Comparative genomics of wild type yeast strains unveils important genome diversity

Carreto, Laura; Eiriz, Maria Francisca; Gomes, Ana Catarina; Pereira, Patrícia M.; Schuller, Dorit Elisabeth; Santos, Manuel A. S.

doi:10.1186/1471-2164-9-524

Cited by 117 publications

(139 citation statements)

References 82 publications

(82 reference statements)

Supporting

Mentioning

124

Contrasting

Unclassified

Order By: Relevance

“…Structural variation, although abundant, was limited to the end sections of chromosomes. A similar pattern has been previously observed in microarray-based surveys of genome variation among different S. cerevisiae strains (Winzeler et al 2003;Carreto et al 2008;Schacherer et al 2009), which found that most polymorphisms, including SNPs and CNVs, were more common within 25 kb of the telomeres. In these studies, however, the full extent of the structural variation in these regions could not be revealed because the microarrays used were based on the S288c genome, and regions of high sequence divergence or sequences that were absent in the reference strain could not be examined.…”

Section: Discussionsupporting

confidence: 60%

“…Microarray-based whole-genome hybridization studies of wild, industrial, and laboratory S. cerevisiae strains (Winzeler et al 2003;Carreto et al 2008;Faddah et al 2009;Schacherer et al 2009) have uncovered a recurrent pattern of copy number variation (CNV) near the ends of chromosomes, suggesting a role for repetitive DNA sequences in structural genome diversification. Despite these valuable insights, two central questions regarding the role of chromosomal rearrangements in genome evolution in S. cerevisiae remain unanswered: First, it is still unclear how these rearrangements contribute to long-term fitness in natural environments; and second, it is not known if they are compatible with the formation of viable meiotic spores that would allow their sexual dissemination between natural S. cerevisiae populations.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

Argueso

Carazzolle

Mieczkowski³

et al. 2009

Genome Res.

251

236

View full text Add to dashboard Cite

Bioethanol is a biofuel produced mainly from the fermentation of carbohydrates derived from agricultural feedstocks by the yeast Saccharomyces cerevisiae. One of the most widely adopted strains is PE-2, a heterothallic diploid naturally adapted to the sugar cane fermentation process used in Brazil. Here we report the molecular genetic analysis of a PE-2 derived diploid (JAY270), and the complete genome sequence of a haploid derivative (JAY291). The JAY270 genome is highly heterozygous (;2 SNPs/kb) and has several structural polymorphisms between homologous chromosomes. These chromosomal rearrangements are confined to the peripheral regions of the chromosomes, with breakpoints within repetitive DNA sequences. Despite its complex karyotype, this diploid, when sporulated, had a high frequency of viable spores. Hybrid diploids formed by outcrossing with the laboratory strain S288c also displayed good spore viability. Thus, the rearrangements that exist near the ends of chromosomes do not impair meiosis, as they do not span regions that contain essential genes. This observation is consistent with a model in which the peripheral regions of chromosomes represent plastic domains of the genome that are free to recombine ectopically and experiment with alternative structures. We also explored features of the JAY270 and JAY291 genomes that help explain their high adaptation to industrial environments, exhibiting desirable phenotypes such as high ethanol and cell mass production and high temperature and oxidative stress tolerance. The genomic manipulation of such strains could enable the creation of a new generation of industrial organisms, ideally suited for use as delivery vehicles for future bioenergy technologies.

show abstract

Section: Discussionsupporting

confidence: 60%

mentioning

confidence: 99%

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

Argueso

Carazzolle

Mieczkowski³

et al. 2009

Genome Res.

251

236

View full text Add to dashboard Cite

show abstract

“…Subtelomeric regions are more generally recognized as extremely dynamic regions of chromosomes (Mefford and Trask 2002;Prieto et al 2004;Gonzalez-Garcia et al 2006;Carreto et al 2008;Nieves et al 2011). In humans, large complex blocks of duplicated sequences-zones of subtelomeric duplication-typically define the last 50-150 kbp of human chromosomes (Mefford and Trask 2002;Riethman et al 2005).…”

mentioning

confidence: 99%

The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2

Ventura¹,

Catacchio²,

Sajjadian³

et al. 2012

Genome Res.

View full text Add to dashboard Cite

Chimpanzee and gorilla chromosomes differ from human chromosomes by the presence of large blocks of subterminal heterochromatin thought to be composed primarily of arrays of tandem satellite sequence. We explore their sequence composition and organization and show a complex organization composed of specific sets of segmental duplications that have hyperexpanded in concert with the formation of subterminal satellites. These regions are highly copy number polymorphic between and within species, and copy number differences involving hundreds of copies can be accurately estimated by assaying read-depth of next-generation sequencing data sets. Phylogenetic and comparative genomic analyses suggest that the structures have arisen largely independently in the two lineages with the exception of a few seed sequences present in the common ancestor of humans and African apes. We propose a model where an ancestral humanchimpanzee pericentric inversion and the ancestral chromosome 2 fusion both predisposed and protected the chimpanzee and human genomes, respectively, to the formation of subtelomeric heterochromatin. Our findings highlight the complex interplay between duplicated sequences and chromosomal rearrangements that rapidly alter the cytogenetic landscape in a short period of evolutionary time.

show abstract

“…Indeed, copy-number variants (CNVs; sometimes also called 'copy-number polymorphisms' or CNPs) have been shown to be widespread in a variety of organisms, including humans (Sebat et al 2004;Conrad et al 2006;McCarroll et al 2006;Redon et al 2006), mice (Graubert et al 2007;She et al 2008), chimpanzees (Perry et al 2006, rhesus macaques (Lee et al 2008), cows (Liu et al 2010), dogs (Chen et al 2009;Nicholas et al 2009), chickens (Griffin et al 2008), maize (Springer et al 2009), Arabidopsis thaliana (Ossowski et al 2008), fruitflies (Dopman & Hartl 2007;Emerson et al 2008), Caenorhabditis elegans (Maydan et al 2010) and Saccharomyces cerevisiae (Carreto et al 2008). Though it is often harder to experimentally identify and genotype CNVs relative to SNPs and indels, many are big enough to encompass whole genes and are therefore more likely to affect organismal fitness.…”

Section: Introductionmentioning

confidence: 99%

Gene copy-number polymorphism in nature

2010

View full text Add to dashboard Cite

Differences between individuals in the copy-number of whole genes have been found in every multicellular species examined thus far. Such differences result in unique complements of protein-coding genes in all individuals, and have been shown to underlie adaptive phenotypic differences. Here, we review the evidence for copy-number variants (CNVs), focusing on the methods used to detect them and the molecular mechanisms responsible for generating this type of variation. Although there are multiple technical and computational challenges inherent to these experimental methods, next-generation sequencing technologies are making such experiments accessible in any system with a sequenced genome. We further discuss the connection between copy-number variation within species and copynumber divergence between species, showing that these values are exactly what one would expect from similar comparisons of nucleotide polymorphism and divergence. We conclude by reviewing the growing body of evidence for natural selection on copy-number variants. While it appears that most genic CNVsespecially deletions-are quickly eliminated by selection, there are now multiple studies demonstrating a strong link between copy-number differences at specific genes and phenotypic differences in adaptive traits. We argue that a complete understanding of the molecular basis for adaptive natural selection necessarily includes the study of copy-number variation.

show abstract

Comparative genomics of wild type yeast strains unveils important genome diversity

Cited by 117 publications

References 82 publications

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2

Gene copy-number polymorphism in nature

Contact Info

Product

Resources

About