Biology subjects

Lien, S.

Publications and source records attributed to Lien, S..

9 recordsLinked to original sources

bioRxiv2018

Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes

BackgroundAfrican cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to understand the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages.\n\nResultsWe re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage PacBio sequencing, and anchored contigs to linkage groups (LGs) using four different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes.\n\nLarge intra-chromosomal structural differences (~2-28Mbp) among species are common, while inter-chromosomal differences are rare (< 10Mbp total). Placement of the centromeres within chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11 and LG20 are associated with reductions in recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element (TE) insertions compared to O. niloticus, suggesting that several TE families have a higher rate of insertion in the haplochromine cichlid lineage.\n\nConclusionThis study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.

genomics↗

bioRxiv2018

A migration-associated supergene reveals loss of biocomplexity in Atlantic cod

Intraspecific phenotypic diversity is integral to ecological resilience and the provision of ecosystem services1. Chromosome structural variation may underpin intraspecific diversity and complex phenotypes2 by reducing recombination within supergenes containing linked, co-adapted alleles. Connecting ecologically-relevant phenotypes to genomic variation can enable more precise conservation of exploited marine species by protecting important genetic diversity3,4. Here, using genome-wide association analysis of a 12K single nucleotide polymorphism (SNP) array we confirm that an ancient, derived chromosomal rearrangement consisting of two adjacent inversions is strongly associated with migratory phenotype and individual-level genetic structure in Atlantic cod (Gadus morhua) across the Northwest Atlantic. The presence of all identified migration-associated loci within this rearrangement indicates that pervasive variation in migration phenotype is in part controlled by a recombination-resistant supergene, facilitating fine-scale individual phenotypic variation within Northern cod. Furthermore, we reconstruct trends in effective population size over the last century, and find genomic signatures of population collapse, and different patterns of population expansion and decline among individuals based on supergene alleles. We demonstrate declines in effective population size consistent with the onset of industrialized harvest (post 1950) and substantially reduced effective size of individuals homozygous for the derived chromosomal rearrangement relative to heterozygous individuals or those homozygous for the ancestral version of this chromosomal region. These results illustrate how chromosomal structural diversity can mediate fine-scale genetic and phenotypic variation in a highly connected marine species, and suggest a loss of biocomplexity from a migration-associated supergene within Northern cod by overfishing.

genomics↗

bioRxiv2018

A zinc knuckle gene on the Y chromosome (zkY) determines sex in Atlantic cod (Gadus morhua)

The genetic mechanisms determining sex in teleost fishes are highly variable, ranging from a single gene to complex patterns of polygenic regulation. The master sex determining gene has only been identified in very few species and there is no information about the gene in the superorder Paracanthopterygii that includes the codfishes, toadfishes and anglerfishes. Here we characterize a male-specific region of 9 kb on linkage group 11 in Atlantic cod (Gadus morhua) harboring a single gene named zkY for zinc knuckle on the Y chromosome. A diagnostic PCR test of phenotypically sexed males and females of Atlantic cod confirmed the sex-specific nature of the Y-sequence. We searched for autosomal gene copies of zkY and identified twelve highly similar genes, of which eight (zk1-zk8) code for proteins containing the zinc knuckle motif. 3D structure modelling suggests that the amino acid changes observed in six of the eight copies might influence the putative RNA-binding specificity. Cod zkY and the autosomal proteins zk1 and zk2 possess an identical zinc knuckle structure, but only the Y-specific gene zkY was expressed at high levels in the developing larvae before the onset of sex differentiation. We propose that cod zkY functions as the master masculinization gene by coding for a suppressor of germ cell division in males. PCR amplification of Y-sequences in Arctic cod (Arctogadus glacialis) and Greenland cod (Gadus macrocephalus ogac) suggests that this novel sex determining mechanism emerged in codfishes more than 7.5 million years ago.\n\nAuthor SummaryStudying the diverse sex determining genes in teleost fish may contribute to increase our understanding of sex chromosome evolution in vertebrates. To date, no sex determinant is known for the superorder Paracanthopterygii, comprising about 1340 species, including the commercially important Atlantic cod. In this study we characterize a Y-specific region of 9 kb on linkage group 11 containing a single gene named zkY for zinc knuckle on the Y chromosome. The gene is transcribed at high levels in larvae before commencement of sex differentiation and encodes a novel zinc knuckle protein that putatively binds RNA target sequences. We propose that cod zkY suppresses germ cell proliferation in the developing males by interacting with the germ-cell specific RNA regulatory network.

genetics↗

bioRxiv2018

Chromosome polymorphisms track trans-Atlantic divergence, admixture and adaptive evolution in salmon

Pleistocene glaciations drove repeated range contractions and expansions shaping contemporary intraspecific diversity. Atlantic salmon (Salmo salar) from the western and eastern Atlantic range diverged >600K YBP, with each clade isolated in independent southern refugia during glacial maxima, driving trans-Atlantic genomic and karyotypic differences. Here, we investigate genomic consequences of glacial isolation and transAtlantic secondary contact using a 220K single nucleotide polymorphism (SNP) array genotyped in 80 North American and European populations. Throughout North America, we identified large inter-individual variation and discrete linkage blocks within and between chromosomes with known rearrangements: Ssa01/Ssa23 translocation and Ssa08/Ssa29 fusion. Spatial genetic analyses suggest independence of rearrangements, with Ssa01/Ssa23 showing high European introgression (>50%) in northern populations indicative of post-glacial trans-Atlantic secondary contact, contrasting low European ancestry genome-wide (3%). Ssa08/Ssa29 showed greater intra-population diversity suggesting a derived chromosome fusion polymorphism within North America. Evidence of selection on both regions suggests adaptive variation associated with karyotypes. Our study highlights how Pleistocene glaciations can drive large-scale intraspecific variation in genomic architecture of northern species.

genomics↗

bioRxiv2018

Development and validation of 58K SNP-array and high-density linkage map in Nile tilapia (O. niloticus)

Despite being the second most important aquaculture species in the world accounting for 7.4% of global production in 2015, tilapia aquaculture has lacked genomic tools like SNP-arrays and high-density linkage maps to improve selection accuracy and accelerate genetic progress. In this paper we describe the development of a genotyping array containing more than 58,000 SNPs for Nile tilapia (Oreochromis niloticus). SNPs were identified from whole genome resequencing of 32 individuals from the commercial population of the Genomar strain, and selected for the SNP-array based on polymorphic information content and physical distribution across the genome using the Orenil1.1 genome assembly as reference sequence. SNP-performance was evaluated by genotyping 4991 individuals, including 689 offspring belonging to 41 full-sib families, which revealed high-quality genotype data for 43,588 of the SNPs. A preliminary genetic linkage map was constructed using Lepmap2 which in turn was integrated with information from the O_niloticus_UMD1 genome assembly to produce an integrated physical and genetic linkage map comprising 40,186 SNPs distributed across 22 linkage groups. Around one-third of the linkage groups showed a different recombination rate between sexes, with male and female map lengths differing by a factor of 1.2 (1359.6cM and 1632.9cM respectively), with most linkage groups displayed a sigmoid recombination profile. Finally, the sex-determining locus in this population was mapped to position 40.53 cM on linkage group 23, in the vicinity of the anti-Mullerian hormone (amh) gene. These new resources has the potential to greatly influence and improve the genetic gain when applying genomic selection and surpass the difficulties of efficient selection for invasive traits in tilapia.

genomics↗

bioRxiv2017

The grayling genome reveals selection on gene expression regulation after whole genome duplication

