An Updated Functional Annotation of Protein-Coding Genes in the Cucumber Genome.

Hongtao Song,Jinglu Hu,Erli Pang,Kui Lin

doi:10.3389/fpls.2018.00325

Hongtao Song, Jinglu Hu + Show 2 more

Open Access

https://doi.org/10.3389/fpls.2018.00325

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Abstract

Background: Although the cucumber reference genome and its annotation were published several years ago, the functional annotation of predicted genes, particularly protein-coding genes, still requires further improvement. In general, accurately determining orthologous relationships between genes allows for better and more robust functional assignments of predicted genes. As one of the most reliable strategies, the determination of collinearity information may facilitate reliable orthology inferences among genes from multiple related genomes. Currently, the identification of collinear segments has mainly been based on conservation of gene order and orientation. Over the course of plant genome evolution, various evolutionary events have disrupted or distorted the order of genes along chromosomes, making it difficult to use those genes as genome-wide markers for plant genome comparisons.Results: Using the localized LASTZ/MULTIZ analysis pipeline, we aligned 15 genomes, including cucumber and other related angiosperm plants, and identified a set of genomic segments that are short in length, stable in structure, uniform in distribution and highly conserved across all 15 plants. Compared with protein-coding genes, these conserved segments were more suitable for use as genomic markers for detecting collinear segments among distantly divergent plants. Guided by this set of identified collinear genomic segments, we inferred 94,486 orthologous protein-coding gene pairs (OPPs) between cucumber and 14 other angiosperm species, which were used as proxies for transferring functional terms to cucumber genes from the annotations of the other 14 genomes. In total, 10,885 protein-coding genes were assigned Gene Ontology (GO) terms which was nearly 1,300 more than results collected in Uniprot-proteomic database. Our results showed that annotation accuracy would been improved compared with other existing approaches.Conclusions: In this study, we provided an alternative resource for the functional annotation of predicted cucumber protein-coding genes, which we expect will be beneficial for the cucumber's biological study, accessible from http://cmb.bnu.edu.cn/functional_annotation. Meanwhile, using the cucumber reference genome as a case study, we presented an efficient strategy for transferring gene functional information from previously well-characterized protein-coding genes in model species to newly sequenced or “non-model” plant species.

Highlights

Cucumber (Cucumis sativus L.) (Huang et al, 2009) is an economically important crop as well as a model system for sex determination studies and plant vascular biology (Tanurdzic and Banks, 2004)
Though the Jaccard similarity between these two sets of collinear genomic segments decreased rapidly with increasing divergence from cucumber, we found that the multiple alignment anchors” (MAAs)-based method identified a greater number of specific collinear segments than the method based on protein-coding genes
We found that the orthomcl2go pipeline could be clustered with opp2go (MAAs-based), with sematic similarity scores of 0.83 for Molecular Function (MF) and 0.67 for Biological Process (BP)

Summary

Introduction

Cucumber (Cucumis sativus L.) (Huang et al, 2009) is an economically important crop as well as a model system for sex determination studies and plant vascular biology (Tanurdzic and Banks, 2004). Together with the currently available genomes of other related angiosperms, it provided an opportunity to perform a more accurate functional annotation for these predicted protein-coding genes in cucumber. Traditional approaches for automatic functional annotation of protein-coding genes in “non-model” species or in newly sequenced genomes rely on homology transfer based on sequence similarity, including Blast2GO (Conesa et al, 2005), identification of conserved domains (Rentzsch and Orengo, 2013) and InterPro2GO (Burge et al, 2012). The cucumber reference genome and its annotation were published several years ago, the functional annotation of predicted genes, protein-coding genes, still requires further improvement. Accurately determining orthologous relationships between genes allows for better and more robust functional assignments of predicted genes. Over the course of plant genome evolution, various evolutionary events have disrupted or distorted the order of genes along chromosomes, making it difficult to use those genes as genome-wide markers for plant genome comparisons

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