Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UFRGS |
Texto Completo: | http://hdl.handle.net/10183/267661 |
Resumo: | Evaluating the quality of a de novo annotation of a complex fungal genome based on RNA-seq data remains a challenge. In this study, we sequentially optimized a Cufflinks-CodingQuary-based bioinformatics pipeline fed with RNA-seq data using the manually annotated model pathogenic yeasts Cryptococcus neoformans and Cryptococcus deneoformans as test cases. Our results show that the quality of the anno tation is sensitive to the quantity of RNA-seq data used and that the best quality is obtained with 5–10 million reads per RNA-seq replicate. We also showed that the number of introns predicted is an excellent a priori indicator of the quality of the final de novo annotation. We then used this pipeline to annotate the genome of the RNAi-deficient species Cryptococcus deuterogattii strain R265 using RNA-seq data. Dynamic transcriptome analysis revealed that intron retention is more prominent in C. deuterogattii than in the other RNAi-proficient spe cies C. neoformans and C. deneoformans. In contrast, we observed that antisense transcription was not higher in C. deuterogattii than in the two other Cryptococcus species. Comparative gene content analysis identified 21 clusters enriched in transcription factors and trans porters that have been lost. Interestingly, analysis of the subtelomeric regions in these three annotated species identified a similar gene enrichment, reminiscent of the structure of primary metabolic clusters. Our data suggest that there is active exchange between subtelo meric regions, and that other chromosomal regions might participate in adaptive diversification of Cryptococcus metabolite assimilation potential. |
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Ferrareze, Patricia Aline GröhsMaufrais, CorinneStreit, Rodrigo Silva AraujoPriest, Shelby J.Cuomo, ChristinaHeitmann, JosephStaats, Charley ChristianJanbon, Guilhem2023-11-25T03:27:26Z20212160-1836http://hdl.handle.net/10183/267661001172371Evaluating the quality of a de novo annotation of a complex fungal genome based on RNA-seq data remains a challenge. In this study, we sequentially optimized a Cufflinks-CodingQuary-based bioinformatics pipeline fed with RNA-seq data using the manually annotated model pathogenic yeasts Cryptococcus neoformans and Cryptococcus deneoformans as test cases. Our results show that the quality of the anno tation is sensitive to the quantity of RNA-seq data used and that the best quality is obtained with 5–10 million reads per RNA-seq replicate. We also showed that the number of introns predicted is an excellent a priori indicator of the quality of the final de novo annotation. We then used this pipeline to annotate the genome of the RNAi-deficient species Cryptococcus deuterogattii strain R265 using RNA-seq data. Dynamic transcriptome analysis revealed that intron retention is more prominent in C. deuterogattii than in the other RNAi-proficient spe cies C. neoformans and C. deneoformans. In contrast, we observed that antisense transcription was not higher in C. deuterogattii than in the two other Cryptococcus species. Comparative gene content analysis identified 21 clusters enriched in transcription factors and trans porters that have been lost. Interestingly, analysis of the subtelomeric regions in these three annotated species identified a similar gene enrichment, reminiscent of the structure of primary metabolic clusters. Our data suggest that there is active exchange between subtelo meric regions, and that other chromosomal regions might participate in adaptive diversification of Cryptococcus metabolite assimilation potential.application/pdfengG3 - Genes|Genomes|Genetics. Bethesda, Md. Vol. 11, no.2 (Feb. 2021), 18 p.CryptococcusGenomaCryptococus deuterogattiiGenome annotation pipelineRNAiMetabolic gene clusterApplication of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi lossEstrangeiroinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFRGSinstname:Universidade Federal do Rio Grande do Sul (UFRGS)instacron:UFRGSTEXT001172371.pdf.txt001172371.pdf.txtExtracted Texttext/plain99672http://www.lume.ufrgs.br/bitstream/10183/267661/2/001172371.pdf.txt2e34e6af726534b02cdc68a931dc732eMD52ORIGINAL001172371.pdfTexto completo (inglês)application/pdf1371782http://www.lume.ufrgs.br/bitstream/10183/267661/1/001172371.pdfa8c18122bb58815434aa19c6c6d7a5c5MD5110183/2676612023-11-26 04:26:22.426177oai:www.lume.ufrgs.br:10183/267661Repositório de PublicaçõesPUBhttps://lume.ufrgs.br/oai/requestopendoar:2023-11-26T06:26:22Repositório Institucional da UFRGS - Universidade Federal do Rio Grande do Sul (UFRGS)false |
