Genome reconstruction and combinatoric analyses of rearrangement evolution

Cancer is often associated with a high number of large-scale, structural rearrangements. In a highly selective environment, some `driver' mutations conferring clonal growth advantage will be positively selected, accounting for further cancer development. Clarifying their nature, as well as their contribution to the pathology is a major current focus of biomedical research. Next generation sequencing technologies can be used nowadays to generate high-resolution data-sets of these alterations in cancer genomes. This project has been developed along two main lines: 1) the reconstruction of cancer aberrant karyotypes, together with their underlying evolutionary history; 2) the elucidation of some combinatorial properties associated with gene duplications. We applied graph theory to the problem of reconstructing the final cancer genome sequence; additionally, we developed an algorithmic approach for the reconstruction of a multi-step evolution consistent with read coverage and paired end data, giving insights on the possible molecular mechanisms underlying rearrangements. Looking at the combinatorics of both tandem and inverted duplication, we developed an algebraic formalism for the representation of these processes. This allowed us to both explore the geometric properties of sequences arising by Tandem Duplication (TD), and obtain a recursion for the number of tandem duplications evolutions after n events. Such results are missing for inverted duplications, whose combinatorial properties have been nevertheless deeply elucidated. Our results have allowed: 1) the identification, through an original approach, of potential rearrangement mechanisms associated with cancer development, and 2) the definition and mathematical description of the complete evolutionary space of specific rearrangement classes

Genomic Evidence for an African Expansion of Anatomically Modern Humans by a Southern Route

There is general agreement among scientists about a recent (less than 200,000 yrs ago) African origin of anatomically modern humans, whereas there is still uncertainty about whether, and to what extent, they admixed with archaic populations, which thus may have contributed to the modern populations’ gene pools. Data on cranial morphology have been interpreted as suggesting that, before the main expansion from Africa through the Near East, anatomically modern humans may also have taken a Southern route from the Horn of Africa through the Arabian peninsula to India, Melanesia and Australia, about 100,000 yrs ago. This view was recently supported by archaeological findings demonstrating human presence in Eastern Arabia 90,000 yrs ago. In this study we analyzed genetic variation at 111,197 nuclear SNPs in nine populations (Kurumba, Chenchu, Kamsali, Madiga, Mala, Irula, Dalit, Chinese, Japanese), chosen because their genealogical relationships are expected to differ under the alternative models of expansion (single vs. multiple dispersals). We calculated correlations between genomic distances, and geographic distances estimated under the alternative assumptions of a single dispersal, or multiple dispersals, and found a significantly stronger association for the multiple dispersal model. If confirmed, this result would cast doubts on the possibility that some non-African populations (i.e., those whose ancestors expanded through the Southern route) may have had any contacts with Neandertals

The complexity of genome rearrangement combinatorics under the infinite sites model

Rearrangements are discrete processes whereby discrete segments of DNA are deleted, replicated and inserted into novel positions. A sequence of such configurations, termed a rearrangement evolution, results in jumbled DNA arrangements, frequently observed in cancer genomes. We introduce a method that allows us to precisely count these different evolutions for a range of processes including breakage-fusion-bridge-cycles, tandem-duplications, inverted-duplications, reversals, transpositions and deletions, showing that the space of rearrangement evolution is superexponential in size. These counts assume the infinite sites model of unique breakpoint usage

MicroRNA Profiling in the Weddell Seal Suggests Novel Regulatory Mechanisms Contributing to Diving Adaptation

Background:The Weddell Seal (Leptonychotes weddelli) represents a remarkable example of adaptation to diving among marine mammals. This species is capable of diving... (See full abstract in article)

Evolution of miRNA-binding sites and regulatory networks in cichlids

The divergence of regulatory regions and gene regulatory network (GRN) rewiring is a key driver of cichlid phenotypic diversity. However, the contribution of miRNA-binding site turnover has yet to be linked to GRN evolution across cichlids. Here, we extend our previous studies by analyzing the selective constraints driving evolution of miRNA and transcription factor (TF)-binding sites of target genes, to infer instances of cichlid GRN rewiring associated with regulatory binding site turnover. Comparative analyses identified increased species-specific networks that are functionally associated to traits of cichlid phenotypic diversity. The evolutionary rewiring is associated with differential models of miRNA- and TF-binding site turnover, driven by a high proportion of fast-evolving polymorphic sites in adaptive trait genes compared with subsets of random genes. Positive selection acting upon discrete mutations in these regulatory regions is likely to be an important mechanism in rewiring GRNs in rapidly radiating cichlids. Regulatory variants of functionally associated miRNA- and TF-binding sites of visual opsin genes differentially segregate according to phylogeny and ecology of Lake Malawi species, identifying both rewired, for example, clade-specific and conserved network motifs of adaptive trait associated GRNs. Our approach revealed several novel candidate regulators, regulatory regions, and three-node motifs across cichlid genomes with previously reported associations to known adaptive evolutionary traits

Evolution of regulatory networks associated with traits under selection in cichlids

