The activity of genome-specific repetitive sequences is the main cause of genome variation between A and D genomes. Through comparative analysis of the two genomes, we retrieved a repetitive element termed motif, which appears frequently in the diploid (D) genome but rarely in the diploid (A) genome. We further explored the existence of the motif in chromosomes of , , and two tetraploid (AADD) cotton species, and , by fluorescence hybridization (FISH), and observed that the motif exists in the D and D-subgenomes but not in the A and A-subgenomes. The motif comprises two components, a variable tandem repeat (TR) region and a conservative sequence (CS). The two constituents each have hundreds of repeats that evenly distribute across 13 chromosomes of the Dgenome. The motif (and its repeats) was revealed as the common conservative region harbored by ancient Long Terminal Repeat Retrotransposons. Identification and investigation of the motif promotes the study of A and D genome differences, facilitates research on genome evolution, and provides assistance to subgenome identification and genome assembling.
Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- The study investigates the genomic similarities and differences within the BOP clade of the Poaceae family, particularly focusing on the genomes of rice, Brachypodium, and various diploid species in the tribe Aveneae, revealing significant genomic expansions and structural variations.
- Findings show that Avena chromosomes experienced a ten to fifteen-fold increase in size, characterized by uniform expansions, conserved gene block arrangements, and notable translocations of gene-rich segments during speciation, indicating deep evolutionary relationships.
- This research enhances understanding of evolutionary processes in the BOP clade, offering insights that can aid in biodiversity assessment, the creation of a comprehensive pangenome, and utilizing genomic diversity for breeding initiatives in grass species.
Background: Repetitive DNA sequences accounts for over 80% of maize genome. Although simple sequence repeats (SSRs) account for only 0.03% of the genome, they have been widely used in maize genetic research and breeding as highly informative codominant DNA markers.
The study examines the karyotypic diversity in Loricariidae, focusing on the effects of chromosomal rearrangements and repetitive DNA sites on their genomes.
It highlights the significance of small nuclear RNAs (snRNAs) as cytogenetic markers for understanding chromosomal changes among closely related species due to their rare analysis.
Findings reveal that the nucleotide sequences of snRNAs show high identity among different species, with notable clustering on specific chromosomes, suggesting a role in chromosome rearrangements and karyotype variations within the family.
Djulis is an ancient crop from Taiwan, related to quinoa, known for its high nutritional value with complete proteins and essential vitamins.
Recent genomic research produced a high-quality genome assembly for djulis, revealing 75,056 potential genes and significant repetitive sequences, particularly in its B sub-genome.
The study also highlighted strong genetic similarities to quinoa, establishing important connections for understanding its genetics and potential conservation efforts amid changing diets and habitat loss among indigenous peoples.
Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland.
Cytogenetics constitutes a branch of genetics that is focused on the cellular components, especially chromosomes, in relation to heredity and genome structure, function and evolution. The use of modern cytogenetic approaches and the latest microscopes with image acquisition and processing systems enables the simultaneous two- or three-dimensional, multicolour visualisation of both single-copy and highly-repetitive sequences in the plant genome. The data that is gathered using the cytogenetic methods in the phylogenetic background enable tracing the evolution of the plant genome that involve changes in: (i) genome sizes; (ii) chromosome numbers and morphology; (iii) the content of repetitive sequences and (iv) ploidy level.
