scholarly journals Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains

2015 ◽  
Vol 81 (18) ◽  
pp. 6253-6267 ◽  
Author(s):  
M. van den Broek ◽  
I. Bolat ◽  
J. F. Nijkamp ◽  
E. Ramos ◽  
M. A. H. Luttik ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Phenotypic Traits ◽  
Genome Sequences ◽  
Content Type ◽  
Chromosome Copy Number ◽  
Group I ◽  
Saccharomyces Pastorianus ◽  
Karyotypic Variability ◽  
Number Variation

ABSTRACTLager brewing strains ofSaccharomyces pastorianusare natural interspecific hybrids originating from the spontaneous hybridization ofSaccharomyces cerevisiaeandSaccharomyces eubayanus. Over the past 500 years,S. pastorianushas been domesticated to become one of the most important industrial microorganisms. Production of lager-type beers requires a set of essential phenotypes, including the ability to ferment maltose and maltotriose at low temperature, the production of flavors and aromas, and the ability to flocculate. Understanding of the molecular basis of complex brewing-related phenotypic traits is a prerequisite for rational strain improvement. While genome sequences have been reported, the variability and dynamics ofS. pastorianusgenomes have not been investigated in detail. Here, using deep sequencing and chromosome copy number analysis, we showed thatS. pastorianusstrain CBS1483 exhibited extensive aneuploidy. This was confirmed by quantitative PCR and by flow cytometry. As a direct consequence of this aneuploidy, a massive number of sequence variants was identified, leading to at least 1,800 additional protein variants inS. pastorianusCBS1483. Analysis of eight additionalS. pastorianusstrains revealed that the previously defined group I strains showed comparable karyotypes, while group II strains showed large interstrain karyotypic variability. Comparison of three strains with nearly identical genome sequences revealed substantial chromosome copy number variation, which may contribute to strain-specific phenotypic traits. The observed variability of lager yeast genomes demonstrates that systematic linking of genotype to phenotype requires a three-dimensional genome analysis encompassing physical chromosomal structures, the copy number of individual chromosomes or chromosomal regions, and the allelic variation of copies of individual genes.

scholarly journals Industrial Relevance of Chromosomal Copy Number Variation in Saccharomyces Yeasts

2017 ◽  
Vol 83 (11) ◽  
Author(s):  
Arthur R. Gorter de Vries ◽  
Jack T. Pronk ◽  
Jean-Marc G. Daran
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Evolutionary Significance ◽  
Evolutionary Engineering ◽  
Content Type ◽  
Recent Developments ◽  
Number Variation ◽  
Chromosomal Copy Number ◽  
Chromosomal Copy ◽  
Chromosomal Copy Number Variation

ABSTRACT Chromosomal copy number variation (CCNV) plays a key role in evolution and health of eukaryotes. The unicellular yeast Saccharomyces cerevisiae is an important model for studying the generation, physiological impact, and evolutionary significance of CCNV. Fundamental studies of this yeast have contributed to an extensive set of methods for analyzing and introducing CCNV. Moreover, these studies provided insight into the balance between negative and positive impacts of CCNV in evolutionary contexts. A growing body of evidence indicates that CCNV not only frequently occurs in industrial strains of Saccharomyces yeasts but also is a key contributor to the diversity of industrially relevant traits. This notion is further supported by the frequent involvement of CCNV in industrially relevant traits acquired during evolutionary engineering. This review describes recent developments in genome sequencing and genome editing techniques and discusses how these offer opportunities to unravel contributions of CCNV in industrial Saccharomyces strains as well as to rationally engineer yeast chromosomal copy numbers and karyotypes.

scholarly journals Two Different Copy Number Variations of the CLCN2 Gene in Chinese Cattle and Their Association with Growth Traits

Animals ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 41
Author(s):  
Jia Tang ◽  
Xuemei Shen ◽  
Yu Yang ◽  
Haiyan Yang ◽  
Ao Qi ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Growth Traits ◽  
Organ Distribution ◽  
Phenotypic Traits ◽  
Cattle Population ◽  
Exon 2 ◽  
Voltage Gated ◽  
Chinese Cattle ◽  
Number Variation

Copy number variation (CNV) can affect gene function and even individual phenotypic traits by changing the transcription and translation level of related genes, and it also plays an important role in species evolution. Chloride voltage-gated channel 2 (CLCN2) encodes a voltage-gated chloride channel (CLC-2), which has a wide organ distribution and is ubiquitously expressed. Based on previous studies, we hypothesize that CLCN2 could be a candidate gene involved in cell volume regulation, transepithelial transport and cell proliferation. This study aimed to explore CNVs in the CLCN2 gene and investigate its association with growth traits in four Chinese cattle breeds (Yunling cattle, Xianan cattle, Qinchuan cattle and Pinan cattle). We identified there are two copy number variation regions (CNV1: 3600 bp, including exon 2–11; CNV2: 4800 bp, including exon 21–22) of the CLCN2 gene. The statistical analysis showed that the CNV1 mutation in the YL cattle population was significantly associated with cannon circumference (p < 0.01). The CNV2 mutation in the XN cattle population had a significant effect on body slanting length, chest girth and body weight (p < 0.05). In the YL cattle, the association analysis of CLCN2 gene CNV1 and CNV2 combination with cannon circumference was significant (p < 0.01). Our results provide evidence that CNV1 and CNV2 in CLCN2 are associated with growth traits in two different cattle populations and could be used as candidate markers for cattle molecular breeding.

scholarly journals MHC gene copy number variation in Tasmanian devils: implications for the spread of a contagious cancer

2010 ◽  
Vol 277 (1690) ◽  
pp. 2001-2006 ◽  
Author(s):  
Hannah V. Siddle ◽  
Jolanta Marzec ◽  
Yuanyuan Cheng ◽  
Menna Jones ◽  
Katherine Belov
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Sequence Similarity ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Tasmanian Devil ◽  
Group I ◽  
Devil Facial Tumour Disease ◽  
Number Variation ◽  
Mhc Diversity

Tasmanian devils face extinction owing to the emergence of a contagious cancer. Devil facial tumour disease (DFTD) is a clonal cancer spread owing to a lack of major histocompatibility complex (MHC) barriers in Tasmanian devil populations. We present a comprehensive screen of MHC diversity in devils and identify 25 MHC types and 53 novel sequences, but conclude that overall levels of MHC diversity at the sequence level are low. The majority of MHC Class I variation can be explained by allelic copy number variation with two to seven sequence variants identified per individual. MHC sequences are divided into two distinct groups based on sequence similarity. DFTD cells and most devils have sequences from both groups. Twenty per cent of individuals have a restricted MHC repertoire and contain only group I or only group II sequences. Counterintuitively, we postulate that the immune system of individuals with a restricted MHC repertoire may recognize foreign MHC antigens on the surface of the DFTD cell. The implication of these results for management of DFTD and this endangered species are discussed.

Sign in / Sign up

Export Citation Format

Share Document