Recent genomic analyses of arthropod defense mechanisms suggest conservation of key elements underlying responses to pathogens, parasites and stresses. At the center of pathogen-induced immune responses are signaling pathways triggered by the recognition of fungal, bacterial and viral signatures. These pathways result in the production of response molecules, such as antimicrobial peptides and lysozymes, which degrade or destroy invaders. Using the recently sequenced genome of the pea aphid (Acyrthosiphon pisum), we conducted the first extensive annotation of the immune and stress gene repertoire of a hemipterous insect, which is phylogenetically distantly related to previously characterized insects models. Strikingly, pea aphids appear to be missing genes present in insect genomes characterized to date and thought critical for recognition, signaling and killing of microbes. In line with results of gene annotation, experimental analyses designed to characterize immune response through the isolation of RNA transcripts and proteins from immune-challenged pea aphids uncovered few immune-related products. Gene expression studies, however, indicated some expression of immune and stress-related genes. The absence of genes suspected to be essential for the insect immune response suggests that the traditional view of insect immunity may not be as broadly applicable as once thought. The limitations of the aphid immune system may be representative of a broad range of insects, or may be aphid specific. We suggest that several aspects of the aphid life style, such as their association with microbial symbionts, could facilitate survival without strong immune protection.

/pdf/immunity-and-other-defenses-in-pea-aphids-acyrthosiphon-3o3373o1rf.pdf

Immunity and other defenses in pea aphids, Acyrthosiphon pisum

The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals (human, chimpanzee, mouse, rat, dog, and cow). The results resolved chromosomal positions for 663,480 contigs, 20,285 putative feline gene orthologs, and 133,499 conserved sequence blocks (CSBs). Additional annotated features include repetitive elements, endogenous retroviral sequences, nuclear mitochondrial (numt) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammalian lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and short tandem repeats (STRs), suitable for linkage or association studies were characterized in the context of long stretches of chromosome homozygosity. In spite of the light coverage capturing approximately 65% of euchromatin sequence from the cat genome, these comparative insights shed new light on the tempo and mode of gene/genome evolution in mammals, promise several research applications for the cat, and also illustrate that a comparative approach using more deeply covered mammals provides an informative, preliminary annotation of a light (1.9-fold) coverage mammal genome sequence.

/pdf/initial-sequence-and-comparative-analysis-of-the-cat-genome-2i19nhwhwm.pdf

Initial sequence and comparative analysis of the cat genome

Full automation of gene prediction has become an important bioinformatics task since the advent of next generation sequencing. The eukaryotic genome annotation pipeline BRAKER1 had combined self-training GeneMark-ET with AUGUSTUS to generate genes’ coordinates with support of transcriptomic data. Here, we introduce BRAKER2, a pipeline with GeneMark-EP+ and AUGUSTUS externally supported by cross-species protein sequences aligned to the genome. Among the challenges addressed in the development of the new pipeline was generation of reliable hints to the locations of protein-coding exon boundaries from likely homologous but evolutionarily distant proteins. Under equal conditions, the gene prediction accuracy of BRAKER2 was shown to be higher than the one of MAKER2, yet another genome annotation pipeline. Also, in comparison with BRAKER1 supported by a large volume of transcript data, BRAKER2 could produce a better gene prediction accuracy if the evolutionary distances to the reference species in the protein database were rather small. All over, our tests demonstrated that fully automatic BRAKER2 is a fast and accurate method for structural annotation of novel eukaryotic genomes.

/pdf/braker2-automatic-eukaryotic-genome-annotation-with-genemark-9j1hds3eqi.pdf

BRAKER2: Automatic Eukaryotic Genome Annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database

https://www.cell.com/current-biology/pdf/S0960-9822(12)00081-4.pdf

Polyphenism in insects.

Injection of siRNA (small interfering RNA) into parthenogenetic adult pea aphids (Acyrthosiphon pisum) is shown here to lead to depletion of a target salivary gland transcript. The siRNA was generated from double stranded RNA that covered most of the open reading frame of the transcript, which we have called Coo2. The Coo2 transcript level decreases dramatically over a 3-day period after injection of siRNA. With a lag of 1 to 2 days, the siCoo2-RNA injected insects died, on average 8 days before the death of control insects injected with siRNA for green fluorescent protein. It appears, therefore, that siRNA injections into adults will be a useful tool in studying the roles of individual transcripts in aphid salivary glands and suggests that siCoo2-RNA injections can be a useful positive control in such studies.

/pdf/rnai-knockdown-of-a-salivary-transcript-leading-to-lethality-4wzbxrla9e.pdf

RNAi knockdown of a salivary transcript leading to lethality in the pea aphid, Acyrthosiphon pisum

Aphids are the leading pests in agricultural crops. A large-scale sequencing of 40,904 ESTs from the pea aphid Acyrthosiphon pisum was carried out to define a catalog of 12,082 unique transcripts. A strong AT bias was found, indicating a compositional shift between Drosophila melanogaster and A. pisum. An in silico profiling analysis characterized 135 transcripts specific to pea-aphid tissues (relating to bacteriocytes and parthenogenetic embryos). This project is the first to address the genetics of the Hemiptera and of a hemimetabolous insect.

/pdf/large-scale-gene-discovery-in-the-pea-aphid-acyrthosiphon-3y34bblgrh.pdf

Cathy Philippe

Papers

Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera)