Transcribing the enigma: the B chromosome as a territory of uncharted RNAs.

B chromosomes are supernumerary elements found in several groups of eukaryotes, including fungi, plants, and animals. Typically, these chromosomes either originate from their hosts through errors in meiosis or interspecifically through horizontal transfer. While many B chromosomes are primarily heterochromatic and possess a low number of coding genes, these additional elements are still capable of transcribing sequences and exerting influence on the expression of host genes. How B chromosomes escape elimination and which impacts can be promoted in the cell always intrigued the cytogeneticists. In pursuit of understanding the behavior and functional impacts of these extra elements, cytogenetic studies meet the advances of molecular biology, incorporating various techniques into investigating B chromosomes from a functional perspective. In this review, we present a timeline of studies investigating B chromosomes and RNAs, highlighting the advances and key findings throughout their history. Additionally, we identified which RNA classes are reported in the B chromosomes and emphasized the necessity for further investigation into new perspectives on the B chromosome functions. In this context, we present a phylogenetic tree that illustrates which branches either report B chromosome presence or have functional RNA studies related to B chromosomes. We propose investigating other unexplored RNA classes and conducting functional analysis in conjunction with cytogenetic studies to enhance our understanding of the B chromosome from an RNA perspective.

Strain-specific evolution and host-specific regulation of transposable elements in the model plant symbiont Rhizophagus irregularis.

Transposable elements (TEs) are repetitive DNA that can create genome structure and regulation variability. The genome of Rhizophagus irregularis, a widely studied arbuscular mycorrhizal fungus (AMF), comprises ∼50% repetitive sequences that include TEs. Despite their abundance, two-thirds of TEs remain unclassified, and their regulation among AMF life stages remains unknown. Here, we aimed to improve our understanding of TE diversity and regulation in this model species by curating repeat datasets obtained from chromosome-level assemblies and by investigating their expression across multiple conditions. Our analyses uncovered new TE superfamilies and families in this model symbiont and revealed significant differences in how these sequences evolve both within and between R. irregularis strains. With this curated TE annotation, we also found that the number of upregulated TE families in colonized roots is 4 times higher than in the extraradical mycelium, and their overall expression differs depending on the plant host. This work provides a fine-scale view of TE diversity and evolution in model plant symbionts and highlights their transcriptional dynamism and specificity during host-microbe interactions. We also provide Hidden Markov Model profiles of TE domains for future manual curation of uncharacterized sequences (https://github.com/jordana-olive/TE-manual-curation/tree/main).

First characterization of PIWI-interacting RNA clusters in a cichlid fish with a B chromosome.

BACKGROUND: B chromosomes are extra elements found in several eukaryote species. Usually, they do not express a phenotype in the host. However, advances in bioinformatics over the last decades have allowed us to describe several genes and molecular functions related to B chromosomes. These advances enable investigations of the relationship between the B chromosome and the host to understand how this element has been preserved in genomes. However, considering that transposable elements (TEs) are highly abundant in this supernumerary chromosome, there is a lack of knowledge concerning the dynamics of TE control in B-carrying cells. Thus, the present study characterized PIWI-interacting RNA (piRNA) clusters and pathways responsible for silencing the mobilization of TEs in gonads of the cichlid fish Astatotilapia latifasciata carrying the B chromosome. RESULTS: Through small RNA-seq and genome assembly, we predicted and annotated piRNA clusters in the A. latifasciata genome for the first time. We observed that these clusters had biased expression related to sex and the presence of the B chromosome. Furthermore, three piRNA clusters, named curupira, were identified in the B chromosome. Two of them were expressed exclusively in gonads of samples with the B chromosome. The composition of these curupira sequences was derived from LTR, LINE, and DNA elements, representing old and recent transposition events in the A. latifasciata genome and the B chromosome. The presence of the B chromosome also affected the expression of piRNA pathway genes. The mitochondrial cardiolipin hydrolase-like (pld6) gene is present in the B chromosome, as previously reported, and an increase in its expression was detected in gonads with the B chromosome. CONCLUSIONS: Due to the high abundance of TEs in the B chromosome, it was possible to investigate the origin of piRNA from these jumping genes. We hypothesize that the B chromosome has evolved its own genomic guardians to prevent uncontrolled TE mobilization. Furthermore, we also detected an expression bias in the presence of the B chromosome over A. latifasciata piRNA clusters and pathway genes.

Comparative Cytogenetics Among Three Sympatric Hypostomus Species (Siluriformes: Loricariidae): An Evolutionary Analysis in a High Endemic Region

ABSTRACT The karyotypes of three armored catfish species (Loricariidae) from the Iguaçu river, southern of the Brazil, were compared using different techniques: C-banding, Ag-NOR and fluorescence in situ hybridization (FISH), which used 5S and 18S rDNAs and total Cot-1 fraction as probes. Hypostomus commersoni and Hypostomus derbyi presented 2n = 68 chromosomes, with karyotype formulae 12m+12sm+14st+30a and 12m+12sm+10st+34a, respectively; whereas Hypostomus myersi presented 2n = 74 chromosomes and 12m+16sm+12st+34a. The chromosomal localization of the Ag-NORs, 5S and 18S rDNAs differed in number of sites and chromosomal localization among the studied species. The total Cot-1 probe permitted the visualization of the repetitive DNA fraction in karyotypes of each species. Cross-hybridizations using total Cot-1 probe revealed that these species have repetitive DNAs in common. However, this does not occur in H. commersoni in relation to the other species. The apparent karyotype similarity suggests a close relationship between the sympatric H. commersoni and H. derbyi species, but the small differences detected in the examined chromosomal markers indicate evolutionary divergence due to gene flow restriction among them. Hence, the present findings indicate different composition of repetitive sequences among studied species, which permit to infer its role in chromosomal differentiation of Hypostomus.

Construction and characterization of a repetitive DNA library in Parodontidae (Atinopterygii:Characiformes): a genomic and evolutionary approach to the degeneration of the w sex cromosome.

Repetitive DNA sequences, including tandem and dispersed repeats, comprise a large portion of eukaryotic genomes and are important for gene regulation, sex chromosome differentiation, and karyotype evolution. In Parodontidae, only the repetitive DNAs WAp and pPh2004 and rDNAs were previously studied using fluorescence in situ hybridization. This study aimed to build a library of repetitive DNA in Parodontidae. We isolated 40 clones using Cot-1; 17 of these clones exhibited similarity to repetitive DNA sequences, including satellites, minisatellites, microsatellites, and class I and class II transposable elements (TEs), from Danio rerio and other organisms. The physical mapping of the clones to chromosomes revealed the presence of a satellite DNA, a Helitron element, and degenerate short interspersed element (SINE), long interspersed element (LINE), and tc1-mariner elements on the sex chromosomes. Some clones exhibited dispersed signals; other sequences were not detected. The 5S rDNA was detected on an autosomal pair. These elements likely function in the molecular degeneration of the W chromosome in Parodontidae. Thus, the location of these elements on the chromosomes is important for understanding the function of these repetitive DNAs and for integrative studies with genome sequencing. The presented data demonstrate that an intensive invasion of TEs occurred during W sex chromosome differentiation in the Parodontidae.