A full-length cDNA resource for the pea aphid

HHMI and Department of Ecology and Evolutionary Biology, Princeton University, NJ, USA. <>
Insect Molecular Biology (Impact Factor: 2.98). 03/2010; 19 Suppl 2(s2):23-31. DOI: 10.1111/j.1365-2583.2009.00946.x
Source: PubMed

ABSTRACT Large collections of full-length cDNAs are important resources for genome annotation and functional genomics. We report the creation of a collection of 50 599 full-length cDNA clones from the pea aphid, Acyrthosiphon pisum. Sequencing from 5' and 3' ends of the clones generated 97 828 high-quality expressed sequence tags, representing approximately 9000 genes. These sequences were imported to AphidBase and are shown to play crucial roles in both automatic gene prediction and manual annotation. Our detailed analyses demonstrated that the full-length cDNAs can further improve gene models and can even identify novel genes that are not included in the current version of the official gene set. This full-length cDNA collection can be utilized for a wide variety of functional studies, serving as a community resource for the study of the functional genomics of the pea aphid.

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Available from: Atsushi Nakabachi, Aug 20, 2015
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    • "Following computational identification , we gathered all available EST and full-length transcript support for our gene models using BlastN searches against Price et al. · doi:10.1093/molbev/msr140 MBE all A. pisum NCBI dbEST data sets and the full-length transcript data set of Shigenobu et al. (2010). The complete list of 40 AATs identified using the above pipeline together with supporting transcriptomic data are listed in supplementary table S1, Supplementary Material online. "
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    ABSTRACT: In insects, some of the most ecologically important symbioses are nutritional symbioses that provide hosts with novel traits and thereby facilitate exploitation of otherwise inaccessible niches. One such symbiosis is the ancient obligate intracellular symbiosis of aphids with the γ-proteobacteria, Buchnera aphidicola. Although the nutritional basis of the aphid/Buchnera symbiosis is well understood, the processes and structures that mediate the intimate interactions of symbiotic partners remain uncharacterized. Here, using a de novo approach, we characterize the complement of 40 amino acid polyamine organocation (APC) superfamily member amino acid transporters (AATs) encoded in the genome of the pea aphid, Acyrthosiphon pisum. We find that the A. pisum APC superfamily is characterized by extensive gene duplications such that A. pisum has more APC superfamily transporters than other fully sequenced insects, including a ten paralog aphid-specific expansion of the APC transporter slimfast. Detailed expression analysis of 17 transporters selected on the basis of their phylogenetic relationship to five AATs identified in an earlier bacteriocyte expressed sequence tag study distinguished a subset of eight transporters that have been recruited for amino acid transport in bacteriocyte cells at the symbiotic interface. These eight transporters include transporters that are highly expressed and/or highly enriched in bacteriocytes and intriguingly, the four AATs that show bacteriocyte-enriched expression are all members of gene family expansions, whereas three of the four that are highly expressed but not enriched in bacteriocytes retain one-to-one orthology with transporters in other genomes. Finally, analysis of evolutionary rates within the large A. pisum slimfast expansion demonstrated increased rates of molecular evolution coinciding with two major shifts in expression: 1) a loss of gut expression and possibly a gain of bacteriocyte expression and 2) loss of expression in all surveyed tissues in asexual females. Taken together, our characterization of nutrient AATs at the aphid/Buchnera symbiotic interface provides the first examination of the processes and structures operating at the interface of an obligate intracellular insect nutritional symbiosis, offering unique insight into the types of genomic change that likely facilitated evolutionary maintenance of the symbiosis.
    Molecular Biology and Evolution 05/2011; 28(11):3113-26. DOI:10.1093/molbev/msr140 · 14.31 Impact Factor
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    • "Biologists working on the pea aphid now have a valuable new set of tools to attack novel questions. In addition to the raw genome sequence we have the functional annotation (Huybrechts et al., 2010; Shigenobu et al., 2009a) and information about gene family evolution (Huerta-Cepas et al., 2010), collections of cDNAs, ESTs and miRNA resources (Legeai et al., 2009a; Shigenobu et al., 2010b), and novel or expanded gene familes to investigate (Nakabachi & Miyagishima, 2010). AphidBase, the centralized bioinformatic platform for annotation of the pea aphid genome (Legeai et al., 2010b), will become increasingly valuable. "
    Insect Molecular Biology 03/2010; 19 Suppl 2:1-4. DOI:10.1111/j.1365-2583.2009.00980.x · 2.98 Impact Factor
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    • "The retrieved nine gene models for the chitinase-like proteins of A. pisum were visually inspected with reference to the full-length cDNA clone sequence information (Shigenobu et al., 2010) and other supportive data, including the orthology-based protein evidence. The structures of Cht5 and Cht6 were corrected based on this manual checking procedure (Table 1). "
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    ABSTRACT: In insects, chitinases play an essential role in the degradation of old exoskeleton and turnover of the gut lining. In silico screening of the entire genome of the pea aphid (Hemimetabola), Acyrthosiphon pisum, detected nine genes encoding putative chitinase-like proteins, including six enzymatically active chitinases, one imaginal disc growth factor, and one endo-beta-N-acetylglucosaminidase. Screening of the genomes of Aedes aegypti, Anopheles gambiae, Apis mellifera, Bombyx mori, Culex quinquefasciatus, Drosophila melanogaster, Nasonia vitripennis, Pediculus humanus corporis, and Tribolium castaneum suggested repeated gene duplications in holometabolous lineages. Quantitative reverse transcription-PCR demonstrated the expression of four and two distinct chitinase-like genes of A. pisum to be highly up-regulated in the embryo and the midgut, respectively, suggesting specific roles in these pea aphid tissues.
    Insect Molecular Biology 03/2010; 19 Suppl 2(Suppl. 2):175-85. DOI:10.1111/j.1365-2583.2009.00985.x · 2.98 Impact Factor
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