Whole genome duplication (WGD) has been a major evolutionary driver of increased genomic complexity in vertebrates. One such event occurred in the salmonid family ~80 million years ago (Ss4R) giving rise to a plethora of structural and regulatory duplicate-driven divergence, making salmonids an exemplary system to investigate the evolutionary consequences of WGD. Here, we present a draft genome assembly of European grayling (Thymallus thymallus) and use this in a comparative framework to study evolution of gene regulation following WGD. Among the Ss4R duplicates identified in European grayling and Atlantic salmon (Salmo salar), one third reflect non-neutral tissue expression evolution, with strong purifying selection, maintained over ~50 million years. Of these, the majority reflect conserved tissue regulation under strong selective constraints related to brain and neural-related functions, as well as higher-order protein-protein interactions. A small subset of the duplicates has evolved tissue regulatory expression divergence in a common ancestor, which have been subsequently conserved in both lineages, suggestive of adaptive divergence following WGD. These candidates for adaptive tissue expression divergence have elevated rates of protein coding- and promoter-sequence evolution and are enriched for immune- and lipid metabolism ontology terms. Lastly, lineage-specific duplicate divergence points towards underlying differences in adaptive pressures on expression regulation in the non-anadromous grayling versus the anadromous Atlantic salmon.\n\nOur findings enhance our understanding of the role of WGD in genome evolution and highlights cases of regulatory divergence of Ss4R duplicates, possibly related to a niche shift in early salmonid evolution.

genomics↗

bioRxiv2017

Diet And Life Stage Associated Remodeling Of Lipid Metabolism Regulation In The Duplicated Atlantic Salmon Genome

Atlantic salmon migrates from rivers to sea to feed, grow and develop gonads before returning to spawn in freshwater. These habitat shifts require great phenotypic plasticity. To address the unresolved question of how the shift in diet between fresh and saltwater affects the regulation of metabolic function, we fed salmon contrasting diets in each of the two life stages. Combining transcriptomics with comparative genomics, we found that lipid metabolism undergoes a concerted shift between fresh- and saltwater stages. Lipogenesis and lipid transport become less active in liver after transition to saltwater, while genes for lipid uptake in gut are more expressed in lipid-rich seawater environments. We assess how the whole-genome duplication that gave rise to the salmonids has impacted the evolution of lipid metabolism, and find signatures of pathway-specific selection pressure on gene duplicates, as well as a limited number of cases of increased gene dosage.

evolutionary biology↗

bioRxiv2017

Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification

The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification is often highly temporally-detached from WGD. Salmonid fish, whose ancestor experienced WGD by autotetraploidization ~95 Ma (i.e. Ss4R), fit such a time-lag model of post-WGD radiation, which occurred alongside a major delay in the rediploidization process. Here we propose a model called Lineage-specific Ohnologue Resolution (LORe) to address the phylogenetic and functional consequences of delayed rediploidization. Under LORe, speciation precedes rediploidization, allowing independent ohnologue divergence in sister lineages sharing an ancestral WGD event. Using cross-species sequence capture, phylogenomics and genome-wide analyses of ohnologue expression divergence, we demonstrate the major impact of LORe on salmonid evolution. One quarter of each salmonid genome, harbouring at least 4,500 ohnologues, has evolved under LORe, with rediploidization and functional divergence occurring on multiple independent occasions > 50 Myr post-WGD. We demonstrate the existence and regulatory divergence of many LORe ohnologues with functions in lineage-specific physiological adaptations that promoted salmonid species radiation. We show that LORe ohnologues are enriched for different functions than older ohnologues that began diverging in the salmonid ancestor. LORe has unappreciated significance as a nested component of post-WGD divergence that impacts the functional properties of genes, whilst providing ohnologues available solely for lineage-specific adaptation. Under LORe, which is predicted following many WGD events, the functional outcomes of WGD need not appear explosively, but can arise gradually over tens of Myr, promoting lineage-specific diversification regimes under prevailing ecological pressures.

genomics↗

bioRxiv2016

Functional Analysis of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

We describe an emerging initiative - the Functional Analysis of All Salmonid Genomes (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, through to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.

genomics↗