Biology subjects

Waterhouse, R. M.

Publications and source records attributed to Waterhouse, R. M..

7 recordsLinked to original sources

bioRxiv2018

Leveraging evolutionary relationships to improve Anopheles genome assemblies

While new sequencing technologies have lowered financial barriers to whole genome sequencing, resulting assemblies are often fragmented and far from finished. Subsequent improvements towards chromosomal-level status can be achieved by both experimental and computational approaches. Requiring only annotated assemblies and gene orthology data, comparative genomics approaches that aim to capture evolutionary signals to predict scaffold neighbours (adjacencies) offer potentially substantive improvements without the costs associated with experimental scaffolding or re-sequencing. We leverage the combined detection power of three such gene synteny-based methods applied to 21 Anopheles mosquito assemblies with variable contiguity levels to produce consensus sets of scaffold adjacency predictions. Three complementary validations were performed on subsets of assemblies with additional supporting data: six with physical mapping data; 13 with paired-end RNA sequencing (RNAseq) data; and three with new assemblies based on re-scaffolding or incorporating Pacific Biosciences (PacBio) sequencing data. Improved assemblies were built by integrating the consensus adjacency predictions with supporting experimental data, resulting in 20 new reference assemblies with improved contiguities. Combined with physical mapping data for six anophelines, chromosomal positioning of scaffolds improved assembly anchoring by 47% for A. funestus and 38% A. stephensi. Reconciling an A. funestus PacBio assembly with synteny-based and RNAseq-based adjacencies and physical mapping data resulted in a new 81.5% chromosomally mapped reference assembly and cytogenetic photomap. While complementary experimental data are clearly key to achieving high-quality chromosomal-level assemblies, our assessments and validations of gene synteny-based computational methods highlight the utility of applying comparative genomics approaches to improve community genomic resources.

genomics↗

bioRxiv2018

Genomic signatures accompanying the dietary shift to phytophagy in polyphagous beetles

BackgroundThe diversity and evolutionary success of beetles (Coleoptera) are proposed to be related to the diversity of plants on which they feed. Indeed the largest beetle suborder, Polyphaga, mostly includes plant-eaters among its ~315,000 species. In particular, plants defend themselves with a diversity of specialized toxic chemicals. These may impose selective pressures that drive genomic diversification and speciation in phytophagous beetles. However, evidence of changes in beetle gene repertoires driven by such interactions remains largely anecdotal and without explicit hypothesis testing.\n\nResultsTo address this, we explored the genomic consequences of beetle-plant trophic interactions by performing comparative gene family analyses across 18 species representing the two most species-rich beetle suborders. We contrasted the gene contents of species from the mostly plant-eating suborder Polyphaga with those of the mainly predatory Adephaga. We found gene repertoire evolution to be more dynamic, with significantly more adaptive lineage-specific expansions, in the more speciose Polyphaga. Testing the specific hypothesis of adaptation to plant-feeding, we identified families of enzymes putatively involved in beetle-plant interactions that underwent adaptive expansions in Polyphaga. There was especially strong support for the selection hypothesis on large gene families for glutathione S-transferase and carboxylesterase detoxification enzymes.\n\nConclusionsOur explicit modeling of the evolution of gene repertoires across 18 species identifies adaptive lineage-specific gene family expansions that accompany the dietary shift towards plants in beetles. These genomic signatures support the popular hypothesis of a key role for interactions with plant chemical defenses, and for plant-feeding in general, in driving beetle diversification.

