Genome-wide signatures of complex introgression and adaptive evolution in the big cats.

The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting ~19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

Background: The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants. This remarkable ability makes M. persicae a highly destructive pest of many important crop species. Results: To investigate the exceptional phenotypic plasticity of M. persicae, we sequenced the M. persicae genome and assessed how one clonal lineage responds to host plant species of different families. We show that genetically identical individuals are able to colonise distantly related host species through the differential regulation of genes belonging to aphid-expanded gene families. Multigene clusters collectively upregulate in single aphids within two days upon host switch. Furthermore, we demonstrate the functional significance of this rapid transcriptional change using RNA interference (RNAi)-mediated knock-down of genes belonging to the cathepsin B gene family. Knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced upregulation of these genes. Conclusions: Previous research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pest M. persicae is able to colonise diverse host plant species in the absence of genetic specialisation. This is achieved through rapid transcriptional plasticity of genes that have duplicated during aphid evolution

Genome-wide signatures of complex introgression and adaptive evolution in the big cats

The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting ~19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages

Next-generation sequencing reveals novel variants and large deletion in FANCA gene in Polish family with Fanconi anemia

Abstract Background Fanconi anemia (FA) is the most common inherited bone marrow failure syndrome. However, establishing its molecular diagnosis remains challenging. Chromosomal breakage analysis is the gold standard diagnostic test for this disease. Nevertheless, molecular analysis is always required for the identification of pathogenic alterations in the FA genes. Results We report here on a family with FA diagnosis in two siblings. Mitomycin C (MMC) test revealed high level of chromosome breaks and radial figures. In both children, array—Comparative Genomic Hybridization (aCGH) showed maternally inherited 16q24.3 deletion, including FANCA gene, and next generation sequencing (NGS) disclosed paternally inherited novel variants in the FANCA gene—Asn1113Tyr and Ser890Asn. A third sibling was shown to be a carrier of FANCA deletion only. Conclusions Although genetic testing in FA patients often requires a multi-method approach including chromosome breakage test, aCGH, and NGS, every effort should be made to make it available for whole FA families. This is not only to confirm the clinical diagnosis of FA in affected individuals, but also to enable identification of carriers of FA gene(s) alterations, as it has implications for diagnostic and genetic counselling process

Patterns of genomic variation in the opportunistic pathogen candida glabrata suggest the existence of mating and a secondary association with humans

Candida glabrata is an opportunistic fungal pathogen that ranks as the second most common cause of systemic candidiasis. Despite its genus name, this yeast is more closely related to the model yeast Saccharomyces cerevisiae than to other Candida pathogens, and hence its ability to infect humans is thought to have emerged independently. Moreover, C. glabrata has all the necessary genes to undergo a sexual cycle but is considered an asexual organism due to the lack of direct evidence of sexual reproduction. To reconstruct the recent evolution of this pathogen and find footprints of sexual reproduction, we assessed genomic and phenotypic variation across 33 globally distributed C. glabrata isolates. We cataloged extensive copy-number variation, which particularly affects genes encoding cell-wall-associated proteins, including adhesins. The observed level of genetic variation in C. glabrata is significantly higher than that found in Candida albicans. This variation is structured into seven deeply divergent clades, which show recent geographical dispersion and large within-clade genomic and phenotypic differences. We show compelling evidence of recent admixture between differentiated lineages and of purifying selection on mating genes, which provides the first evidence for the existence of an active sexual cycle in this yeast. Altogether, our data point to a recent global spread of previously genetically isolated populations and suggest that humans are only a secondary niche for this yeast.The T.G. group acknowledges the support of the Spanish Ministry of Economy and Competitiveness grants “Centro de Excelencia Severo Ochoa 2013–2017” SEV-2012-0208 and BFU2015-67107 cofunded by the European Regional Development Fund (ERDF); European Union and ERC Seventh Framework Programme (FP7/2007–2013) under grant agreement ERC-2012-StG-310325; Catalan Research Agency (AGAUR) SGR857; CERCA Programme/Generalitat de Catalunya; and a grant from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreement H2020-MSCA-ITN-2014-642095. C.F.’s and T.G.’s groups acknowledge support from the GDRI “iGenolevures” of the French CNRS for travel and meeting funds. T.G., O.B., and E.G.-M. acknowledge funding from the European Unionunder grant agreement FP7-PEOPLE-2013-ITN-606786 “ImresFun.

Phylogenomics identifies an ancestral burst of gene duplications predating the diversification of aphidomorpha

Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106-227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings.This research was funded by European Regional Development Fund (ERDF) and Ministerio de Economía y Competitividad (Spain) (Grant Nos. PGC2018-099344-B-100 and BFU2015-67107). T.G. group also acknowledges support from the Catalan Research Agency (AGAUR) SGR857, and grants from the European Union’s Horizon 2020 research and innovation program under the grant agreements ERC-2016-724173 and MSC-747607. T.G. also receives support from an INB (Grant No. PT17/0009/0023—ISCIII-SGEFI/ERDF). The genome, annotation and sequencing reads have been deposited at the European Nucleotide Archive (ENA) under the project accession PRJEB3341

