Dataset Information

TGFam-Finder: a novel solution for target-gene family annotation in plants.

ABSTRACT: Whole-genome annotation error that omits essential protein-coding genes hinders further research. We developed Target Gene Family Finder (TGFam-Finder), an alternative tool for the structural annotation of protein-coding genes containing target domain(s) of interest in plant genomes. TGFam-Finder took considerably reduced annotation run-time and improved accuracy compared to conventional annotation tools. Large-scale re-annotation of 50 plant genomes identified an average of 150, 166 and 86 additional far-red-impaired response 1, nucleotide-binding and leucine-rich-repeat, and cytochrome P450 genes, respectively, that were missed in previous annotations. We detected significantly higher number of translated genes in the new annotations using mass spectrometry data from seven plant species compared to previous annotations. TGFam-Finder along with the new gene models can provide an optimized platform for comprehensive functional, comparative, and evolutionary studies in plants.

SUBMITTER: Kim S

PROVIDER: S-EPMC7496378 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Publications

TGFam-Finder: a novel solution for target-gene family annotation in plants.

Kim Seungill S Cheong Kyeongchae K Park Jieun J Kim Myung-Shin MS Kim Jihyun J Seo Min-Ki MK Chae Geun Young GY Jang Min Jeong MJ Mang Hyunggon H Kwon Sun-Ho SH Kim Yong-Min YM Koo Namjin N Min Cheol Woo CW Kim Kwang-Soo KS Oh Nuri N Kim Ki-Tae KT Jeon Jongbum J Kim Hyunbin H Lee Yoon-Young YY Sohn Kee Hoon KH McCann Honour C HC Ye Sang-Kyu SK Kim Sun Tae ST Park Kyung-Soon KS Lee Yong-Hwan YH Choi Doil D

The New phytologist 20200605 5

Whole-genome annotation error that omits essential protein-coding genes hinders further research. We developed Target Gene Family Finder (TGFam-Finder), an alternative tool for the structural annotation of protein-coding genes containing target domain(s) of interest in plant genomes. TGFam-Finder took considerably reduced annotation run-time and improved accuracy compared to conventional annotation tools. Large-scale re-annotation of 50 plant genomes identified an average of 150, 166 and 86 addi ...[more]

PMID: 32392385

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Project description:BackgroundTo date more than 2,1 million gene products from more than 100000 different species have been described specifying their function, the processes they are involved in and their cellular localization using a very well defined and structured vocabulary, the gene ontology (GO). Such vast, well defined knowledge opens the possibility of compare gene products at the level of functionality, finding gene products which have a similar function or are involved in similar biological processes without relying on the conventional sequence similarity approach. Comparisons within such a large space of knowledge are highly data and computing intensive. For this reason this project was based upon the use of the computational GRID, a technology offering large computing and storage resources.ResultsWe have developed a tool, GENe AnaloGue FINdEr (ENGINE) that parallelizes the search process and distributes the calculation and data over the computational GRID, splitting the process into many sub-processes and joining the calculation and the data on the same machine and therefore completing the whole search in about 3 days instead of occupying one single machine for more than 5 CPU years. The results of the functional comparison contain potential functional analogues for more than 79000 gene products from the most important species. 46% of the analyzed gene products are well enough described for such an analysis to individuate functional analogues, such as well-known members of the same gene family, or gene products with similar functions which would never have been associated by standard methods.ConclusionENGINE has produced a list of potential functionally analogous relations between gene products within and between species using, in place of the sequence, the gene description of the GO, thus demonstrating the potential of the GO. However, the current limiting factor is the quality of the associations of many gene products from non-model organisms that often have electronic associations, since experimental information is missing. With future improvements of the GO, this limit will be reduced. ENGINE will manifest its power when it is applied to the whole GODB of more than 2,1 million gene products from more than 100000 organisms. The data produced by this search is planed to be available as a supplement to the GO database as soon as we are able to provide regular updates.

Dataset Information

TGFam-Finder: a novel solution for target-gene family annotation in plants.

Publications

TGFam-Finder: a novel solution for target-gene family annotation in plants.

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