dc.title.pt_BR.fl_str_mv |
Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss |
title |
Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss |
spellingShingle |
Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss Ferrareze, Patricia Aline Gröhs Cryptococcus Genoma Cryptococus deuterogattii Genome annotation pipeline RNAi Metabolic gene cluster |
title_short |
Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss |
title_full |
Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss |
title_fullStr |
Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss |
title_full_unstemmed |
Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss |
title_sort |
Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss |
author |
Ferrareze, Patricia Aline Gröhs |
author_facet |
Ferrareze, Patricia Aline Gröhs Maufrais, Corinne Streit, Rodrigo Silva Araujo Priest, Shelby J. Cuomo, Christina Heitmann, Joseph Staats, Charley Christian Janbon, Guilhem |
author_role |
author |
author2 |
Maufrais, Corinne Streit, Rodrigo Silva Araujo Priest, Shelby J. Cuomo, Christina Heitmann, Joseph Staats, Charley Christian Janbon, Guilhem |
author2_role |
author author author author author author author |
dc.contributor.author.fl_str_mv |
Ferrareze, Patricia Aline Gröhs Maufrais, Corinne Streit, Rodrigo Silva Araujo Priest, Shelby J. Cuomo, Christina Heitmann, Joseph Staats, Charley Christian Janbon, Guilhem |
dc.subject.por.fl_str_mv |
Cryptococcus Genoma |
topic |
Cryptococcus Genoma Cryptococus deuterogattii Genome annotation pipeline RNAi Metabolic gene cluster |
dc.subject.eng.fl_str_mv |
Cryptococus deuterogattii Genome annotation pipeline RNAi Metabolic gene cluster |
description |
Evaluating the quality of a de novo annotation of a complex fungal genome based on RNA-seq data remains a challenge. In this study, we sequentially optimized a Cufflinks-CodingQuary-based bioinformatics pipeline fed with RNA-seq data using the manually annotated model pathogenic yeasts Cryptococcus neoformans and Cryptococcus deneoformans as test cases. Our results show that the quality of the anno tation is sensitive to the quantity of RNA-seq data used and that the best quality is obtained with 5–10 million reads per RNA-seq replicate. We also showed that the number of introns predicted is an excellent a priori indicator of the quality of the final de novo annotation. We then used this pipeline to annotate the genome of the RNAi-deficient species Cryptococcus deuterogattii strain R265 using RNA-seq data. Dynamic transcriptome analysis revealed that intron retention is more prominent in C. deuterogattii than in the other RNAi-proficient spe cies C. neoformans and C. deneoformans. In contrast, we observed that antisense transcription was not higher in C. deuterogattii than in the two other Cryptococcus species. Comparative gene content analysis identified 21 clusters enriched in transcription factors and trans porters that have been lost. Interestingly, analysis of the subtelomeric regions in these three annotated species identified a similar gene enrichment, reminiscent of the structure of primary metabolic clusters. Our data suggest that there is active exchange between subtelo meric regions, and that other chromosomal regions might participate in adaptive diversification of Cryptococcus metabolite assimilation potential. |
publishDate |
2021 |
dc.date.issued.fl_str_mv |
2021 |
dc.date.accessioned.fl_str_mv |
2023-11-25T03:27:26Z |
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2160-1836 |
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001172371 |
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http://hdl.handle.net/10183/267661 |
dc.language.iso.fl_str_mv |
eng |
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dc.relation.ispartof.pt_BR.fl_str_mv |
G3 - Genes|Genomes|Genetics. Bethesda, Md. Vol. 11, no.2 (Feb. 2021), 18 p. |
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info:eu-repo/semantics/openAccess |
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