Distinct Retrotransposon Evolution Profile in the Genome of Rabbit (Oryctolagus cuniculus)

Abstract

Although the rabbit genome has already been annotated, it’s mobilome remains largely unknown. Here, multiple pipelines were used to de novo mine and annotate the mobilome in rabbit. Four families and 19 subfamilies of LINE1s, two families and nine subfamilies of SINEs, and 12 ERV families were defined in rabbit based on sequence identity, structural organization, and phylogenetic tree. The analysis of insertion age and polymerase chain reaction (PCR) suggest that a number of families are very young and may remain active, such as L1B, L1D, OcuSINEA, and OcuERV1. RepeatMasker annotation revealed a distinct TE landscape within the genome, with approximately 2 million copies of SINEs, representing the greatest proportion of the genome (19.61%), followed by LINEs (15.44%), and LTRs (4.11%), respectively, considerably different from most other mammal mobilomes except hedgehog and tree shrew, in which LINEs have the highest proportion. Furthermore, a very high rate of insertion polymorphisms (>85%) for the youngest subfamily (OcuSINEA1) was identified by PCR. The majority of retrotransposon insertions overlapped with protein-coding regions (>80%) and lncRNA (90%) genes. Genomic distribution bias was observed for retrotransposons, with those immediately upstream (-1 kb) and downstream (1 kb) of genes significantly depleted. Local GC content in 50 kb widows had significantly negative correlations with LINE (rs = -0.996) and LTR (rs = -0.829) insertions. The current study revealed a distinct mobilome landscape in rabbit, which will assist in the elucidation of the evolution of the genome of lagomorphs, and even other mammals.

Four classic “de novo” genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences

“…Even if the gene perform does some function, it does not follow that it would be useful, thereby allowing it to be preserved by natural selection. The de novo recruitment of some ncDNA into an existing protein-coding gene is entirely possible, such as through retrotransposon insertion (Poretti et al 2023; Yang et al 2021), although this describes an expansion of an already functioning gene rather than one that is born “from scratch”. Also, if a peptide is, in fact, confirmed not to exist anywhere else within the protein repertoire, this may not by itself be that significant.…”

Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes

“…Nowadays, more researchers turn sight to SV exploration work from plant [36] to animal [51] phenotype and even in human healthy [52]. Particularly, RIPs, as important sources of SVs, play important roles in genomic shaping and phenotype variations [53]. In animals, several cases of the coat color phenotype variations derived from RIPs have been reported.…”

THE SOURCES OF GENOME VARIABILITY AS DOMESTICATION DRIVERS (review)

“…Сравнение распределения мобильных генетических элементов между домашним кроликом (Oryctolagus cuniculus domesticus) и пищухой (Ochotona princeps) показало заметно большую частоту встречаемости у домашнего вида по сравнению с диким (60). Сходные различия выявлены и при сравнении домашней кошки (Felis silvestris catus) и близкородственного дикого вида (Felis silvestris silvestris) (61).…”

“…В процессе формирования новой многокомпонентой ниши человек (доместикатор)-растения/животные (доместицируемые) в геноме доместицируемого формируется повышенная плотность мобильных генетических элементов, основанная на пониженной резистентности геномов к интеграции транспозонов. В пользу этого предположения свидетельствуют вовлеченность транспозонов в эпигенетическую изменчивость (31,51) и в организацию архитектоники интерфазного ядра (35), высокая скорость их эволюции (34), частоты рекомбинаций между ними (43,58), разичия между домашними и дикими видами по распространенности некоторых транспозонов в геномах (56,(59)(60)(61). В наших предыдущих исследованиях мы отмечали, что основным нерешенным вопросом в поисках ведущих геномных особенностей у доместицированных видов при сравнении с близкородственными дикими является источник изменчивости, отличающий эти близкородственные формы (62,63).…”