Genome sequence of the olive tree, Olea europaea

The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticated cultivars, or between domesticated olive trees and their wild relatives, remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n). A total of 543 Gb of raw DNA sequence from whole genome shotgun sequencing, and a fosmid library containing 155,000 clones from a 1,000+ year-old olive tree (cv. Farga) were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 443 kb, and a total length of 1.31 Gb, which represents 95 % of the estimated genome length (1.38 Gb). In addition, the associated fungus Aureobasidium pullulans was partially sequenced. Genome annotation, assisted by RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes, suggesting recent genomic expansion. Genome completeness, as estimated using the CEGMA pipeline, reached 98.79 %. The assembled draft genome of O. europaea will provide a valuable resource for the study of the evolution and domestication processes of this important tree, and allow determination of the genetic bases of key phenotypic traits. Moreover, it will enhance breeding programs and the formation of new varieties

Genome sequence of the olive tree, Olea europaea

Background: The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticated cultivars, or between domesticated olive trees and their wild relatives, remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n). Findings: A total of 543 Gb of raw DNA sequence from whole genome shotgun sequencing, and a fosmid library containing 155,000 clones from a 1,000+ year-old olive tree (cv. Farga) were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 443 kb, and a total length of 1.31 Gb, which represents 95 % of the estimated genome length (1.38 Gb). In addition, the associated fungus Aureobasidium pullulans was partially sequenced. Genome annotation, assisted by RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes, suggesting recent genomic expansion. Genome completeness, as estimated using the CEGMA pipeline, reached 98.79 %. Conclusions: The assembled draft genome of O. europaea will provide a valuable resource for the study of the evolution and domestication processes of this important tree, and allow determination of the genetic bases of key phenotypic traits. Moreover, it will enhance breeding programs and the formation of new varieties

The draft genome sequence of the rice weevil Sitophilus oryzae as a model to explore the host-symbiont interactions in a nascent stage of endosymbiosis

International audienceOrganisms across the tree of life are associated with diverse microbial partners that impact host adaptive traits and exhibit phenotypes ranging from parasitism to mutualism. For example, insects thriving on nutritionally unbalanced habitats are prone to house mutualistic intracellular bacteria (endosymbionts) that complement their diet, thus greatly improving their ecological performances. Within insects, endosymbiosis is very common in the Curculionoidea weevils superfamily, which constitutes a group with considerable worldwide biodiversity. Weevils include some of the most invasive insects and cause huge crop damages. Recent phylogenetic and molecular studies have shown that endosymbiosis history has been marked by several symbiotic displacements within this insect group. The most recent event may have occurred less than one million year ago within the cereal weevil Sitophilus clade resulting in the replacement of an ancestral symbiont Candidatus Nardonella by Sodalis pierantonius symbiont. S. pierantonius genome exhibits peculiar molecular features associated with a massive pseudogenization and the occurrence of a huge amount of repeated elements. Whether these phenomena are adaptive, and whether they impact host genome reshaping are puzzling questions that will be addressed thanks to the genome level investigation of the Sitophilus-Sodalis recent association.Here, we present the draft genome sequence of the rice weevil Sitophilus oryzae. The full genome sequence has been obtained through a combination of short-read (Illumina HiSeq and Roche/454 GS FLX) and long-read (Pacific Biosciences PacBio RS) sequencing methods. After error correction, the data were assembled using the Platanus algorithm for an initial scaffolding and gap-filling. These scaffolds were then re-scaffolded several times using PacBio data. The final assembly consisted in 17,365 scaffolds of a total length of 652 Mbp (the S. oryzae genome size was estimated to be about 650 Mbp using flow cytometry), a N50 value of 110 kbp, a coverage of 101X and a GC content of 38.4%. Intriguingly, transposable elements (TE) analysis using both automated tools (dnaPipeTE, RepeatModeler and MITEhunter) and manual annotations revealed an unexpected high amount of repeated DNA (>50%) in this weevil genome. Gene prediction was then performed using a combination of MAKER, GeneMark, Augustus and SNAP algorithms and taking advantage of the available transcriptomic data (EST and RNA-seq data) on S. oryzae to build more accurate gene models. Finally, the official gene set contained 17,026 protein-coding genes. Based on this gene set, the complete catalogue of gene phylogenies (phylome) was predicted through the PhylomeDB pipeline and will be publicly available in this database (www.phylomedb.org). The weevil metabolic and signalling networks were also reconstructed using the CycADS pipeline in order to generate the SitorCyc database (a BioCyc interface of the S. oryzae metabolism). These metabolic pathways were integrated in the ArthropodaCyc database collection dedicated to comparative metabolic analyses among arthropods (http://arthropodacyc.cycadsys.org/). The interdependence of the metabolic networks of S. oryzae and its endosymbiont S. pierantonius will then be characterized thanks to their integration into the ArtSymbioCyc database that is being developed and will be dedicated to arthropod symbioses. All these annotations (TE, phylome and metabolic networks) will be integrated in a comprehensive genome database providing a genome browser with crosslinks to available resources.Altogether, these results are expected to unravel basic molecular mechanisms and evolutionary features associated with the establishment and the maintenance of endosymbiosis in animals, and to permit identifying potential gene targets useful for the development of new ecologically-friendly strategies for pest insects control and management