Background Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is known about gene regulatory network (GRN) evolution associated with phenotypic effect across ecologically diverse species. Here we use a novel approach for comparative GRN analysis in vertebrate species to study GRN evolution in representative species of the most striking examples of adaptive radiations, the East African cichlids. We previously demonstrated how the explosive phenotypic diversification of East African cichlids can be attributed to diverse molecular mechanisms, including accelerated regulatory sequence evolution and gene expression divergence. Results To investigate these mechanisms across species at a genome-wide scale, we develop a novel computational pipeline that predicts regulators for co-extant and ancestral co-expression modules along a phylogeny, and candidate regulatory regions associated with traits under selection in cichlids. As a case study, we apply our approach to a well-studied adaptive trait—the visual system—for which we report striking cases of network rewiring for visual opsin genes, identify discrete regulatory variants, and investigate their association with cichlid visual system evolution. In regulatory regions of visual opsin genes, in vitro assays confirm that transcription factor binding site mutations disrupt regulatory edges across species and segregate according to lake species phylogeny and ecology, suggesting GRN rewiring in radiating cichlids. Conclusions Our approach reveals numerous novel potential candidate regulators and regulatory regions across cichlid genomes, including some novel and some previously reported associations to known adaptive evolutionary traits

Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes

Cichlid fish of the genus Oreochromis form the basis of the global tilapia aquaculture and fisheries industries. Broodstocks for aquaculture are often collected from wild populations, which in Africa may be from locations containing multiple Oreochromis species. However, many species are difficult to distinguish morphologically, hampering efforts to maintain good quality farmed strains. Additionally, non-native farmed tilapia populations are known to be widely distributed across Africa and to hybridize with native Oreochromis species, which themselves are important for capture fisheries. The morphological identification of these hybrids is particularly unreliable. Here, we describe the development of a single nucleotide polymorphism (SNP) genotyping panel from whole-genome resequencing data that enables targeted species identification in Tanzania. We demonstrate that an optimized panel of 96 genome-wide SNPs based on FST outliers performs comparably to whole genome resequencing in distinguishing species and identifying hybrids. We also show this panel outperforms microsatellite-based and phenotype-based classification methods. Case studies indicate several locations where introduced aquaculture species have become established in the wild, threatening native Oreochromis species. The novel SNP markers identified here represent an important resource for assessing broodstock purity in hatcheries and helping to conserve unique endemic biodiversity

An improved microRNA annotation of the canine genome

The domestic dog, Canis familiaris, is a valuable model for studying human diseases. The publication of the latest Canine genome build and annotation, CanFam3.1 provides an opportunity to enhance our understanding of gene regulation across tissues in the dog model system. In this study, we used the latest dog genome assembly and small RNA sequencing data from 9 different dog tissues to predict novel miRNAs in the dog genome, as well as to annotate conserved miRNAs from the miRBase database that were missing from the current dog annotation. We used both miRCat and miRDeep2 algorithms to computationally predict miRNA loci. The resulting, putative hairpin sequences were analysed in order to discard false positives, based on predicted secondary structures and patterns of small RNA read alignments. Results were further divided into high and low confidence miRNAs, using the same criteria. We generated tissue specific expression profiles for the resulting set of 811 loci: 720 conserved miRNAs, (207 of which had not been previously annotated in the dog genome) and 91 novel miRNA loci. Comparative analyses revealed 8 putative homologues of some novel miRNA in ferret, and one in microbat. All miRNAs were also classified into the genic and intergenic categories, based on the Ensembl RefSeq gene annotation for CanFam3.1. This additionally allowed us to identify four previously undescribed MiRtrons among our total set of miRNAs. We additionally annotated piRNAs, using proTRAC on the same input data. We thus identified 263 putative clusters, most of which (211 clusters) were found to be expressed in testis. Our results represent an important improvement of the dog genome annotation, paving the way to further research on the evolution of gene regulation, as well as on the contribution of post-transcriptional regulation to pathological conditions

MicroRNA profiling in the Weddell seal suggests novel regulatory mechanisms contributing to diving adaptation

Background: The Weddell Seal (Leptonychotes weddelli) represents a remarkable example of adaptation to diving among marine mammals. This species is capable of diving > 900 m deep and remaining underwater for more than 60 min. A number of key physiological specializations have been identified, including the low levels of aerobic, lipid-based metabolism under hypoxia, significant increase in oxygen storage in blood and muscle; high blood volume and extreme cardiovascular control. These adaptations have been linked to increased abundance of key proteins, suggesting an important, yet still understudied role for gene reprogramming. In this study, we investigate the possibility that post-transcriptional gene regulation by microRNAs (miRNAs) has contributed to the adaptive evolution of diving capacities in the Weddell Seal. Results: Using small RNA data across 4 tissues (brain, heart, muscle and plasma), in 3 biological replicates, we generate the first miRNA annotation in this species, consisting of 559 high confidence, manually curated miRNA loci. Evolutionary analyses of miRNA gain and loss highlight a high number of Weddell seal specific miRNAs. Four hundred sixteen miRNAs were differentially expressed (DE) among tissues, whereas 80 miRNAs were differentially expressed (DE) across all tissues between pups and adults and age differences for specific tissues were detected in 188 miRNAs. mRNA targets of these altered miRNAs identify possible protective mechanisms in individual tissues, particularly relevant to hypoxia tolerance, anti-apoptotic pathways, and nitric oxide signal transduction. Novel, lineage-specific miRNAs associated with developmental changes target genes with roles in angiogenesis and vasoregulatory signaling. Conclusions: Altogether, we provide an overview of miRNA composition and evolution in the Weddell seal, and the first insights into their possible role in the specialization to diving