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Article: Re-annotation of protein-coding genes in 10 complete genomes of Neisseriaceae family by combining similarity-based and composition-based methods
Title | Re-annotation of protein-coding genes in 10 complete genomes of Neisseriaceae family by combining similarity-based and composition-based methods |
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Authors | |
Keywords | The Neisseriaceae family Re-annotation Newly found genes Eliminated non-coding ORFs Newly assigned functions |
Issue Date | 2013 |
Publisher | Oxford University Press for Kazusa DNA Research Institute. The Journal's web site is located at http://dnaresearch.oxfordjournals.org |
Citation | DNA Research, 2013, v. 20 n. 3, p. 273-286 How to Cite? |
Abstract | In this paper, we performed a comprehensive re-annotation of protein-coding genes by a systematic method combining composition- and similarity-based approaches in 10 complete bacterial genomes of the family Neisseriaceae. First, 418 hypothetical genes were predicted as non-coding using the composition-based method and 413 were eliminated from the gene list. Both the scatter plot and cluster of orthologous groups (COG) fraction analyses supported the result. Second, from 20 to 400 hypothetical proteins were assigned with functions in each of the 10 strains based on the homology search. Among newly assigned functions, 397 are so detailed to have definite gene names. Third, 106 genes missed by the original annotations were picked up by an ab initio gene finder combined with similarity alignment. Transcriptional experiments validated the effectiveness of this method in Laribacter hongkongensis and Chromobacterium violaceum. Among the 106 newly found genes, some deserve particular interests. For example, 27 transposases were newly found in Neiserria meningitidis alpha14. In Neiserria gonorrhoeae NCCP11945, four new genes with putative functions and definite names (nusG, rpsN, rpmD and infA) were found and homologues of them usually are essential for survival in bacteria. The updated annotations for the 10 Neisseriaceae genomes provide a more accurate prediction of protein-coding genes and a more detailed functional information of hypothetical proteins. It will benefit research into the lifestyle, metabolism, environmental adaption and pathogenicity of the Neisseriaceae species. The re-annotation procedure could be used directly, or after the adaption of detailed methods, for checking annotations of any other bacterial or archaeal genomes. |
Persistent Identifier | http://hdl.handle.net/10722/184602 |
ISSN | 2023 Impact Factor: 3.9 2023 SCImago Journal Rankings: 1.131 |
PubMed Central ID | |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Guo, F | - |
dc.contributor.author | Xiong, L | - |
dc.contributor.author | Teng, JLL | - |
dc.contributor.author | Yuen, KY | - |
dc.contributor.author | Lau, SKP | - |
dc.contributor.author | Woo, PCY | - |
dc.date.accessioned | 2013-07-15T09:57:36Z | - |
dc.date.available | 2013-07-15T09:57:36Z | - |
dc.date.issued | 2013 | - |
dc.identifier.citation | DNA Research, 2013, v. 20 n. 3, p. 273-286 | - |
dc.identifier.issn | 1340-2838 | - |
dc.identifier.uri | http://hdl.handle.net/10722/184602 | - |
dc.description.abstract | In this paper, we performed a comprehensive re-annotation of protein-coding genes by a systematic method combining composition- and similarity-based approaches in 10 complete bacterial genomes of the family Neisseriaceae. First, 418 hypothetical genes were predicted as non-coding using the composition-based method and 413 were eliminated from the gene list. Both the scatter plot and cluster of orthologous groups (COG) fraction analyses supported the result. Second, from 20 to 400 hypothetical proteins were assigned with functions in each of the 10 strains based on the homology search. Among newly assigned functions, 397 are so detailed to have definite gene names. Third, 106 genes missed by the original annotations were picked up by an ab initio gene finder combined with similarity alignment. Transcriptional experiments validated the effectiveness of this method in Laribacter hongkongensis and Chromobacterium violaceum. Among the 106 newly found genes, some deserve particular interests. For example, 27 transposases were newly found in Neiserria meningitidis alpha14. In Neiserria gonorrhoeae NCCP11945, four new genes with putative functions and definite names (nusG, rpsN, rpmD and infA) were found and homologues of them usually are essential for survival in bacteria. The updated annotations for the 10 Neisseriaceae genomes provide a more accurate prediction of protein-coding genes and a more detailed functional information of hypothetical proteins. It will benefit research into the lifestyle, metabolism, environmental adaption and pathogenicity of the Neisseriaceae species. The re-annotation procedure could be used directly, or after the adaption of detailed methods, for checking annotations of any other bacterial or archaeal genomes. | - |
dc.language | eng | - |
dc.publisher | Oxford University Press for Kazusa DNA Research Institute. The Journal's web site is located at http://dnaresearch.oxfordjournals.org | - |
dc.relation.ispartof | DNA Research | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.subject | The Neisseriaceae family | - |
dc.subject | Re-annotation | - |
dc.subject | Newly found genes | - |
dc.subject | Eliminated non-coding ORFs | - |
dc.subject | Newly assigned functions | - |
dc.title | Re-annotation of protein-coding genes in 10 complete genomes of Neisseriaceae family by combining similarity-based and composition-based methods | - |
dc.type | Article | - |
dc.identifier.email | Guo, F: fbguohku@hku.hk | - |
dc.identifier.email | Teng, JLL: llteng@hku.hk | - |
dc.identifier.email | Yuen, KY: kyyuen@hkucc.hku.hk | - |
dc.identifier.email | Lau, SKP: skplau@hkucc.hku.hk | - |
dc.identifier.email | Woo, PCY: pcywoo@hkucc.hku.hk | - |
dc.identifier.authority | Teng, JLL=rp00277 | - |
dc.identifier.authority | Yuen, KY=rp00366 | - |
dc.identifier.authority | Lau, SKP=rp00486 | - |
dc.identifier.authority | Woo, PCY=rp00430 | - |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.1093/dnares/dst009 | - |
dc.identifier.pmid | 23571676 | - |
dc.identifier.pmcid | PMC3686433 | - |
dc.identifier.scopus | eid_2-s2.0-84884186033 | - |
dc.identifier.hkuros | 216406 | - |
dc.identifier.volume | 20 | - |
dc.identifier.issue | 3 | - |
dc.identifier.spage | 273 | - |
dc.identifier.epage | 286 | - |
dc.identifier.isi | WOS:000321404200007 | - |
dc.publisher.place | United Kingdom | - |
dc.identifier.issnl | 1340-2838 | - |