Abstract
Recent sequencing of the Oriental pear (P. bretschneideri Rehd.) genome and the availability of the draft genome sequence of Occidental pear (P. communis L.), has provided a good opportunity to characterize the abundance, distribution, timing, and evolution of long terminal repeat retrotransposons (LTR-RTs) in these two important fruit plants. Here, a total of 7247 LTR-RTs, which can be classified into 148 families, have been identified in the assembled Oriental pear genome. Unlike in other plant genomes, approximately 90% of these elements were found to be randomly distributed along the pear chromosomes. Further analysis revealed that the amplification timeframe of elements varies dramatically in different families, super-families and lineages, and the Copia-like elements have highest activity in the recent 0.5 million years (Mys). The data also showed that two genomes evolved with similar evolutionary rates after their split from the common ancestor ~0.77–1.66 million years ago (Mya). Overall, the data provided here will be a valuable resource for further investigating the impact of transposable elements on gene structure, expression, and epigenetic modification in the pear genomes.
Highlights
Retrotransposons are abundant and widespread mobile DNA in eukaryotic genomes
The Copia-like Maximus lineage has been lost in the Rosaceae species and the two pear species have evolved with similar evolutionary rates since they split from their common ancestor ~0.77–1.66 million years ago (Mya)
To accurately characterize the structure of long terminal repeat retrotransposons (LTR-RTs) and their organization in the pear genome, we annotated LTR-RTs in the high-quality assembled Oriental pear (P. bretschneideri) genome based on previously used methods[10,25], and detailed manual inspections have been conducted to confirm each predicted element and define its structure and boundaries
Summary
Identification and Structural Characterization of LTR-RTs in the Pear (P. bretschneideri). In order to further understand the distribution of LTR-RTs in pear, we investigated and compared the abundance, activities, and amplification timeframes of the LTR-RTs from different super-families This effort yielded several clear observations 1) the average insertion time of LTR-RTs for Copia-like, Gypsy-like, TRIM and LARD super-families is 1.36, 2.22, 1.75, and 3.17 Mys, respectively; 2) most of the Copia-like elements (559, 42.2%) are amplified in the last 1 Mys, whereas most Gypsy-like (481, 77.7%), TRIM (962, 76.8%), and LARD (21, 87.5%) elements proliferated during the last 1–4 Mys; 3) Of the 491 LTR-RTs that proliferated within the last 0.5 Mys, 382 (77.8%) elements belong to Copia-like super-family; 4) Of the 121 elements with two identical LTRs, 113, 8, 0 and 0 are Copia-like, Gypsy-like, and TRIM or LARD elements, respectively (Fig. 3c). Five out of the six Copia-like lineages are shared by pear and other plant species, but the Maximus lineage was not found in the pear genome (Fig. 4a), which may be caused by the likely accumulated mutations including the deletion of the RT protein sequence and became non-autonomous and truncated elements. We investigated whether the env-like protein of Maximus lineage is absent
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
