scholarly journals Genomic diversity and global distribution of Saccharomyces eubayanus, the wild ancestor of hybrid lager-brewing yeasts

2019 ◽  
Author(s):  
Quinn K. Langdon ◽  
David Peris ◽  
Juan I. Eizaguirre ◽  
Dana A. Opulente ◽  
Kelly V. Buh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
South America ◽  
Phenotypic Diversity ◽  
Isolation By Distance ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Phenotypic Data ◽  
In The Wild ◽  
Saccharomyces Eubayanus ◽  
Brewing Yeasts

AbstractS. eubayanus, the wild, cold-tolerant parent of hybrid lager-brewing yeasts, has a complex and understudied natural history. The exploration of this diversity can be used both to develop new brewing applications and to enlighten our understanding of the dynamics of yeast evolution in the wild. Here, we integrate whole genome sequence and phenotypic data of 200 S. eubayanus strains, the largest collection to date. S. eubayanus has a multilayered population structure, consisting of two major populations that are further structured into six subpopulations. Four of these subpopulations are found exclusively in the Patagonian region of South America; one is found predominantly in Patagonia and sparsely in Oceania and North America; and one is specific to the Holarctic ecozone. S. eubayanus is most abundant and genetically diverse in Patagonia, where some locations harbor more genetic diversity than is found outside of South America. All but one subpopulation shows isolation-by-distance, and gene flow between subpopulations is low. However, there are strong signals of ancient and recent outcrossing, including two admixed lineages, one that is sympatric with and one that is mostly isolated from its parental populations. Despite S. eubayanus’ extensive genetic diversity, it has relatively little phenotypic diversity, and all subpopulations performed similarly under most conditions tested. Using our extensive biogeographical data, we constructed a robust model that predicted all known and a handful of additional regions of the globe that are climatically suitable for S. eubayanus, including Europe. We conclude that this industrially relevant species has rich wild diversity with many factors contributing to its complex distribution and biology.

scholarly journals Signatures of selection and genomic diversity of Muskellunge (Esox masquinongy) from two populations in North America.

2021 ◽  
Author(s):  
Josue Chinchilla-Vargas ◽  
Max F. Rothschild ◽  
Francesca Bertolini
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Related Species ◽  
Reference Genome ◽  
Genetic Differences ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Closely Related Species ◽  
Esox Masquinongy ◽  
Signatures Of Selection

Abstract Background Muskellunge (Esox masquinongy) is the largest and most prized game fish for anglers in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used whole genome sequence from 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from Saint-Lawrence river in Canada to study the genetic differences between populations, analyze signatures of selection that might shed light on environmental adaptations, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available for Muskellunge, reads were aligned to the genome of Pike (Esox lucius), a closely-related species. Results Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high quality SNPs that overlap with the Canadian samples. The Ti/Tv values were 1.09 and 1.29 for samples from Iowa and Canada, respectively. PCA and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Moreover, PCA showed a clustering by sex in the Iowan population although widow-based Fst did not find outlier regions. Window based pooled heterozygosity found 6 highly heterozygous windows containing 244 genes in the Iowa population and Fst comparing the Iowa and Canadian populations found 14 windows with Fst values larger than 0.9 containing 641 genes. One enriched GO term (sensory perception of pain) was found through pooled heterozygosity analyzes. Although not significant, several enriched GO terms associated to growth and development were found through Fst analyses. Inbreeding calculated as Froh was 0.03 on average for the Iowa population and 0.32 on average for the Canadian samples. The inbreeding rate appears is presumably due to isolation of subpopulations. Conclusions This study is the first of its kind in Muskellunge from Iowa in which captured brood stock showed marked genetic differences with the Canadian population. Additionally, despite genetic differentiation based on sex has been observed, no major locus has been detected . Inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, isolation of subpopulations has caused levels of homozygosity to increase in the Canadian Muskellunge population. These results prove the validity of using genomes of closely related species to perform genomic analyses when no reference genome assembly is available.

scholarly journals Signatures of selection and genomic diversity of Muskellunge (Esox masquinongy) from two populations in North America.

