Abstract
To better understand PBI-DdeI satellite DNA located in the centromeric region of python, molecular evolution analysis was conducted on 40 snake species. A ladder-like pattern of DNA bands with repetition of the 194–210 bp monomer was observed in 15 species using PCR. Molecular cloning was performed to obtain 97 AT-rich monomer sequences. Phylogenetic and network analyses showed three PBI-DdeI subfamilies with sequences grouped in species-specific clusters, suggesting rapid evolution. Slow evolution was found in eight species with shared PBI-DdeI sequences, suggesting recent species diversification, allowing PBI-DdeI no time to diverge, with limited homogenization and fixation processes. Quantitative real-time PCR showed large differences in copy number between Python bivittatus and other snakes, consistent with repeat scanning of whole genome sequences. Copy numbers were significantly higher in female Naja kaouthia than in males, concurring with chromosomal distribution of PBI-DdeI specifically localized to female W chromosomes. PBI-DdeI might act as an evolutionary driver with several repeats to promote W chromosome differentiation and heterochromatinization in N. kaouthia. Analysis revealed PBI-DdeI with a reduced copy number, compared to P. bivittatus, in most snakes studied, and it is possible that it subsequently dispersed and amplified on W chromosomes with different functional roles in N. kaouthia.
Highlights
Several recent snake genome analyses have revealed that the remarkable variability in genome size results from large differences in the amount of repeated sequences[1]
This might be important for chromatin condensation or interaction between protein and DNA22, and suggests that PBI-DdeI plays an important role under selective pressure
A satellite DNA (satDNA) family may be replaced by another satDNA family/subfamily, known as the library model3,11. quantitative real-time polymerase chain reaction (qPCR) analysis showed different copy numbers of PBI-DdeI with approximately 5.73 × 106 copies, accounting for 82.53% of the P. bivittatus genome
Summary
Several recent snake genome analyses have revealed that the remarkable variability in genome size results from large differences in the amount of repeated sequences[1]. Different satDNA families/subfamilies may coexist in the genome of a species and can efficiently change the arrangement of DNA sequences in heterochromatin by replacing one dominant satDNA family with another that is less well represented, differing in nucleotide sequences and/or copy numbers in related species, following “the library model”[11] This consequence varies among satDNA families based on mutation rate, species, chromosome morphology, population size, and reproductive mode[12]. This process occurs rapidly among species, resulting in the expansion of new mutations horizontally throughout the genome of distantly related species[6,13]. This allowed us to delineate the evolutionary dynamics of PBI-DdeI and investigate its significance
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