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Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss.

Publication ,  Journal Article
Gröhs Ferrareze, PA; Maufrais, C; Silva Araujo Streit, R; Priest, SJ; Cuomo, CA; Heitman, J; Staats, CC; Janbon, G
Published in: G3 (Bethesda)
February 9, 2021

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 annotation 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 species 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 transporters 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 subtelomeric regions, and that other chromosomal regions might participate in adaptive diversification of Cryptococcus metabolite assimilation potential.

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Published In

G3 (Bethesda)

DOI

EISSN

2160-1836

Publication Date

February 9, 2021

Volume

11

Issue

2

Location

England

Related Subject Headings

  • RNA Interference
  • Multigene Family
  • Molecular Sequence Annotation
  • Genomics
  • Genome, Fungal
  • Cryptococcus neoformans
  • 4905 Statistics
  • 3105 Genetics
  • 3101 Biochemistry and cell biology
  • 0604 Genetics
 

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Gröhs Ferrareze, P. A., Maufrais, C., Silva Araujo Streit, R., Priest, S. J., Cuomo, C. A., Heitman, J., … Janbon, G. (2021). Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss. G3 (Bethesda), 11(2). https://doi.org/10.1093/g3journal/jkaa070
Gröhs Ferrareze, Patrícia Aline, Corinne Maufrais, Rodrigo Silva Araujo Streit, Shelby J. Priest, Christina A. Cuomo, Joseph Heitman, Charley Christian Staats, and Guilhem Janbon. “Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss.G3 (Bethesda) 11, no. 2 (February 9, 2021). https://doi.org/10.1093/g3journal/jkaa070.
Gröhs Ferrareze PA, Maufrais C, Silva Araujo Streit R, Priest SJ, Cuomo CA, Heitman J, et al. Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss. G3 (Bethesda). 2021 Feb 9;11(2).
Gröhs Ferrareze, Patrícia Aline, et al. “Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss.G3 (Bethesda), vol. 11, no. 2, Feb. 2021. Pubmed, doi:10.1093/g3journal/jkaa070.
Gröhs Ferrareze PA, Maufrais C, Silva Araujo Streit R, Priest SJ, Cuomo CA, Heitman J, Staats CC, Janbon G. Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss. G3 (Bethesda). 2021 Feb 9;11(2).

Published In

G3 (Bethesda)

DOI

EISSN

2160-1836

Publication Date

February 9, 2021

Volume

11

Issue

2

Location

England

Related Subject Headings

  • RNA Interference
  • Multigene Family
  • Molecular Sequence Annotation
  • Genomics
  • Genome, Fungal
  • Cryptococcus neoformans
  • 4905 Statistics
  • 3105 Genetics
  • 3101 Biochemistry and cell biology
  • 0604 Genetics