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Phased Diploid Genome Assemblies for Three Strains of Candida albicans from Oak Trees

Although normally a harmless commensal, Candida albicans, it is also one of the most common causes of bloodstream infections in the U.S. Candida albicans has long been considered an obligate commensal, however, recent studies suggest it can live outside animal hosts. Here, we have generated PacBio s...

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Autores principales: Hamlin, Jennafer A. P., Dias, Guilherme B., Bergman, Casey M., Bensasson, Douda
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6829152/
https://www.ncbi.nlm.nih.gov/pubmed/31540974
http://dx.doi.org/10.1534/g3.119.400486
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author Hamlin, Jennafer A. P.
Dias, Guilherme B.
Bergman, Casey M.
Bensasson, Douda
author_facet Hamlin, Jennafer A. P.
Dias, Guilherme B.
Bergman, Casey M.
Bensasson, Douda
author_sort Hamlin, Jennafer A. P.
collection PubMed
description Although normally a harmless commensal, Candida albicans, it is also one of the most common causes of bloodstream infections in the U.S. Candida albicans has long been considered an obligate commensal, however, recent studies suggest it can live outside animal hosts. Here, we have generated PacBio sequences and phased genome assemblies for three C. albicans strains from oak trees (NCYC 4144, NCYC 4145, and NCYC 4146). PacBio datasets are high depth (over 400 fold coverage) and more than half of the sequencing data are contained in reads longer than 15 kb. Primary assemblies showed high contiguity with several chromosomes for each strain recovered as single contigs, and greater than half of the alternative haplotype sequence was assembled in haplotigs at least 174 kb long. Using these assemblies we were able to identify structural polymorphisms, including a polymorphic inversion over 100 kb in length. These results show that phased de novo diploid assemblies for C. albicans can enable the study of genomic variation within and among strains of an important fungal pathogen.
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spelling pubmed-68291522019-11-06 Phased Diploid Genome Assemblies for Three Strains of Candida albicans from Oak Trees Hamlin, Jennafer A. P. Dias, Guilherme B. Bergman, Casey M. Bensasson, Douda G3 (Bethesda) Genome Report Although normally a harmless commensal, Candida albicans, it is also one of the most common causes of bloodstream infections in the U.S. Candida albicans has long been considered an obligate commensal, however, recent studies suggest it can live outside animal hosts. Here, we have generated PacBio sequences and phased genome assemblies for three C. albicans strains from oak trees (NCYC 4144, NCYC 4145, and NCYC 4146). PacBio datasets are high depth (over 400 fold coverage) and more than half of the sequencing data are contained in reads longer than 15 kb. Primary assemblies showed high contiguity with several chromosomes for each strain recovered as single contigs, and greater than half of the alternative haplotype sequence was assembled in haplotigs at least 174 kb long. Using these assemblies we were able to identify structural polymorphisms, including a polymorphic inversion over 100 kb in length. These results show that phased de novo diploid assemblies for C. albicans can enable the study of genomic variation within and among strains of an important fungal pathogen. Genetics Society of America 2019-09-20 /pmc/articles/PMC6829152/ /pubmed/31540974 http://dx.doi.org/10.1534/g3.119.400486 Text en Copyright © 2019 Hamlin et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genome Report
Hamlin, Jennafer A. P.
Dias, Guilherme B.
Bergman, Casey M.
Bensasson, Douda
Phased Diploid Genome Assemblies for Three Strains of Candida albicans from Oak Trees
title Phased Diploid Genome Assemblies for Three Strains of Candida albicans from Oak Trees
title_full Phased Diploid Genome Assemblies for Three Strains of Candida albicans from Oak Trees
title_fullStr Phased Diploid Genome Assemblies for Three Strains of Candida albicans from Oak Trees
title_full_unstemmed Phased Diploid Genome Assemblies for Three Strains of Candida albicans from Oak Trees
title_short Phased Diploid Genome Assemblies for Three Strains of Candida albicans from Oak Trees
title_sort phased diploid genome assemblies for three strains of candida albicans from oak trees
topic Genome Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6829152/
https://www.ncbi.nlm.nih.gov/pubmed/31540974
http://dx.doi.org/10.1534/g3.119.400486
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