Community annotation: Procedures, protocols, and supporting tools: Table 1.

Elsik, Christine G.; Worley, Kim C.; Zhang, Lan; Milshina, Natalia V.; Jiang, Huaiyang; Reese, Justin; Childs, Kevin L.; Venkatraman, Anand; Dickens, C. Michael; Weinstock, George M.; Gibbs, Richard A.

doi:10.1101/gr.5580606

Cited by 43 publications

(39 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…While most eucaryal metazoan genomes have been intensively curated (e.g. Arabidopsis thaliana [17] and Apis mellifera [18]), most microbial genomes have not. Microbial genome papers that do cite manual annotation typically provided no details of how it was performed [19].…”

Section: Supplementary Informationmentioning

confidence: 99%

The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation

et al. 2009

View full text Add to dashboard Cite

burtonii has a high "IQ" (a measure of adaptive potential) compared to many methanogens.Numerous genes in these two over-represented COG categories appear to have been acquired from ε-and δ-proteobacteria, as do specific genes involved in central metabolism such as a novel B form of aconitase. Transposases also distinguish M. burtonii from other archaea, and their genomic characteristics indicate they play an important role in evolving the M. burtonii genome. Our study reveals a capacity for this model psychrophile to evolve through genome plasticity (including nucleotide skew, horizontal gene transfer and transposase activity) that enables adaptation to the cold, and to the biological and physical changes that have occurred over the last several thousand years as it adapted from a marine, to an Antarctic lake environment.

show abstract

Section: Supplementary Informationmentioning

confidence: 99%

The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation

et al. 2009

View full text Add to dashboard Cite

show abstract

“…bcm.tmc.edu/projects/honeybee) (Elsik et al, 2006; The Honey Bee Genome Sequencing Consortium, 2006). For mapping the respective ESTs to the genomic scaffolds of the honey bee genome (Amel 3.0), we used ARTEMIS (version 8.0) as a platform (Rutherford et al, 2000).…”

Section: Rda-adaptersmentioning

confidence: 99%

“…The ESTs shown in Table II are those that could be mapped to exons or putative UTRs of predicted genes. The table lists the corresponding genomic region (oriented or unoriented linkage group), the identifier (GB number) of the Official Gene Set of the honey bee (Elsik et al, 2006;The Honey Bee Genome Sequencing Consortium, 2006), as well as the number of ESTs that clustered to each predicted gene. The BLASTP results report best matches to Drosophila or human orthologs and their respective similarity scores.…”

Section: Representational Difference Analysis For Mucus Glands Of Newmentioning

confidence: 99%

“…Three ESTs sequenced in our study mapped to intronic regions of GLEAN3-predicted genes and another 32 ESTs did not match any predicted gene in the Official Gene Set. The fact that they could all be unambiguously assigned to specific genome regions is strong evidence that they may represent novel genes that either encode proteins that were not predicted by the GLEAN3 algorithms (Elsik et al, 2006), due to low CDS conservation, or they could be non-coding RNAs, such as revealed in large amounts in tiling arrays of the human genome (Kapranov et al, 2007). However, since we could confirm the presence of ORFs for all of these no-match ESTs, it is quite probable that they indeed represent novel proteincoding genes specific to the honey bee.…”

Section: Rda Screens As Tools To Detectmentioning

confidence: 99%

See 1 more Smart Citation

Differential gene expression profiling in mucus glands of honey bee(Apis mellifera)drones during sexual maturation

Colonello-Frattini

Hartfelder

2009

Apidologie

View full text Add to dashboard Cite

-The mating sign that each drone leaves when mating with a queen essentially consists of mucus gland proteins. We employed a Representational Difference Analysis (RDA) methodology to identify genes that are differentially expressed in mucus glands during sexual maturation of drones. The RDA library for mucus glands of newly emerged drones was more complex than that of 8 day-old drones, with matches to 20 predicted genes. Another 26 reads matched to the Apis genome but not to any predicted gene. Since these ESTs were located within ORFs they may represent novel honey bee genes, possibly fast evolving mucus gland proteins. In the RDA library for mucus glands of 8 day-old drones, most reads corresponded to a capsid protein of deformed wing virus, indicating high viral loads in these glands. The expression of two genes encoding venom allergens, acid phosphatase-1 and hyaluronidase, in drone mucus glands argues for their homology with the female venom glands, both associated with the reproductive system. male accessory gland / Representational Difference Analysis / honeybee / reproduction / deformed wing virus

show abstract

“…In addition to the six species of Hymenoptera analyzed here, the predicted genes of three annotated model genomes were utilized, including: Drosophila melanogaster (Diptera), Bombyx mori (Lepidoptera), and Apis mellifera (Hymenoptera). These coding sequences were downloaded from the following resources: Flybase (The FlyBase Consortium, 2008;Tweedie et al, 2009), SilkDB (Beijing Genomics Institute, 2006Wang et al, 2005), and BeeBase (Elsik et al, 2006; The Honeybee Genome Sequencing Consortium, 2008), respectively.…”

Section: Contig Assembly and Identification Of Orthologsmentioning

confidence: 99%

Expressed Sequence Tags (ESTs)

Parkinson¹

2009

Methods in Molecular Biology

View full text Add to dashboard Cite

a b s t r a c tHymenoptera is one of the most diverse groups of animals on the planet and have vital importance for ecosystem function as pollinators and parasitoids. Higher-level relationships among Hymenoptera have been notoriously difficult to resolve with both morphological and traditional molecular approaches. Here we examined the utility of expressed sequence tags for resolving relationships among hymenopteran superfamilies. Transcripts were assembled for 6 disparate Hymenopteran taxa with additional sequences added from public databases for a final dataset of 24 genes for 16 taxa and over 10 kb of sequence data. The concatenated dataset recovered a robust and well-supported topology demonstrating the monophyly of Holometabola, Hymenoptera, Apocrita, Aculeata, Ichneumonoidea, and a sister relationship between the two most closely related proctotrupomorphs in the dataset (Cynipoidea + Proctotrupoidea). The data strongly supported a sister relationship between Aculeata and Proctotrupomorpha, contrary to previously proposed hypotheses. Additionally there was strong evidence indicating Ichneumonoidea as sister to Aculeata + Proctotrupomorpha. These relationships were robust to missing data, nucleotide composition biases, low taxonomic sampling, and conflicting signal across gene trees. There was also strong evidence indicating that Chalcidoidea is not contained within Proctotrupomorpha.

show abstract

Community annotation: Procedures, protocols, and supporting tools: Table 1.

Cited by 43 publications

References 33 publications

The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation

The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation

Differential gene expression profiling in mucus glands of honey bee(Apis mellifera)drones during sexual maturation

Expressed Sequence Tags (ESTs)

Contact Info

Product

Resources

About