[Show abstract][Hide abstract] ABSTRACT: Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but also is a major vector of Chagas disease, an illness that affects approximately seven million people worldwide. We sequenced the genome of R. prolixus, generated assembled sequences covering 95% of the genome (∼702 Mb), including 15,456 putative protein-coding genes, and completed comprehensive genomic analyses of this obligate blood-feeding insect. Although immune-deficiency (IMD)-mediated immune responses were observed, R. prolixus putatively lacks key components of the IMD pathway, suggesting a reorganization of the canonical immune signaling network. Although both Toll and IMD effectors controlled intestinal microbiota, neither affected Trypanosoma cruzi, the causal agent of Chagas disease, implying the existence of evasion or tolerance mechanisms. R. prolixus has experienced an extensive loss of selenoprotein genes, with its repertoire reduced to only two proteins, one of which is a selenocysteine-based glutathione peroxidase, the first found in insects. The genome contained actively transcribed, horizontally transferred genes from Wolbachia sp., which showed evidence of codon use evolution toward the insect use pattern. Comparative protein analyses revealed many lineage-specific expansions and putative gene absences in R. prolixus, including tandem expansions of genes related to chemoreception, feeding, and digestion that possibly contributed to the evolution of a blood-feeding lifestyle. The genome assembly and these associated analyses provide critical information on the physiology and evolution of this important vector species and should be instrumental for the development of innovative disease control methods.
Full-text · Article · Nov 2015 · Proceedings of the National Academy of Sciences
[Show abstract][Hide abstract] ABSTRACT: Lucilia cuprina is a parasitic fly of major economic importance worldwide. Larvae of this fly invade their animal host, feed on tissues and excretions and progressively cause severe skin disease (myiasis). Here we report the sequence and annotation of the 458-megabase draft genome of Lucilia cuprina. Analyses of this genome and the 14,544 predicted protein-encoding genes provide unique insights into the fly's molecular biology, interactions with the host animal and insecticide resistance. These insights have broad implications for designing new methods for the prevention and control of myiasis.
Full-text · Article · Jun 2015 · Nature Communications
[Show abstract][Hide abstract] ABSTRACT: Author Summary
Arthropods are the most abundant animals on earth. Among them, insects clearly dominate on land, whereas crustaceans hold the title for the most diverse invertebrates in the oceans. Much is known about the biology of these groups, not least because of genomic studies of the fruit fly Drosophila , the water flea Daphnia , and other species used in research. Here we report the first genome sequence from a species belonging to a lineage that has previously received very little attention‚Äîthe myriapods. Myriapods were among the first arthropods to invade the land over 400 million years ago, and survive today as the herbivorous millipedes and venomous centipedes, one of which‚Äî Strigamia maritima ‚Äîwe have sequenced here. We find that the genome of this centipede retains more characteristics of the presumed arthropod ancestor than other sequenced insect genomes. The genome provides access to many aspects of myriapod biology that have not been studied before, suggesting, for example, that they have diversified receptors for smell that are quite different from those used by insects. In addition, it shows specific consequences of the largely subterranean life of this particular species, which seems to have lost the genes for all known light-sensing molecules, even though it still avoids light.
[Show abstract][Hide abstract] ABSTRACT: Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa.
Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable
differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous
reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase
Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted
protein–encoding genes led to multiple discoveries, including chromosomal integrations of bacterial
(Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of
host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These
genome data provide a foundation for research into trypanosomiasis prevention and yield important
insights with broad implications for multiple aspects of tsetse biology.
[Show abstract][Hide abstract] ABSTRACT: The evolutionary importance of hybridization and introgression has long been debated. Hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring beneficial traits between species. Here we use genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation. We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,669 predicted genes, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organization has remained broadly conserved since the Cretaceous period, when butterflies split from the Bombyx (silkmoth) lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, Heliconius melpomene, Heliconius timareta and Heliconius elevatus, especially at two genomic regions that control mimicry pattern. We infer that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation.
[Show abstract][Hide abstract] ABSTRACT: VectorBase (http://www.vectorbase.org) is a NIAID-supported bioinformatics resource for invertebrate vectors of human pathogens. It hosts data for nine genomes: mosquitoes (three Anopheles gambiae genomes, Aedes aegypti and Culex quinquefasciatus), tick (Ixodes scapularis), body louse (Pediculus humanus), kissing bug (Rhodnius prolixus) and tsetse fly (Glossina morsitans). Hosted data range from genomic features and expression data to population genetics and ontologies. We describe improvements and integration of new data that expand our taxonomic coverage. Releases are bi-monthly and include the delivery of preliminary data for emerging genomes. Frequent updates of the genome browser provide VectorBase users with increasing options for visualizing their own high-throughput data. One major development is a new population biology resource for storing genomic variations, insecticide resistance data and their associated metadata. It takes advantage of improved ontologies and controlled vocabularies. Combined, these new features ensure timely release of multiple types of data in the public domain while helping overcome the bottlenecks of bioinformatics and annotation by engaging with our user community.
Full-text · Article · Dec 2011 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: Ensembl Genomes (http://www.ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology
(for genome annotation, analysis and dissemination) developed in the context of the (vertebrate-focused) Ensembl project and
provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive
interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and
comparative analysis. Since its launch in 2009, Ensembl Genomes has undergone rapid expansion, with the goal of providing
coverage of all major experimental organisms, and additionally including taxonomic reference points to provide the evolutionary
context in which genes can be understood. Against the backdrop of a continuing increase in genome sequencing activities in
all parts of the tree of life, we seek to work, wherever possible, with the communities actively generating and using data,
and are participants in a growing range of collaborations involved in the annotation and analysis of genomes.
Full-text · Article · Nov 2011 · Nucleic Acids Research