous satellite DNA in the related genomes C. cricetus and P. eremicus (Rodentia, Cricetidae)

S Louzada (1), A Vieira-da-Silva (1), A Paco (1), S Kubickova (2), F Adega (1), H Guedes-Pinto (1), J Rubes (2), R Chaves (1)

1. Institute for Biotechnology and Bioengineering, Centre of Genetics and Biotechnology, UTAD (CGB-UTAD/IBB), 1013, 5001-801 Vila Real (Portugal)
2. Veterinary Research Institute (VRI), Hudcova 70, 62100 Brno (Czech Republic)

A significant fraction of the eukaryotic genome is comprised of repetitive sequences, including satellite DNA (satDNA) which is organized into long and uninterrupted tandem arrays. Different satDNA families can coexist in the same genome, and the same family of satellite DNA can be found in the genomes of related species. Cricetus cricetus (2n=22) and Peromyscus eremicus (2n=48) belong to Cricetidae family (order Rodentia). Here we report the isolation of C. cricetus centromeric repetitive sequences from chromosome 4 (CCR4/10sat), using the laser microdissection and pressure catapulting procedure. The in situ hybridization of these sequences onto C. cricetus and P. eremicus chromosomes revealed its presence in both genomes, displaying very different chromosome location. With few exceptions, CCR4/10sat displays a co-localization with the constitutive heterochromatin, evidenced by classic C-banding or in situ RE+C-Banding. The occurrence of these orthologous sequences in both species genomes is revealing of a common ancestor; however, its different chromosomal location foresees different trails for these genomes evolutionary history.

Supported by: project POCI/BIA-BMC/58541/2004, PhD and Pos-doc grants SFRH/BD/25813/2005,SFRH/BD/41942/2007,SFRH/BD/41574/2007,SFRH/BPD/32661/2006 of the Science and Technology Foundation (FCT) -Portugal. We thank Dr. V.Volobouev for Rodentia cell cultures.


A proposal of the standard karyotype of donkey (Equus asinus, 2n=62) chromosomes on the basis of G- and R-banding comparison

G.P. Di Meo (1), A. Perucatti (1) ,V. Peretti (2), F. Ciotola (3), L. Liotta (4), D. Di Berardino (5), B. Chowdhary, L. Iannuzzi (1).

1. National Research Council (CNR), ISPAAM, Lab. of Animal Cytogenetics and Gene Mapping, Naples (Italy);
2. Dept. of Animal Sciences and Food Inspection, Univ. of Naples Federico II, Naples (Italy);
3. Dept. of Experimental and Clinical Medicine, University Magna Graecia, Catanzaro (Italy);
4. Dept. MOBIFIPA, Vet. Medicine Faculty, University of Messina, Messina (Italy);
5. Dept. of Soil, Plant, Environmental Science, Univ. Federico II, Portici (Italy);
6. Dept. of Veterinary Integrative Bio-Sciences, College of Veterinary Medicine, Texas A&M University, College Station, TX (USA)

Donkey belongs to the Equidae family (which includes asses, horses and zebras), order Perissodactyla. The chromosomes of this species have attracted the attention of the cytogeneticists primarily to identify similarities or differences with horse chromosomes (Equus caballus, ECA, 2n=64), essentially to better understand the reasons of the sterility in their hybrids. Donkey chromosomes were earlier characterized separately by C-, G- and R-banding techniques. However, direct comparisons between G- and R-banding patterns have still not been carried out in this species. The present study reports this comparison at the 450 band level by using replicating banding patterns. Two sets of synchronized lymphocyte cultures were set up to obtain early- (G-banding) and late- (R-banding) BrdU incorporation. Slides were stained with acridine orange and observed under a fluorescence microscope. Reverse GBG- and RBG-banded karyotypes were constructed on the basis of previous GTG-banded karyotype reported by Raudsepp et al. (2000). To verify G- and R-banding patterns in some acrocentric chromosomes, sequential GBG/Ag-NORs and RBG/Ag-NORs were also performed. Results of CBA-banding patterns were obtained in 15 animals from two breeds. Ideogrammatic representations of G- and R-banded karyotypes were constructed. The findings contribute to current efforts to develop a standard karyotype for donkey chromosomes.


Molecular analysis and Physical distribution of LINE-1 sequences in three rodent species, Cricetus cricetus, Peromyscus eremicus (Cricetidae family) and Praomys tullbergi (Muridae family)

A Paco, F Adega, H Guedes-Pinto, R Chaves

Institute for Biotechnology and Bioengineering, Centre of Genetics and Biotechnology, UTAD (IBB/CGB-UTAD), 1013, 5001-801 Vila Real (Portugal)

Long interspersed elements-1 (LINE-1) are autonomous retroelements currently active in mammalian genomes, composing about 20% of the mouse genome. These sequences have traditionally been referred as selfish elements, persisting over time due to their replicative advantage over the host genome. However nowadays, according to its non-random chromosome distribution, a functional meaning has been addressed to LINE-1 sequences, as they play an important role in gene expression and in X-chromosome inactivation. In this work it was isolated and sequenced for the first time, a fraction of the LINE-1 sequence from three rodent species, Cricetus cricetus, Peromyscus eremicus (Cricetidae family) and Praomys tullbergi (Muridae family), corresponding to an ORFII fraction with approximately 300bp. The molecular analysis of these sequences and its comparison with other rodent LINE-1 sequences available in NCBI database, allowed establishing considerations about the phylogenetic relationships among different rodent species. Moreover, the physical chromosomal location of these sequences in the genome of the three rodent species analysed, performed by fluorescent in situ hybridization, allowed to draw some considerations about the possible role of LINE-1 sequences in X-chromosome inactivation.

