Draft Genome Sequence of a Diploid and Hybrid Candida Strain, Candida sanyaensis UCD423, Isolated from Compost in Ireland.

Adam Ryan,Hawraa Almotawaa,Ada Mcdonagh,Isabelle Daly,Julia O’Leary,Aaron Martin,Emma Watson,Kevin P Byrne,Matthieu Osborne,Ghozlan Alhajeri,Sophia Heneghan,Roslyn Kavanagh,Kellie Horan,Sean A Bergin,Christopher Keane,Geraldine Butler,Kenneth H Wolfe,Eoin Ó Cinnéide,Jason E Stajich

doi:10.1128/mra.00761-21

Abstract

ABSTRACTCandida sanyaensis is a CUG-Ser1 clade yeast that is associated with soil. Assembly of short-read and long-read data shows that C. sanyaensis has a diploid and hybrid genome, with approximately 97% identity between the haplotypes. The haploid genome size is approximately 15.4 Mb.

Highlights

The yeast Candida sanyaensis is a member of the subphylum Saccharomycotina and the phylum Ascomycota and is closely related to Candida sojae and Candida tropicalis (1)
Using the diploid parameters with Canu resulted in an assembly that largely kept two haplotypes separate (Fig. 1)
C. sanyaensis has a diploid genome and the haplotypes differ by ;3.3%, suggesting that the genome results from hybridization between related but not identical parents (9)

Summary

Introduction

The yeast Candida sanyaensis is a member of the subphylum Saccharomycotina and the phylum Ascomycota and is closely related to Candida sojae and Candida tropicalis (1). Low-quality reads (Q scores of ,15) were removed from the Illumina data using Skewer v0.2.2 (4), and reads were assembled using SPAdes v3.14.0 (5) with default parameters. The MinION data were filtered using NanoFilt v2.7.1 (6), removing reads with quality scores of ,10 and lengths of ,10 kb. Reads were assembled using Canu v2.0 (7) with default parameters for a haploid assembly or with the options corOutCoverage = 200 and batOptions = -dg 3 -db 3 -dr 1 -ca 500 -cp 50 for a diploid assembly, assuming a genome size of 18 Mb. Assembly statistics were visualized using QUAST (8) (Table 1).

Results

Conclusion