The mutational load in natural populations is significantly affected by high primary rates of retroposition

The phenomenon of retroposition (the reintegration of reverse-transcribed RNA into the genome) has been well studied in comparisons between species and has been identified as a source of evolutionary innovation. However, less attention has been paid to possible negative effects of retroposition. To trace the evolutionary dynamics of these negative effects, our study uses a unique genomic dataset of house mouse populations. It reveals that the initial retroposition rate is very high and that most of these newly transposed retrocopies have a deleterious impact, apparently through modifying the expression of their parental genes. In humans, this effect is expected to cause disease alleles, and we propose that genetic screening should include the search for newly transposed retrocopies.Gene retroposition is known to contribute to patterns of gene evolution and adaptations. However, possible negative effects of gene retroposition remain largely unexplored since most previous studies have focused on between-species comparisons where negatively selected copies are mostly not observed, as they are quickly lost from populations. Here, we show for natural house mouse populations that the primary rate of retroposition is orders of magnitude higher than the long-term rate. Comparisons with single-nucleotide polymorphism distribution patterns in the same populations show that most retroposition events are deleterious. Transcriptomic profiling analysis shows that new retroposed copies become easily subject to transcription and have an influence on the expression levels of their parental genes, especially when transcribed in the antisense direction. Our results imply that the impact of retroposition on the mutational load has been highly underestimated in natural populations. This has additional implications for strategies of disease allele detection in humans.The raw strand-specific RNA-Seq data generated in this study are available in the European Nucleotide Archive under study accession number PRJEB36991

Ancient segmentally duplicated LCORL retrocopies in equids.

LINE-1 is an active transposable element encoding proteins capable of inserting host gene retrocopies, resulting in retro-copy number variants (retroCNVs) between individuals. Here, we performed retroCNV discovery using 86 equids and identified 437 retrocopy insertions. Only 5 retroCNVs were shared between horses and other equids, indicating that the majority of retroCNVs inserted after the species diverged. A large number (17-35 copies) of segmentally duplicated Ligand Dependent Nuclear Receptor Corepressor Like (LCORL) retrocopies were present in all equids but absent from other extant perissodactyls. The majority of LCORL transcripts in horses and donkeys originate from the retrocopies. The initial LCORL retrotransposition occurred 18 million years ago (17-19 95% CI), which is coincident with the increase in body size, reduction in digit number, and changes in dentition that characterized equid evolution. Evolutionary conservation of the LCORL retrocopy segmental amplification in the Equidae family, high expression levels and the ancient timeline for LCORL retrotransposition support a functional role for this structural variant

レトロ遺伝子PIPSLの転写機構に関する研究

長浜バイオ大学201

Sequencing and Assembling the Nuclear Genome of the Antarctic Psychrophilic Green Alga Chlamydomonas sp. UWO241: Unravelling the Evolution of Cold Adaptation

DNA sequencing technologies have undergone tremendous advancements in recent years, but assembling, annotating, and analyzing a nuclear genome is still a huge undertaking, especially for small laboratory groups, partly because many eukaryotic genomes are repeat-rich and contain thousands of genes and introns. The Antarctic harbors a variety of algae that can withstand extreme cold but do not grow at warmer temperatures (psychrophiles), including the unicellular green alga Chlamydomonas sp. UWO241 (a.k.a. UWO241). Little is known, however, about how psychrophilic algae evolved from their respective mesophilic ancestors by adapting to particular cold environments. To present insights into this issue,I critically determined the draft nuclear genome (~212 Mb, 16,325 protein-coding genes) sequence of UWO241 and performed comparative genomic analyses. Firstly, an assembly pipeline was developed for processing high throughput sequencing (DNA-Seq) reads into genomic contigs. These contigs, alongside transcriptome sequencing (RNA-Seq) reads, were fed into an annotation pipeline, containing the commonly used bioinformatics gene-profiling software. Computational analyses were carried out on a powerful in-house computer. Finally, comparative genomic analyses were performed between UWO241 and its close green algal relatives in the Chlamydomonadales revealing: (1) UWO241 harbors hundreds of highly similar duplicate genes involved in diverse cellular processes, some of which I argue are aiding its survival in the Antarctic via gene dosage; (2) UWO241 encodes a large number (³37) of ice-binding proteins (IBPs), putatively originating from horizontal gene transfer; and (3) UWO241 appears to have an expanded set of orthologous gene families for reverse transcriptase, IBPs and antenna proteins. These investigations deepen our understanding of evolution between psychrophilic and mesophilic algae and help unravel the existence of common mechanisms in the adaptation to cold environments