Space-efficient computation of k-mer dictionaries for large values of k.

Computing k-mer frequencies in a collection of reads is a common procedure in many genomic applications. Several state-of-the-art k-mer counters rely on hash tables to carry out this task but they are often optimised for small k as a hash table keeping keys explicitly (i.e., k-mer sequences) takes O ( N k w ) computer words, N being the number of distinct k-mers and w the computer word size, which is impractical for long values of k. This space usage is an important limitation as analysis of long and accurate HiFi sequencing reads can require larger values of k. We propose Kaarme, a space-efficient hash table for k-mers using O ( N + u k w ) words of space, where u is the number of reads. Our framework exploits the fact that consecutive k-mers overlap by k - 1 symbols. Thus, we only store the last symbol of a k-mer and a pointer within the hash table to a previous one, which we can use to recover the remaining k - 1 symbols. We adapt Kaarme to compute canonical k-mers as well. This variant also uses pointers within the hash table to save space but requires more work to decode the k-mers. Specifically, it takes O ( σ k ) time in the worst case, σ being the DNA alphabet, but our experiments show this is hardly ever the case. The canonical variant does not improve our theoretical results but greatly reduces space usage in practice while keeping a competitive performance to get the k-mers and their frequencies. We compare canonical Kaarme to a regular hash table storing canonical k-mers explicitly as keys and show that our method uses up to five times less space while being less than 1.5 times slower. We also show that canonical Kaarme uses significantly less memory than state-of-the-art k-mer counters when they do not resort to disk to keep intermediate results.

Detection of selection signatures in the genome of a farmed population of anadromous rainbow trout (Oncorhynchus mykiss).

Domestication processes and artificial selection are likely to leave signatures that can be detected at a molecular level in farmed rainbow trout (Oncorhynchus mykiss). These signatures of selection are genomic regions that contain functional genetic variants conferring a higher fitness to their bearers. We genotyped 749 rainbow trout from a commercial population using a rainbow trout Axiom 57 K SNP array panel and identified putative genomic regions under selection using the pcadapt, Composite Likelihood Ratio (CLR) and Integrated Haplotype Score (iHS) methods. After applying quality-control pipelines and statistical analyses, we detected 12, 96 and 16 SNPs putatively under selection, associated with 96, 781 and 115 candidate genes, respectively. Several of these candidate genes were associated with growth, early development, reproduction, behavior and immune system traits. In addition, some of the SNPs were found in interesting regions located in autosomal inversions on Omy05 and Omy20. These findings could represent a genome-wide map of selection signatures in farmed rainbow trout and could be important in explaining domestication and selection for genetic traits of commercial interest.

Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus).

Nile tilapia belongs to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs and domestication process of Nile tilapia may have modified the genome through selective pressure, leaving signals that can be detected at the molecular level. In this work, signatures of selection were identified using genome-wide SNP data, by two haplotype-based (iHS and Rsb) and one FST based method. Whole-genome re-sequencing of 326 individuals from three strains (A, B and C) of farmed tilapia maintained in Brazil and Costa Rica was carried out using Illumina HiSeq 2500 technology. After applying conventional SNP-calling and quality-control filters, ~ 1.3 M high-quality SNPs were inferred and used as input for the iHS, Rsb and FST based methods. We detected several candidate genes putatively subjected to selection in each strain. A considerable number of these genes are associated with growth (e.g. NCAPG, KLF3, TBC1D1, TTN), early development (e.g. FGFR3, PFKFB3), and immunity traits (e.g. NLRC3, PIGR, MAP1S). These candidate genes represent putative genomic landmarks that could be associated to traits of biological and commercial interest in farmed Nile tilapia.

Fine Mapping Using Whole-Genome Sequencing Confirms Anti-Müllerian Hormone as a Major Gene for Sex Determination in Farmed Nile Tilapia (Oreochromis niloticus L.).

Nile tilapia (Oreochromis niloticus) is one of the most cultivated and economically important species in world aquaculture. Intensive production promotes the use of monosex animals, due to an important dimorphism that favors male growth. Currently, the main mechanism to obtain all-male populations is the use of hormones in feeding during larval and fry phases. Identifying genomic regions associated with sex determination in Nile tilapia is a research topic of great interest. The objective of this study was to identify genomic variants associated with sex determination in three commercial populations of Nile tilapia. Whole-genome sequencing of 326 individuals was performed, and a total of 2.4 million high-quality bi-allelic single nucleotide polymorphisms (SNPs) were identified after quality control. A genome-wide association study (GWAS) was conducted to identify markers associated with the binary sex trait (males = 1; females = 0). A mixed logistic regression GWAS model was fitted and a genome-wide significant signal comprising 36 SNPs, spanning a genomic region of 536 kb in chromosome 23 was identified. Ten out of these 36 genetic variants intercept the anti-Müllerian (Amh) hormone gene. Other significant SNPs were located in the neighboring Amh gene region. This gene has been strongly associated with sex determination in several vertebrate species, playing an essential role in the differentiation of male and female reproductive tissue in early stages of development. This finding provides useful information to better understand the genetic mechanisms underlying sex determination in Nile tilapia.