@article{6c27db3d844544bfac249a5c1f4a9ba2,
title = "Cell wall protein variation, break-induced replication, and subtelomere dynamics in Candida glabrata",
abstract = "Candida glabrata is an opportunistic pathogen of humans, responsible for up to 30% of disseminated candidiasis. Adherence of C. glabrata to host cells is mediated by adhesin-like proteins (ALPs), about half of which are encoded in the subtelomeres. We performed a de novo assembly of two C. glabrata strains, BG2 and BG3993, using long single-molecule real-time (SMRT) reads, and constructed high-quality telomere-to-telomere assemblies of all 13 chromosomes to assess differences between C. glabrata strains. We documented variation between strains, and in agreement with earlier studies, found high (~0.5%–1%) frequencies of SNVs across the genome, including within subtelomeric regions. We documented changes in ALP gene structure and complement: there are large length differences in ALP genes in different strains, resulting from copy number variation in tandem repeats. We compared strains to characterize chromosome rearrangement events including within the poorly characterized subtelomeric regions. We show that rearrangements within the subtelomere regions all affect ALP-encoding genes, and 14/16 involve just the most terminal ALP gene. We present evidence that these rearrangements are mediated by break-induced replication. This study highlights the constrained nature of subtelomeric changes impacting ALP gene complement and subtelomere structure.",
keywords = "BIR, GPI-CWP, fungal adhesins",
author = "Zhuwei Xu and Brian Green and Nicole Benoit and Sobel, {Jack D.} and Schatz, {Michael C.} and Sarah Wheelan and Cormack, {Brendan P.}",
note = "Funding Information: We thank Sara Goodwin and Cold Spring Harbor{\textquoteright}s Next Generation Genomics Shared Resource for sequencing on the PacBio SMRT sequencing platform. We thank the Experimental and Computational Genomics Core (ECGC) at the Sidney Kimmel Comprehensive Cancer Center for sequencing on the Illumina sequencing platform. We thank Paul Hook for help with BG2 assembly efforts. We thank Nancy Craig and Carol Greider for insight and suggestions, and for reading the manuscript. We thank an anonymous reviewer for a careful and thorough review which improved the manuscript. This work was supported by grant R01AI046223 to BPC and by a National Science Foundation Award (DBI‐1627442) to MCS. Funding Information: We thank Sara Goodwin and Cold Spring Harbor{\textquoteright}s Next Generation Genomics Shared Resource for sequencing on the PacBio SMRT sequencing platform. We thank the Experimental and Computational Genomics Core (ECGC) at the Sidney Kimmel Comprehensive Cancer Center for sequencing on the Illumina sequencing platform. We thank Paul Hook for help with BG2 assembly efforts. We thank Nancy Craig and Carol Greider for insight and suggestions, and for reading the manuscript. We thank an anonymous reviewer for a careful and thorough review which improved the manuscript. This work was supported by grant R01AI046223 to BPC and by a National Science Foundation Award (DBI-1627442) to MCS. Publisher Copyright: {\textcopyright} 2021 John Wiley & Sons Ltd",
year = "2021",
month = jul,
doi = "10.1111/mmi.14707",
language = "English (US)",
volume = "116",
pages = "260--276",
journal = "Molecular Microbiology",
issn = "0950-382X",
publisher = "Wiley-Blackwell",
number = "1",
}