Genome structure and evolution in the cruciferous tribe Thlaspideae (Brassicaceae).

Whole-genome duplications (WGDs) and chromosome rearrangements (CRs) play the key role in driving the diversification and evolution of plant lineages. Although the direct link between WGDs and plant diversification is well documented, relatively few studies focus on the evolutionary significance of CRs. The cruciferous tribe Thlaspideae represents an ideal model system to address the role of large-scale chromosome alterations in genome evolution, as most Thlaspideae species share the same diploid chromosome number (2n = 2x = 14). Here we constructed the genome structure in 12 Thlaspideae species, including field pennycress (Thlaspi arvense) and garlic mustard (Alliaria petiolata). We detected and precisely characterized genus- and species-specific CRs, mostly pericentric inversions, as the main genome-diversifying drivers in the tribe. We reconstructed the structure of seven chromosomes of an ancestral Thlaspideae genome, identified evolutionary stable chromosomes versus chromosomes prone to CRs, estimated the rate of CRs, and uncovered an allohexaploid origin of garlic mustard from diploid taxa closely related to A. petiolata and Parlatoria cakiloidea. Furthermore, we performed detailed bioinformatic analysis of the Thlaspideae repeatomes, and identified repetitive elements applicable as unique species- and genus-specific barcodes and chromosome landmarks. This study deepens our general understanding of the evolutionary role of CRs, particularly pericentric inversions, in plant genome diversification, and provides a robust base for follow-up whole-genome sequencing efforts.

Chromosome mapping of repetitive DNAs in sergeant major fishes (Abudefdufinae, Pomacentridae): a general view on the chromosomal conservatism of the genus.

Species of the Abudefduf genus (sergeant-majors) are widely distributed in the Indian, Pacific and Atlantic oceans, with large schools inhabiting rocky coastal regions and coral reefs. This genus consists of twenty recognized species are of generalist habit, showing typical characteristics of colonizers. Some populations maintain gene flow between large oceanic areas, a condition that may influence their cytogenetic features. A number of species have been shown to be invaders and able to hybridize with local species. However, cytogenetic data in this genus are restricted to few species. In this way, the present study includes the chromosomal investigation, using conventional (Giemsa staining, Ag-NOR and C-banding) and molecular (in situ mapping of six different repetitive DNA classes) approaches in four Abudefduf species from different oceanic regions (A. bengalensis and A. sexfasciatus from the Indo-Pacific, A. vaigiensis from the Indian and A. saxatilis from the Atlantic oceans, respectively), to investigate the evolutionary events associated with the chromosomal diversification in this group. All species share a similar karyotype (2n = 48; NF = 52), except A. sexfasciatus (2n = 48; NF = 50), which possesses a characteristic pericentric inversion in the NOR-bearing chromosomal pair. Mapping of repetitive sequences suggests a chromosomal conservatism in this genus. The high karyotypic similarity between allopatric species of Abudefduf may be related to the success of natural viable hybrids among species with recent secondary contact.

Comparative cytogenetics in three Sciaenid species (Teleostei, Perciformes): evidence of interspecific chromosomal diversification.

BACKGROUND: Species belonging to the Sciaenidae family present a karyotype composed by 48 acrocentric chromosomes and are thus considered a striking example of chromosomal conservation. In this family, three species are extensively studied including Larimichthys crocea, Larimichthys polyactis and Nibea albiflora due to their importance in fishery and aquaculture in East Asia. Despite abundant data of population genetics available for some of them, cytogenetic information on these species is still scarce and obtained by conventional cytogenetic protocols. Therefore, a more detailed cytogenomic investigation was performed in these species to analyze their karyotype differentiation using conventional staining techniques and fluorescence in situ hybridization to map several repetitive DNAs. RESULTS: The three species showed a slight karyotype differentiation with 4sm + 2st + 42a in L. polyactis, 20st + 28a in L. crocea and 48a in N. albiflora. Additionally, the mapping of repetitive sequences further revealed a number of interspecific differences among them. Particularly, 18S and 5S rDNA sites showed syntenic arrangements in N. albiflora and non-syntenic arrangements in both Larimichthys species. The microsatellites (CA)15 and (GA)15 showed conspicuous terminal clusters in some chromosomes of all species. On the other hand, (CGG)10 repeats, Rex6 elements and U2 snRNA displayed a scattered distribution on the chromosomes. CONCLUSIONS: Although the three Sciaenid species examined displayed a general pattern of karyotypic conservatism, we explored chromosomal diversification among them. The diversificated karyotypic macrostructure is followed by intergeneric evolutionary diversification of the repetitive sequences. The data indicate some degree of intergeneric evolutionary diversification at chromosomal level, and suggest the evolutionary dynamics among Sciaenid species, higher than previously thought. The present cytogenetic data provide new insight into the chromosomal diversification in Sciaenidae, and contribute to inferring the chromosomal rearrangements and trends of karyotype evolution in this fish group.

