Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

Haas, Brian J.; Salzberg, Steven L.; Zhu, Wei; Pertea, Mihaela; Allen, Jonathan; Orvis, Joshua; White, Owen; Buell, C. Robin; Wortman, Jennifer

doi:10.1186/gb-2008-9-1-r7

Cited by 2,847 publications

(2,413 citation statements)

References 49 publications

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“…To accurately compare the gene numbers and gene distribution in each fungus, the gene structures were predicted for H. rhossiliensis as well as for all other fungi with the same algorithms, Evidence Modeler (Haas et al 2008), using Fusarium graminearum sequence as a reference. Finally, functional predictions were performed by BLASTX search against a protein database and InterProscan searches against protein domain databases (Zdobnov and Apweiler 2001).…”

Section: Methodsmentioning

confidence: 99%

Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

Zhang

Wang

et al. 2018

Mycology

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Hypocrealean fungi (Ascomycota) are known for their diversity of lifestyles. Their vital influences on agricultural and natural ecosystems have resulted in a number of sequenced genomes, which provide essential data for genomic analysis. Totally, 45 hypocrealean fungal genomes constructed a phylogeny. The phylogeny showed that plant pathogens in Nectriaceae diverged earliest, followed by animal pathogens in Cordycipitaceae, Ophiocordycipitaceae and Clavicipitaceae with mycoparasites in Hypocreaceae. Insect/nematode pathogens and grass endophytes in Clavicipitaceae diverged at last. Gene families associated with host-derived nutrients are significantly contracted in diverged lineages compared with the ancestral species. Introgression was detected in certain lineages of hypocrealean fungi, and the main functions of the genes located in the introgressed regions are involved in host recognition, transcriptional regulation, stress response and cell growth regulation. These results indicate that contraction of gene families and introgression might be main mechanisms to drive lifestyle differentiation and evolution and host shift of hypocrealean fungi.

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Section: Methodsmentioning

confidence: 99%

Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

Zhang

Wang

et al. 2018

Mycology

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“…Augustus [27], GeneID [28], and GeneMark-ES [29] programs were used to predict the gene models for the genome, and then the gene models generated by EVM [30] were updated by PASA. All predicted gene models were subjected to Gene Ontology (GO) [31], EuKaryotic Orthologous Groups (KOG) [32], FunCat [33] and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis [34].…”

Section: Mapping Assembly Of the Transcriptome And Differential Exprementioning

confidence: 99%

Comparative transcriptome analysis of the lichen-forming fungus Endocarpon pusillum elucidates its drought adaptation mechanisms

Wang

Zhang

Zhou

et al. 2014

Sci. China Life Sci.

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The lichen-forming fungus was isolated from the desert lichen Endocarpon pusillum that is extremely drought resistant. To understand the molecular mechanisms of drought resistance in the fungus, we employed RNA-seq and quantitative real-time PCR to compare and characterize the differentially expressed genes in pure culture at two different water levels and with that in desiccated lichen. The comparative transcriptome analysis indicated that a total of 1781 genes were differentially expressed between samples cultured under normal and PEG-induced drought stress conditions. Similar to those in drought resistance plants and non-lichenized fungi, the common drought-resistant mechanisms were differentially expressed in E. pusillum. However, the expression change of genes involved in osmotic regulation in E. pusillum is different, which might be the evidence for the feature of drought adaptation. Interestingly, different from other organisms, some genes involved in drought adaption mechanisms showed significantly different expression patterns between the presence and absence of drought stress in E. pusillum. The expression of 23 candidate stress responsive genes was further confirmed by quantitative real-time PCR using dehydrated E. pusillum lichen thalli. This study provides a valuable resource for future research on lichen-forming fungi and shall facilitate future functional studies of the specific genes related to drought resistance. lichen, mycobiont, dehydration, drought adaption, drought resistant Citation:Wang YY, Zhang XY, Zhou QM, Zhang XL, Wei JC. Comparative transcriptome analysis of the lichen-forming fungus Endocarpon pusillum elucidates its drought adaptation mechanisms.

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“…Cufflinks (version 2.1.1) 63 (http://cufflinks.cbcb.umd.edu/) was then used to assemble the transcripts into gene models. All gene models predicted from the above three approaches were combined by EvidenceModeler (EVM) into a nonredundant set of gene structures 64 . The gene models were further filtered based on their Cscore, peptide coverage and its CDS overlapping with TEs.…”

mentioning

confidence: 99%

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

et al. 2015

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Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

Abstract: EVidenceModeler (EVM) is an automated annotation tool that predicts protein-coding regions, alternatively spliced transcripts and untranslated regions of eukaryotic genes.

Cited by 2,847 publications

References 49 publications

Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

Comparative transcriptome analysis of the lichen-forming fungus Endocarpon pusillum elucidates its drought adaptation mechanisms

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

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