Similarities and differences in the nuclear genome organization within Pooideae species revealed by comparative genomic in situ hybridization (GISH)

Abstract

In this paper, we highlight the affinity between the genomes of key representatives of the Pooideae subfamily, revealed at the chromosomal level by genomic in situ hybridization (GISH). The analyses were conducted using labeled probes from each species to hybridize with chromosomes of every species used in this study based on a “round robin” rule. As a result, the whole chromosomes or chromosome regions were distinguished or variable types of signals were visualized to prove the different levels of the relationships between genomes used in this study. We observed the unexpected lack of signals in secondary constrictions of rye (RR) chromosomes probed by triticale (AABBRR) genomic DNA. We have also identified unlabeled chromosome regions, which point to species-specific sequences connected with disparate pathways of chromosome differentiation. Our results revealed a conservative character of coding sequence of 35S rDNA among selected species of the genera Aegilops, Brachypodium, Festuca, Hordeum, Lolium, Secale, and Triticum. In summary, we showed strong relationships in genomic DNA sequences between species which have been previously reported to be phylogenetically distant.

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

“…The set of our CGH experiments aimed to compare genomes among the different notopterid genera ( Xenomystus , Papyrocranus,Notopterus , and Chitala ), suggest an advanced stage of sequence divergence, except fot the bright signals, highly likely corresponding to NOR sites (as might be compared with previous rDNA FISH analysis 9 ). Such result is typical for distantly related or substantially diverged genomes, see 67,68 ). The decrease of shared sequences is hardly surprising considering the ancient time of divergence between the clades.…”

Karyotype reshufflings of Festuca pratensis × Lolium perenne hybrids

“…Clone 395, derived from the library representing the most frequently present sequences in the F. pratensis genome, was labeled by nick translation with fluorochrome Atto647 (Jena BioScience) (Majka et al 2017b ). The ribosomal sequence 35S rDNA was labeled with digoxigenin-11-dUTP by nick translation.…”

Sex Chromosome Evolution and Genomic Divergence in the Fish Hoplias malabaricus (Characiformes, Erythrinidae)

“…The development of recent molecular methologies has allowed a qualitative improvement on chromosome researches of different biological taxa. Among them, the genomic in situ hybridization (GISH) and comparative genomic hybridization (CGH), originally developed for clinical studies (Kallioniemi et al, 1992 ), are now successfully applied for several other purposes, such as the identification of parental genomes in hybrids/allopolyploids (Bi and Bogart, 2006 ; Knytl et al, 2013 ; Symonová et al, 2013a , 2015 ; Doležálková et al, 2016 ; Majtánová et al, 2016 ), the detection of sex-specific content on homomorphic sex chromosomes (Ezaz et al, 2006 ; Altmanová et al, 2016 ; Rovatsos et al, 2016 ; Freitas et al, 2017 ) and the genome comparisons among related species (Valente et al, 2009 ; Symonová et al, 2013b ; Majka et al, 2016 ; Carvalho et al, 2017 ; Moraes et al, 2017 ). All these (and many other) studies proved that GISH and CGH technologies, despite representing rather “rough” molecular tools, may be successful in providing clues about the genome evolution, with their resolution being based on the differential distribution of already divergent genome-specific repetitive DNA classes (Kato et al, 2005 ; Chester et al, 2010 ), as these sequences are generally highly abundant in eukaryotic genomes and display faster evolutionary rates than the single-copy ones (Charlesworth et al, 1994 ; Cioffi and Bertollo, 2012 ; López-Flores and Garrido-Ramos, 2012 ).…”