evolutionary biology↗

bioRxiv2018

Evolutionary landscape of mosquito viral integrations

The sequenced genome of the arboviral vector mosquito, Aedes albopictus, is replete with repetitive DNA and it harbors an unusually large number of endogenous viral sequences, collectively called Nonretroviral Integrated RNA Virus Sequences (NIRVS). NIRVS are enriched both within protein-coding gene exons and PIWI-interacting RNA (piRNA) clusters, where they encode piRNAs. Based on these features, NIRVS have been proposed to function as novel mosquito antiviral immune factors. However, the relative importance and contributions of different NIRVS as functional antiviral elements and their mechanisms of action remain open questions.\n\nWe apply an analytical approach that intersects computational, evolutionary and molecular methods to identify NIRVS most likely affecting mosquito immunity. Using this strategy, we show that NIRVS are a highly dynamic component of the Ae. albopictus repeatome, which nevertheless maintains a core set of seemingly the oldest NIRVS with similarity to Rhabdoviruses. Population-level polymorphism of NIRVS varies depending on whether they occur in intergenic regions, piRNA clusters or are part of gene exons. NIRVS from piRNA clusters are differentially widespread in diverse populations but conserved at the sequence level. This is consistent with the hypothesis that they act analogously to fragments of transposable elements in piRNA clusters and contribute to piRNA-based immunity. Among NIRVS from gene exons, AlbRha52 and AlbRha12 have the hallmarks of domestication as they are fixed across populations, stably expressed, and as polymorphic at the sequence level as fast-evolving genes. Overall these results support the hypothesis that NIRVS contribute to mosquito immunity, potentially through diverse modes of action.

evolutionary biology↗

bioRxiv2018

Genome sequence of the wheat stem sawfly, Cephus cinctus, a primitive hymenopteran and wheat pest, illuminates evolution of hymenopteran chemoreceptors

The wheat stem sawfly, Cephus cinctus, is a major pest of wheat and key ecological player in the grasslands of western North America. It also represents a distinctive lineage of sawflies that appeared early during the hymenopteran radiation, but after the clade of Eusymphyta sawflies that is the sister lineage of all other Hymenoptera. We present a high-quality draft genome assembly of 162 Mbp in 1,976 scaffolds with a scaffold N50 of 622 kbp. Automated gene annotation identified 11,210 protein-coding gene models and 1,307 non-coding RNA models. Thirteen percent of the assembly consists of ~58,000 transposable elements partitioned equally between Class-I and Class-II elements. Orthology analysis reveals that 86% of Cephus proteins have identifiable orthologs in other insects. Phylogenomic analysis of conserved subsets of these proteins supports the placement of the Cephidae between the Eusymphyta and the parasitic woodwasp superfamily Orussoidea. Manual annotation and phylogenetic analysis of families of odorant, gustatory, and ionotropic receptors, plus odorant binding proteins, shows that Cephus has representatives for most conserved and expanded gene lineages in the Apocrita (wasps, ants, and bees). Cephus has also maintained several insect gene lineages that have been lost from the Apocrita, most prominently the carbon dioxide receptor subfamily. Furthermore, Cephus encodes a few small lineage-specific chemoreceptor gene family expansions that might be involved in adaptations to new grasses including wheat. These comparative analyses identify gene family members likely to have been present in the hymenopteran ancestor and provide a new perspective on the evolution of the chemosensory gene repertoire.

genomics↗

bioRxiv2017

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

BackgroundThe Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.\n\nResultsThe 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid-nutrition feeding.\n\nConclusionsWith the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.

genomics↗

bioRxiv2017

BUSCO applications from quality assessments to gene prediction and phylogenomics

Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). Now in its third release, BUSCO utilities extend beyond quality control to applications in comparative genomics, gene predictor training, metagenomics, and phylogenomics.

bioinformatics↗

bioRxiv2016

Rapid evolution of female-biased genes among four species of Anopheles malaria mosquitoes

Understanding how phenotypic differences between males and females arise from the sex-biased expression of nearly identical genomes can often reveal important insights into the biology and evolution of a species. Among Anopheles mosquito species, these phenotypic differences include vectorial capacity, as it is only females that blood feed and thus transmit human malaria. Here, we use RNA-seq data from multiple tissues of four vectors spanning the Anopheles phylogeny to explore the genomic and evolutionary properties of sex-biased genes. We find that in these mosquitoes, in contrast to what has been found in many other organisms, female-biased genes are more rapidly evolving in sequence, expression, and genic turnover, than male-biased genes. Our results suggests that this atypical pattern may be due to the combination of sex-specific life history challenges encountered by females, such as blood feeding. Furthermore, female propensity to only mate once in nature in male swarms likely diminishes sexual selection of post-reproductive traits related to sperm competition among males. We also develop a comparative framework to systematically explore tissue- and sex-specific splicing, to document its conservation throughout the genus and identify a set of candidate genes for future functional analyses of sex-specific isoform usage. Finally, our data reveals that the deficit of male-biased genes on the X chromosomes in Anopheles is a conserved feature in this genus and can be directly attributed to chromosome-wide transcriptional regulation that demasculinizes the X in male reproductive tissues.

genomics↗