Sex determining gene transposition as an evolutionary platform for chromosome turnover

SummaryDespite the key role that sex-determination plays in evolutionary processes, it is still poorly understood in many species. In salmonids, which are the best studied family of fishes, the master sex-determining gene sexually dimorphic on the Y-chromosome (sdY) has been identified. However, sdY displays unexplained discordance to the phenotypic sex, with a variable frequency of phenotypic females being reported as genetic males. Multiple sex determining loci in Atlantic salmon have also been reported, possibly as a result of transposition, suggesting a recent and non-random sex chromosome turnover in this species. We hypothesized the existence of an autosomic pseudocopy of sdY that is transmitted in accordance with Mendelian inheritance. To test this we developed a qPCR methodology to detect the number of sdY copies present in the genome. Based on the observed phenotype/genotype frequencies and linkage analysis among 2025 offspring from 64 pedigree-controlled families of accurately phenotyped Atlantic salmon, we identified both males and females carrying one or two autosomic copies in addition to the Y-specific copy present in males. Copy number frequencies were consistent with Mendelian inheritance. Pseudocopy loci were mapped to different chromosomes evidencing non-random transitions of the sex determining gene in Atlantic salmon and the existence of functional constraints for chromosome turnover.

Landscape of gene transposition-duplication within the Brassicaceae family

ABSTRACTWe developed the CLfinder-OrthNet pipeline that detects co-linearity in gene arrangement among multiple closely related genomes; find ortholog groups; and encodes the evolutionary history of each ortholog group into a representative network (OrthNet). Using a search based on network topology, out of a total of 17,432 OrthNets in six Brassicaceae genomes, we identified 1,394 that included gene transposition-duplication (tr-d) events in one or more genomes. Occurrences of tr-d shared by subsets of Brassicaceae genomes mirrored the divergence times between the genomes and their repeat contents. The majority of tr-d events resulted in truncated open reading frames (ORFs) in the duplicated loci. However, the duplicates with complete ORFs were significantly more frequent than expected from random events. They also had a higher chance of being expressed and derived from older tr-d events. We also found an enrichment, compared to random chance, of tr-d events with complete loss of intergenic sequence conservation between the original and duplicated loci. Finally, we identified tr-d events uniquely found in two extremophytes among the six Brassicaceae genomes, including tr-d of SALT TOLERANCE 32 and ZINC TRANSPORTER 3. The CLfinder-OrthNet pipeline provides a flexible and a modular toolkit to compare gene order, encode and visualize evolutionary paths among orthologs as networks, and identify all gene loci that share the same evolutionary history using network topology searches.Funding source: This work was supported by National Science Foundation (MCB 1616827) and the Next Generation BioGreen21 Program (PJ011379) of the Rural Development Administration, Republic of Korea.Online-only Supplementary materials includes supplementary text (S1-S10), methods (M1-M4), figures (S1-S7), and tables (S1-S3), in two PDF files, one for text and methods and the other for figures and tables. Additionally, Supplementary Dataset S1 is available at the Figshare repository (https://doi.org/10.6084/m9.figshare.5825937) and Dataset S2 and S3 as separate Excel files.

Tagged Mutagenesis by Efficient Minos-Based Germ Line Transposition

ABSTRACT Germ line gene transposition technology has been used to generate “libraries” of flies and worms carrying genomewide mutations. Phenotypic screening and DNA sequencing of such libraries provide functional information resulting from insertional events in target genes. There is also a great need to have a fast and efficient way to generate mouse mutants in vivo to model developmental defects and human diseases. Here we describe an optimized mammalian germ line transposition system active during early mouse spermatogenesis using the Minos transposon. Transposon-positive progeny carry on average more than 2 new transpositions, and 45 to 100% of the progeny carry an insertion in a gene. The optimized Minos-based system was tested in a small rapid dominant functional screen to identify mutated genes likely to cause measurable cardiovascular “disease” phenotypes in progeny/embryos. Importantly this system allows rapid screening for modifier genes.