Prevalence of Cytogenetic Anomalies in Couples with Recurrent Miscarriages: A Case-control Study.

BACKGROUND: About 15%-20% of couples get affected by recurrent miscarriages (RM) and chromosomal abnormality in one partner affects 3%-6% of RM couples. AIMS: The present study aimed to determine the prevalence of cytogenetic anomalies in couples with RM. SETTINGS AND DESIGN: A case-control study was undertaken, in which 243 couples who had experienced 2 or >2 miscarriages were investigated for chromosomal abnormalities and compared with 208 healthy, age-matched control couples who had at least one healthy live born and no history of miscarriages. MATERIAL AND METHODS: Peripheral blood (PB) lymphocytes were cultured using PB-Max Karyotyping medium (GIBCO) for chromosomal analysis and 20 metaphases were analyzed for each individual. STATISTICAL ANALYSIS: Student's t-test was used for statistical evaluation and P < 0.05 was considered statistically significant for all instances. RESULTS: The current study revealed 3.1% RM cases showing structural chromosomal aberrations, of which balanced translocations and Robertsonian translocations constituted 66.7% and 26.7% cases, respectively, while inversions constituted 6.7% abnormal RM cases. Polymorphic variations were observed in 1.9% RM patients and 1.2% controls as well. However, the number of abortions were significantly more (P = 0.027) in male carriers of balanced translocations as compared to female carriers in the RM group. There was no significant difference for age (P = 0.539) between RM women and control women. CONCLUSIONS: Although similar studies exist in literature, our study is the first of its kind from our region that has compared the chromosomal anomalies between the RM group and the control group. We observed 3.1% of balanced translocations and an increased number (though nonsignificant) of polymorphic variations and satellite associations in the RM group as compared to the control group.

First report of B chromosomes in three neotropical thorny catfishes (Siluriformes, Doradidae).

The family Doradidae (Siluriformes) is an important group of fishes endemic to freshwater ecosystems in South America. Some cytogenetic studies have been conducted focused on the group; however, there are no reports on the occurrence of B chromosomes for the family. In this paper the chromosomal characteristics of Platydoras armatulus (Valenciennes, 1840), Pterodoras granulosus (Valenciennes, 1821) and Ossancora punctata (Kner, 1855) were investigated through classical cytogenetics approaches. The conventional staining reveals 2n=58 in Platydoras armatulus and Pterodoras granulosus, however with distinct karyotypic formulae, possibly originated by pericentric inversions. In Ossancora punctata a derivate karyotype was described with 2n=66 and predominance of acrocentric chromosomes. The C banding pattern was resolutive in discriminating the three species, being considered an important cytotaxonomic marker. All species showed B chromosomes totally heterochromatic with non-Mendelian segregation during meiosis and low frequencies in mitotic cells. The probably origin of these additional elements was through fragmentations of chromosomes of the standard complement, which occurred recently and independently in these three species. The diploid number observed in Ossancora punctata is an evidence of centric fusions and up to the moment it is the highest diploid number reported for Doradidae.

Are Pericentric Inversions Reorganizing Wedge Shell Genomes?

Wedge shells belonging to the Donacidae family are the dominant bivalves in exposed beaches in almost all areas of the world. Typically, two or more sympatric species of wedge shells differentially occupy intertidal, sublittoral, and offshore coastal waters in any given locality. A molecular cytogenetic analysis of two sympatric and closely related wedge shell species, Donax trunculus and Donax vittatus, was performed. Results showed that the karyotypes of these two species were both strikingly different and closely alike; whilst metacentric and submetacentric chromosome pairs were the main components of the karyotype of D. trunculus, 10-11 of the 19 chromosome pairs were telocentric in D. vittatus, most likely as a result of different pericentric inversions. GC-rich heterochromatic bands were present in both species. Furthermore, they showed coincidental 45S ribosomal RNA (rRNA), 5S rRNA and H3 histone gene clusters at conserved chromosomal locations, although D. trunculus had an additional 45S rDNA cluster. Intraspecific pericentric inversions were also detected in both D. trunculus and D. vittatus. The close genetic similarity of these two species together with the high degree of conservation of the 45S rRNA, 5S rRNA and H3 histone gene clusters, and GC-rich heterochromatic bands indicate that pericentric inversions contribute to the karyotype divergence in wedge shells.

Similarities and differences among the chromosomes of the wild guinea pig Cavia tschudii and the domestic guinea pig Cavia porcellus (Rodentia, Caviidae).

