Donovan Paul D, Schröder Markus S, Higgins Desmond G, Butler Geraldine
School of Biomedical and Biomolecular Science and UCD Conway Institute of Biomolecular and Biomedical Research, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
School of Medicine and UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.
PLoS One. 2016 Sep 22;11(9):e0163235. doi: 10.1371/journal.pone.0163235. eCollection 2016.
The Candida CTG clade is a monophyletic group of fungal species that translates CTG as serine, and includes the pathogens Candida albicans and Candida parapsilosis. Research has typically focused on identifying protein-coding genes in these species. Here, we use bioinformatic and experimental approaches to annotate known classes of non-coding RNAs in three CTG-clade species, Candida parapsilosis, Candida orthopsilosis and Lodderomyces elongisporus. We also update the annotation of ncRNAs in the C. albicans genome. The majority of ncRNAs identified were snoRNAs. Approximately 50% of snoRNAs (including most of the C/D box class) are encoded in introns. Most are within mono- and polycistronic transcripts with no protein coding potential. Five polycistronic clusters of snoRNAs are highly conserved in fungi. In polycistronic regions, splicing occurs via the classical pathway, as well as by nested and recursive splicing. We identified spliceosomal small nuclear RNAs, the telomerase RNA component, signal recognition particle, RNase P RNA component and the related RNase MRP RNA component in all three genomes. Stem loop IV of the U2 spliceosomal RNA and the associated binding proteins were lost from the ancestor of C. parapsilosis and C. orthopsilosis, following the divergence from L. elongisporus. The RNA component of the MRP is longer in C. parapsilosis, C. orthopsilosis and L. elongisporus than in S. cerevisiae, but is substantially shorter than in C. albicans.
念珠菌CTG进化枝是一组真菌物种的单系群，它们将CTG翻译为丝氨酸，包括病原体白色念珠菌和近平滑念珠菌。研究通常集中于鉴定这些物种中的蛋白质编码基因。在此，我们使用生物信息学和实验方法对三种CTG进化枝物种——近平滑念珠菌、正平滑念珠菌和长孢洛德酵母中的已知非编码RNA类别进行注释。我们还更新了白色念珠菌基因组中非编码RNA的注释。鉴定出的大多数非编码RNA是核仁小RNA（snoRNA）。大约50%的snoRNA（包括大多数C/D盒类）编码于内含子中。大多数存在于无蛋白质编码潜力的单顺反子和多顺反子转录本中。五个snoRNA多顺反子簇在真菌中高度保守。在多顺反子区域，剪接通过经典途径以及嵌套和递归剪接发生。我们在所有三个基因组中鉴定出了剪接体小核RNA、端粒酶RNA组分、信号识别颗粒、核糖核酸酶P RNA组分以及相关的核糖核酸酶MRP RNA组分。在与长孢洛德酵母分化后，U2剪接体RNA的茎环IV及其相关结合蛋白在近平滑念珠菌和正平滑念珠菌的祖先中丢失。MRP的RNA组分在近平滑念珠菌、正平滑念珠菌和长孢洛德酵母中比在酿酒酵母中更长，但比在白色念珠菌中短得多。