Supported by: project POCI/BIA-BMC/58541/2004, PhD and Pos-doc grants SFRH/BD/41574/2007, SFRH/BPD/32661/2006 of the Science and Technology Foundation-Portugal. We thank Dr.V.Volobouev for Rodentia cell cultures.


Physical distribution of LINE-1 in Acomys sp. (Rodentia, Muridae), Microtus sp. (Rodentia, Cricetidae) and Cricetomys sp. (Rodentia, Nesomyidae)

A. Vieira-da-Silva, F. Adega, H. Guedes-Pinto, R. Chaves

Institute for Biotechnology and Bioengineering, Centre of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (IBB/CGB-UTAD), 1013, 5001- 801 Vila Real (Portugal)

"Long Interspersed Nuclear Elements" (LINEs) are an ancient family of retroelements found across a wide phylogenetic range, being the LINE-1 the most recent lineage. LINE-1 are thought to have been present in the ancestral genome prior to the mammalian radiation, and nowadays represent an important component of mammalian genomes, suggesting that they provide an advantage to the genomes they inhabit.
Different authors suggested that LINE-1 are not transposed randomly and the target sites might be conserved among mammalian species. In order to study genomic organization on rodents Acomys sp. (Rodentia, Muridae), Microtus sp. (Rodentia, Cricetidae) and Cricetomys sp. (Rodentia, Nesomyidae), we analysed the chromosome distribution of LINE-1 by isolating these elements from these genomes and performing its physical mapping. The same chromosome preparations were then submitted to classical C-banding. In two of the three genomes there was detected a preferential accumulation of LINE-1 on certain chromosomes and, on all the species, the sequential C-banding showed that LINE-1 are preferentially located in euchromatin.

This work was supported by: project POCI/BIA-BCM/58541/2004, PhD and Pos-doc grants SFRH/BD/41942/2007, SFRH/BPD/32661/2006, of the Science and Technology Foundation(FCT)/Portugal. We thank Dr. V. Volobouev for the Rodentia cell cultures.


High-resolution comparative FISH mapping on chicken and Japanese quail lampbrush chromosomes

A. Zlotina (1), A. Daks (1), S. Galkina (1), S. Deryusheva (1), A. Krasikova (1), R. Crooijmans (2), M. Groenen (2), E. Gaginskaya (1)

1. Saint-Petersburg State University, Saint-Petersburg (Russia);
2. Wageningen University, Wageningen (The Netherlands)

Giant lampbrush chromosomes (LBCs), which are characteristic of the diplotene stage of prophase I during avian oogenesis, represent a very promising system for precise physical gene mapping. Comparative FISH mapping of chicken BAC clones from the Wageningen BAC library on chicken (Gallus gallus domesticus) and Japanese quail (Coturnix coturnix japonica) LBCs allowed us to define gene order more precisely. Centromeres on LBCs were detected using antibodies against cohesion proteins. Present data conform and extend the data earlier obtained on mitotic chromosomes. In addition to well-established inversions, which differ chromosomes 1 and 2 in the chicken and Japanese quail, we found a pericentric inversion in quail chromosome 3 as compared to chicken. Our data clearly demonstrate that the difference in centromere position in chicken and quail chromosomes 1, 3, 4 and 8 cannot be explained by inversions only. The centromeres seem to form de novo during karyotype evolution in Galliformes. Detailed analysis of the region from 0 Mb to 23 Mb on chicken LBC3 allowed us to assign centromere to the gap at the 2.4 Mb position in GGA3 sequence assembly; the gap at the 5.6 Mb position and current centromeric gap at the 11.6-13.1Mb position correspond to long clusters of tandem repeat CNM. This work was supported by RFBR.


How many species of Thrichomys (Rodentia, Echimyidae) are there? A karyological and molecular approach

R.V. Vilela, T. Machado, Y. Yonenaga-Yassuda

Departamento de Genetica e Biologia Evolutiva, Instituto de Biociincias, Universidade de São Paulo. São Paulo, SP (Brazil).

Molecular phylogeny, karyological, and biogeographic analyses suggest that the genus Thrichomys is a composite of at least five species. Our dataset included 24 sequences of the cytochrome-b gene of Thrichomys specimens captured in ten localities in Brazil and 19 sequences from GenBank. We present karyotypes from localities not yet sampled. From our phylogenies we associated clades to karyotypes described in the literature and their geographic distribution. We recognized: T. inermis (2n=26, FN=48), T. pachyurus (2n=30, FN=56), T. fosteri (2n=34, FN=64), T. sp. n. (2n=26, FN=48), and T. apereoides. Differently from previous studies, T. apereoides had little support as a monophyletic group, and was divided in, at least, three clades: (1) 2n=28, FN=50 or 52, (2) 2n=30, FN=54, and (3) 2n=28, FN=52; or 2n=30, FN=54 or 56. Although mostly moderately supported and having sequence divergence values ranging from slight to substantial among them, these three clades have different karyologic composition. The clades of T. apereoides appear to be undergoing speciation or alternatively they have experienced recent speciation with little gene flow and T. apereoides may be a complex of species. Another species, T. laurentius, was previously recognized based on morphological and morphometric data. Its karyotype (2n=30, FN=54) is similar to that of clade ’2’ of T. apereoides.