Cavia tschudii Fitzinger, 1867 is a wild guinea pig species living in South America that according to the analysis of mitochondrial genes is the closest wild form of the domestic guinea pig. To investigate the genetic divergence between the wild and domestic species of guinea pigs from a cytogenetic perspective, we characterized and compared the C, G and AgNOR banded karyotypes of molecularly identified Cavia tschudii and Cavia porcellus Linnaeus, 1758 specimens for the first time. Both species showed 64 chromosomes of similar morphology, although C. tschudii had four medium size submetacentric pairs that were not observed in the C. porcellus karyotype. Differences in the C bands size and the mean number of AgNOR bands between the karyotypes of the two species were detected. Most of the two species chromosomes showed total G band correspondence, suggesting that they probably represent large syntenic blocks conserved over time. Partial G band correspondence detected among the four submetacentric chromosomes present only in the C. tschudii karyotype and their subtelocentric homologues in C. porcellus may be explained by the occurrence of four pericentric inversions that probably emerged and were fixed in the C. tschudii populations under domestication. The role of the chromosomal and genomic differences in the divergence of these two Cavia species is discussed.

Comparative chromosomal analysis and evolutionary considerations concerning two species of genus Tatia (Siluriformes, Auchenipteridae).

Auchenipteridae is divided in two subfamilies, Centromochlinae and Auchenipterinae. Centromochlinae has 31 valid species, from which 13 are included in the genus Tatia Miranda Ribeiro, 1911. Among these, Tatia jaracatia Pavanelli & Bifi, 2009 and Tatia neivai (Ihering, 1930) are the only two representative species from the Paraná-Paraguay basins. This study aimed to analyze cytogenetically these two species and thus provide the first chromosomal data for the genus. Although Tatia jaracatia and Tatia neivai presented 2n=58 chromosomes, some differences were observed in the karyotypic formula. The heterochromatin was dispersed in the centromeric and terminal regions of most chromosomes of Tatia jaracatia, and only in the terminal region of most chromosomes of Tatia neivai. The AgNORs were detected in the subtelocentric pair 28 for both species, which was confirmed by FISH with 18S rDNA probe. The 5S rDNA sites were detected in four chromosome pairs in Tatia jaracatia and three chromosome pairs in Tatia neivai. Both species of Tatia presented great chromosomal similarities among themselves; however, when compared to other species of Auchenipteridae, it was possible to identify some differences in the karyotype macrostructure, in the heterochromatin distribution pattern and in the number and position of 5S rDNA sites, which until now seems to be intrinsic to the genus Tatia.

First cytogenetic record for a species of Otothyropsis Ribeiro, Carvalho & Melo, 2005 (Loricariidae, Hypoptopomatinae)

Hypoptopomatinae is a monophyletic subfamily that includes 147 species, distributed in 20 genera. Otothyropsis is a genus of Hypoptopomatinae, recently described. Here, we provided the first cytogenetic information of Otothyropsis . The specimens were collected from córrego Dourado, a small tributary of rio Iguatemi, which flows into rio Paraná. The specimens of Otothyropsis cf. polyodon were analyzed with respect to diploid number, C-Band and Ag-NOR patterns. The diploid number was 54 chromosomes, distributed in 18 metacentric, 28 submetacentric, and 8 subtelocentric chromosomes, with single Ag-NOR and conspicuous heterochromatic blocks on the short and long arms of the 24th pair of chromosomes. Our study highlights the conservation trend of the diploid number (2n=54) and fundamental number (FN = 108) among the species of Hypoptopomatinae. However, the karyotype formula (18m+28sm+8st) seems to be specific to O. cf. polyodon , considering the other Hypoptopomatinae species already analyzed.

Hypoptopomatinae é uma subfamília monofilética que inclui 147 espécies distribuídas em 20 gêneros, sendo Otothyropsis um gênero recentemente descrito. Aqui, fornecemos a primeira informação citogenética do gênero Otothyropsis . Espécimes foram coletados no córrego Dourado, um pequeno tributário do rio Iguatemi, o qual deságua no rio Paraná. Espécimes de Otothyropsis cf. polyodon foram analisados em relação ao número diploide e padrões de Banda-C e Ag-NOR. O número diploide foi de 54 cromossomos, distribuídos em 18 metacêntricos, 28 submetacêntricos e 8 subtelocêntricos, com Ag-NOR simples e blocos heterocromáticos evidentes no braços curto e longo do par de cromossomos 24. Nosso estudo destaca a tendência de conservação do número diploide (2n=54) e número fundamental (NF=108) entre as espécies de Hypoptopomatinae. Entretanto, a fórmula cariotípica (18m+28sm+8st) parece ser específica para O. cf. polyodon, considerando as outras espécies de Hypoptopomatinae já analisadas.