Emerging patterns of genome organization in Notopteridae species (Teleostei, Osteoglossiformes) as revealed by Zoo-FISH and Comparative Genomic Hybridization (CGH)

Notopteridae (Teleostei, Osteoglossiformes) represents an old fish lineage with ten currently recognized species distributed in African and Southeastern Asian rivers. Their karyotype structures and diploid numbers remained conserved over long evolutionary periods, since African and Asian lineages diverged approximately 120 Mya. However, a significant genetic diversity was already identified for these species using molecular data. Thus, why the evolutionary relationships within Notopteridae are so diverse at the genomic level but so conserved in terms of their karyotypes? In an attempt to develop a more comprehensive picture of the karyotype and genome evolution in Notopteridae, we performed comparative genomic hybridization (CGH) and cross-species (Zoo-FISH) whole chromosome painting experiments to explore chromosome-scale intergenomic divergence among seven notopterid species, collected in different African and Southeast Asian river basins. CGH demonstrated an advanced stage of sequence divergence among the species and Zoo-FISH experiments showed diffuse and limited homology on inter-generic level, showing a temporal reduction of evolutionarily conserved syntenic regions. The sharing of a conserved chromosomal region revealed by Zoo-FISH in these species provides perspectives that several other homologous syntenic regions have remained conserved among their genomes despite long temporal isolation. In summary, Notopteridae is an interesting model for tracking the chromosome evolution as it is (i) ancestral vertebrate group with Gondwanan distribution and (ii) an example of animal group exhibiting karyotype stasis. The present study brings new insights into degree of genome divergence vs. conservation at chromosomal and sub-chromosomal level in representative sampling of this group.

From Chromosomes to Genome: Insights into the Evolutionary Relationships and Biogeography of Old World Knifefishes (Notopteridae; Osteoglossiformes)

In addition to its wide geographical distribution, osteoglossiform fishes represent one of the most ancient freshwater teleost lineages; making it an important group for systematic and evolutionary studies. These fishes had a Gondwanan origin and their past distribution may have contributed to the diversity present in this group. However, cytogenetic and genomic data are still scarce, making it difficult to track evolutionary trajectories within this order. In addition, their wide distribution, with groups endemic to different continents, hinders an integrative study that allows a globalized view of its evolutionary process. Here, we performed a detailed chromosomal analysis in Notopteridae fishes, using conventional and advanced molecular cytogenetic methods. Moreover, the genetic distances of examined species were assessed by genotyping using diversity arrays technology sequencing (DArTseq). These data provided a clear picture of the genetic diversity between African and Asian Notopteridae species, and were highly consistent with the chromosomal, geographical, and historical data, enlightening their evolutionary diversification. Here, we discuss the impact of continental drift and split of Pangea on their recent diversity, as well as the contribution to biogeographical models that explain their distribution, highlighting the role of the Indian subcontinent in the evolutionary process within the family.

Do genoma aos cromossomos: Inferências sobre as relações evolutivas e a biogeografia de peixes da família Notopteridae (Teleostei, Osteoglossiformes)

Além de sua ampla distribuição geográfica, a ordem Osteoglossiformes representa uma das mais antigas linhagens de Teleósteos. Estes peixes tiveram uma origem Gondwanica (~ 227 Mya) e sua distribuição atual é reflexo direto das movimentações tectônicas ocorridas ao longo da história evolutiva da Terra. No entanto, os dados citogenéticos e genômicos são ainda esporádicos e bastante incompletos neste grupo de peixes, tornando impossível determinar as tendências evolutivas que ocorrem nesta ordem. A família Notopteridae possui 10 espécies distribuídas pelo continente Africano (3) e Asiático (7) e seus membros são popularmente conhecidos como “Peixes-faca”. No presente estudo foram realizadas abordagens cromossômicas e genômicas em 07 espécies de peixes-faca oriundas da Tailândia (Chitala blanci, C. ornata, C. lopis e Notopterus notopterus), Índia (C. chitala) e Nigéria (Xenomystus nigri e Papyrocranus afer), visando auxiliar na compreensão da diversidade apresentada por este grupo frente a sua atual distribuição geográfica. As espécies apresentam 2n=42 cromossomos acrocêntricos, com exceção de C. lopis e P. afer as quais apresentam 2n=38 e 2n=50, respectivamente. Adicionalmente, P. afer diferenciou-se das demais espécies por ser a única a apresentar também cromossomos de dois braços. O mapeamento cromossômico de diversas classes de DNAs repetitivos evidenciou um padrão geral compartilhado entre as espécies, com exceção de algumas poucas particularidades evidenciadas nas espécies P. afer, C. lopis e C. chitala. Adicionalmente, C. lopis também apresenta uma concentração de sequencias repetitivas co-localizadas como sítios teloméricos intersticiais (ITS) nos pares 1 e 3, evidenciando rearranjos cromossômicos ocorridos durante sua evolução cariotípica. Análise da diversidade genômica entre os grupos corroborou os dados cromossômicos e biogeográficos apontando C. chitala como possível espécie intermediaria entre os notopterídeos Africanos e Asiáticos. Atualmente a hipótese “Out-of-India” é a mais aceita para explicar a distribuição geográfica do grupo. Entretanto, aqui levantamos alternativas baseando nos tempos de divergência e na história biogeográfica da separação das massas Madagascar-Seychelles-Índia, indo de encontro com a diversidade cromossômica e molecular do grupo e sua distribuição geográfica atual.

Evolutionary Relationships and Cytotaxonomy Considerations in the Genus Pyrrhulina (Characiformes, Lebiasinidae)

Although fishes exhibit the greatest biodiversity among the vertebrates, a large percentage of this fauna is still underexplored on evolutionary cytogenetic questions, particularly the miniature species. The Lebiasinidae family is a particular example for such case. This study is the first one presenting differential cytogenetic methods, such as C-banding, repetitive DNAs mapping, comparative genomic hybridization (CGH), and whole chromosome painting in lebiasinid species. Pyrrhulina australis and Pyrrhulina aff. australis were deeply investigated concerning their chromosomal patterns and evolutionary relationships. These species have a very similar morphology, but they can be distinguished by a longitudinal midlateral faintly dark stripe exclusive for Pyrrhulina aff. australis. Both species presented 2n = 40 chromosomes (4st +36a), without heteromorphic sex chromosomes. However, despite their morphological and karyotype resemblance, it was evidenced that both species have already gone through a significant genomic divergence, thus corresponding to distinct evolutionary units. Furthermore, to give additional support to some proposals on evolutionary relationship among Lebiasinidae with other fish families, a chromosomal comparative approach with Erythrinus erythrinus, a representative species of the Erythrinidae family, was also performed. In addition to have similar karyotype structure, mainly composed by acrocentric chromosomes, both species share uncommon genomic similarities, such as (i) syntenic location of 5S and 18S rDNA sequences; (ii) huge dispersion of multiple 5S rDNA sites in the karyotypes; and (iii) complex association between 5S rDNA and Rex3 elements. CGH experiments, despite reinforcing some shared genomic homologies, also highlighted that both Pyrrhulina and Erythrinus have a range of nonoverlapping species-specific signals. The overall chromosomal data proved to be effective markers for the cytotaxonomy and evolutionary process among Lebiasinidae fishes.