A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes

Abstract

LTR retrotransposons (LTR-RTs) are ubiquitous and represent the dominant repeat element in plant genomes, playing important roles in functional variation, genome plasticity and evolution. With the advent of new sequencing technologies, a growing number of whole-genome sequences have been made publicly available, making it possible to carry out systematic analyses of LTR-RTs. However, a comprehensive and unified annotation of LTR-RTs in plant groups is still lacking. Here, we constructed a plant intact LTR-RTs dataset, which is designed to classify and annotate intact LTR-RTs with a standardized procedure. The dataset currently comprises a total of 2,593,685 intact LTR-RTs from genomes of 300 plant species representing 93 families of 46 orders. The dataset is accompanied by sequence, diverse structural and functional annotation, age determination and classification information associated with the LTR-RTs. This dataset will contribute valuable resources for investigating the evolutionary dynamics and functional implications of LTR-RTs in plant genomes.

Annotation of Siberian Larch (Larix sibirica Ledeb.) Nuclear Genome—One of the Most Cold-Resistant Tree Species in the Only Deciduous GENUS in Pinaceae

“…In the gymnosperms, 10–15 MYA insertion times have been reported [ 80 ]. Based on the LTRs identification by Zhou et al [ 81 ], the approximate time of LTR expansion in the gymnosperms can be estimated to be 2–4 MYA. In the larch, the time estimate can be influenced either by the efficient repeat elimination mechanism combined with the true ancient repeat insertion, or by the fragmented nature of the draft assembly, and consequently, the low number of found LTRs.…”

“…Zhou et al [ 81 ] have carried out a thorough search for LTR-RTs and generated an LTRs resource for 301 plant genomes, including publicly available draft genomes of 10 gymnosperms. For the L. sibirica draft genome, they identified 367 LTR-RT elements.…”

Retrotransposons: How the continuous evolutionary front shapes plant genomes for response to heat stress

“…LTR retrotransposons from genomes of about 300 plant species have been identified and are associated with diverse structural, functional annotation, and classification information (Zhou et al, 2021). Thus, this information may provide useful resources for investigating the evolutionary dynamics and functional implications of LTR retrotransposons in plant genomes (Kalendar et al, 2004;Moisy et al, 2014;Kalendar et al, 2020).…”

Evolution of complex genome architecture in gymnosperms

“…It is worth mentioning that the outlier Welwitschia has suffered from a very recent expansion of both autonomous and nonautonomous LTRs in less than 1 to 2 Ma, which probably resulted from a cascade of events triggered by intense aridity [ 27 ]. The high-resolution categories of retroelements and the use of appropriate mutation rates [ 60 ] are both required to distinguish the species-specific expansions that contribute to the diversity in genome growth rhythms [ 61 , 62 ].…”