Can-SINE dynamics in the giant panda and three other Caniformia genomes

Abstract

BackgroundAlthough repeat sequences constitute about 37% of carnivore genomes, the characteristics and distribution of repeat sequences among carnivore genomes have not been fully investigated. Based on the updated Repbase library, we re-annotated transposable elements (TEs) in four Caniformia genomes (giant panda, polar bear, domestic dog, and domestic ferret) and performed a systematic, genome-wide comparison focusing on the Carnivora-specific SINE family, Can-SINEs.ResultsWe found the majority of young recently integrated transposable elements are LINEs and SINEs in carnivore genomes. In particular, SINEC1_AMe, SINEC1B_AMe and SINEC_C1 are the top three most abundant Can-SINE subfamilies in the panda and polar bear genomes. Transposition in transposition analysis indicates that SINEC1_AMe and SINEC1B_AMe are the most active subfamilies in the panda and the polar bear genomes. SINEC2A1_CF and SINEC1A_CF subfamilies show a higher retrotransposition activity in the dog genome, and MVB2 subfamily is the most active Can-SINE in the ferret genome. As the giant panda is an endangered icon species, we then focused on the identification of panda specific Can-SINEs. With the panda-associated two-way genome alignments, we identified 250 putative panda-specific (PPS) elements (139 SINEC1_AMes and 111 SINEC1B_AMes) that inserted in the panda genome but were absent at the orthologous regions of the other three genomes. Further investigation of these PPS elements allowed us to identify a new Can-SINE subfamily, the SINEC1_AMe2, which was distinguishable from the current SINEC1_AMe consensus by four non-CpG sites. SINEC1_AMe2 has a high copy number (> 100,000) in the panda and polar bear genomes and the vast majority (> 96%) of the SINEC1_AMe2 elements have divergence rates less than 10% in both genomes.ConclusionsOur results suggest that Can-SINEs show lineage-specific retransposition activity in the four genomes and have an important impact on the genomic landscape of different Caniformia lineages. Combining these observations with results from the COSEG, Network, and target site duplication analysis, we suggest that SINEC1_AMe2 is a young mobile element subfamily and currently active in both the panda and polar bear genomes.Electronic supplementary materialThe online version of this article (10.1186/s13100-018-0137-0) contains supplementary material, which is available to authorized users.

Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae

“…The overall repeat landscape of the tayra genome assembly is comparable to other carnivore genomes (Liu et al, 2020;Peng et al, 2018). It is similar to that of the sable genome, differing mostly in the number of L1 LINE elements, which have been recently proliferating and accumulating within the tayra genome more than in other Guloninae genomes.…”

Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae

“…The overall 'repeat landscape' of the tayra genome assembly is comparable to other carnivore genomes (C. Peng et al 2018;G. Liu et al 2020).…”

“…The overall repeat landscape of the tayra genome assembly is comparable to other carnivore genomes Peng et al, 2018). It is similar to that of the sable genome, differing mostly in the number of L1 LINE elements, which have been recently proliferating and accumulating within the tayra genome more than in other Guloninae genomes.…”

A 4-lineage statistical suite to evaluate the support of large-scale retrotransposon insertion data to reconstruct evolutionary trees

“…The copyright holder for this this version posted December 11, 2020. ; https://doi.org/10.1101/2020.12.10.419374 doi: bioRxiv preprint thousand years ago and have since been diversified into approximately 400 different breeds (Galibert et al, 2011). The large number of dog-specific SINE elements that were active over a long period of time (Peng et al, 2018) and the rapid diversification of lineages boosted by domestication makes domesticated dogs a good example for testing the 4-LIN statistical approach. We first used 2-n-way (Churakov et al, 2020) to find and extract diagnostic presence/absence markers from 2-way alignments generated from the genomes of the boxer, beagle, German shepherd, and dingo.…”