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Comparative Analysis of Transposable Elements and the Identification of Candidate Centromeric Elements in the Subgenus and Its Relatives.

Authors:
Lei Wang Yan Wang Jing Zhang Yan Feng Qing Chen Zhen-Shan Liu Cong-Li Liu Wen He Hao Wang Shao-Feng Yang Yong Zhang Ya Luo Hao-Ru Tang Xiao-Rong Wang

Genes (Basel) 2022 04 2;13(4). Epub 2022 Apr 2.

College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China.

The subgenus and its relatives include many crucial economic drupe fruits and ornamental plants. Repetitive elements make up a large part of complex genomes, and some of them play an important role in gene regulation that can affect phenotypic variation. However, the variation in their genomes remains poorly understood. This work conducted a comprehensive repetitive sequence identification across the draft genomes of eight taxa of the genus , including four of the subgenus ( , , and ) as well as congeneric species (, , and ). Annotation results showed high proportions of transposable elements in their genomes, ranging from 52.28% () to 61.86% (). The most notable differences in the contents of long terminal repeat retrotransposons (LTR-RTs) and tandem repeats (TRs) were confirmed with identification based on the structure of each genome, which significantly contributed to their genome size variation, especially in and . Sequence comparisons showed many similar LTR-RTs closely related to their phylogenetic relationships, and a highly similar monomer unit of the TR sequence was conserved among species. Additionally, the predicted centromere-associated sequence was located in centromeric regions with FISH in the 12 taxa of . It presented significantly different signal intensities, even within the diverse interindividual phenotypes for . This study provides insight into the LTR-RT and TR variation within and increases our knowledge about its role in genome evolution.

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http://dx.doi.org/10.3390/genes13040641DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9028240PMC
April 2022

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