2021 ◽  
Author(s):  
Josue Chinchilla-Vargas ◽  
Jonathan Meerbeek ◽  
Max F. Rothschild ◽  
Francesca Bertolini
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Related Species ◽  
Reference Genome ◽  
Genetic Differences ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Closely Related Species ◽  
Esox Masquinongy ◽  
Signatures Of Selection

Abstract Background Muskellunge (Esox masquinongy) is the largest and most prized game fish for anglers in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used whole genome sequence from 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from Saint-Lawrence river in Canada to study the genetic differences between populations, analyze signatures of selection that might shed light on environmental adaptations, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available for Muskellunge, reads were aligned to the genome of Pike (Esox lucius), a closely-related species.ResultsVariant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high quality SNPs that overlap with the Canadian samples. The Ti/Tv values were 1.09 and 1.29 for samples from Iowa and Canada, respectively. PCA and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Moreover, PCA showed a clustering by sex in the Iowan population although widow-based Fst did not find outlier regions. Window based pooled heterozygosity found 6 highly heterozygous windows containing 244 genes in the Iowa population and Fst comparing the Iowa and Canadian populations found 14 windows with Fst values larger than 0.9 containing 641 genes. One enriched GO term (sensory perception of pain) was found through pooled heterozygosity analyzes. Although not significant, several enriched GO terms associated to growth and development were found through Fst analyses.Inbreeding calculated as Froh was 0.03 on average for the Iowa population and 0.32 on average for the Canadian samples. The Canadian inbreeding rate appears is presumably due to isolation of subpopulations.ConclusionsThis study is the first of its kind in Muskellunge from Iowa in which captured brood stock showed marked genetic differences with the Canadian population. Additionally, despite genetic differentiation based on sex has been observed, no major locus has been detected. Inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, but apparent isolation of subpopulations has caused levels of homozygosity to increase in the Canadian Muskellunge population.These results prove the validity of using genomes of closely related species to perform genomic analyses when no reference genome assembly is available.

scholarly journals Genetic Diversity and Potential Paths of Transmission of Mycobacterium bovis in the Amazon: The Discovery of M. bovis Lineage Lb1 Circulating in South America

2021 ◽  
Vol 8 ◽  
Author(s):  
Paulo Alex Carneiro ◽  
Cristina Kraemer Zimpel ◽  
Taynara Nunes Pasquatti ◽  
Taiana T. Silva-Pereira ◽  
Haruo Takatani ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
South America ◽  
River Basin ◽  
Mycobacterium Bovis ◽  
Genomic Diversity ◽  
Amazon River ◽  
Amazon River Basin ◽  
River Region ◽  
Significant Difference ◽  
Marajó Island

Bovine tuberculosis (bTB) has yet to be eradicated in Brazil. Herds of cattle and buffalo are important sources of revenue to people living in the banks of the Amazon River basin. A better understanding of Mycobacterium bovis (M. bovis) populational structure and transmission dynamics affecting these animals can significantly contribute in efforts to improve their sanitary status. Herein, we sequenced the whole genome of 22 M. bovis isolates (15 from buffalo and 7 from cattle) from 10 municipalities in the region of the Lower Amazon River Basin in Brazil and performed phylogenomic analysis and Single Nucleotide Polymorphism (SNP)-based transmission inference to evaluate population structure and transmission networks. Additionally, we compared these genomes to others obtained in unrelated studies in the Marajó Island (n = 15) and worldwide (n = 128) to understand strain diversity in the Amazon and to infer M. bovis lineages. Our results show a higher genomic diversity of M. bovis genomes obtained in the Lower Amazon River region when compared to the Marajó Island, while no significant difference was observed between M. bovis genomes obtained from cattle and buffalo (p ≥ 0.05). This high genetic diversity is reflected by the weak phylogenetic clustering of M. bovis from the Lower Amazon River region based on geographic proximity and in the detection of only two putative transmission clusters in the region. One of these clusters is the first description of inter-species transmission between cattle and buffalo in the Amazon, bringing implications to the bTB control program. Surprisingly, two M. bovis lineages were detected in our dataset, namely Lb1 and Lb3, constituting the first description of Lb1 in South America. Most of the strains of this study (13/22) and all 15 strains of the Marajó Island carried no clonal complex marker, suggesting that the recent lineage classification better describe the diversity of M. bovis in the Amazon.

scholarly journals R-locus for roaned coat is associated with a tandem duplication in an intronic region of USH2A in dogs and also contributes to Dalmatian spotting

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248233
Author(s):  
Takeshi Kawakami ◽  
Meghan K. Jensen ◽  
Andrea Slavney ◽  
Petra E. Deane ◽  
Ausra Milano ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Tandem Duplication ◽  
Coat Color ◽  
Phenotypic Diversity ◽  
Genetic Difference ◽  
Large Fraction ◽  
Whole Genome Sequence ◽  
Probe Intensity ◽  
Intronic Region ◽  
Coat Pattern

Structural variations (SVs) represent a large fraction of all genetic diversity, but how this genetic diversity is translated into phenotypic and organismal diversity is unclear. Explosive diversification of dog coat color and patterns after domestication can provide a unique opportunity to explore this question; however, the major obstacle is to efficiently collect a sufficient number of individuals with known phenotypes and genotypes of hundreds of thousands of markers. Using customer-provided information about coat color and patterns of dogs tested on a commercial canine genotyping platform, we identified a genomic region on chromosome 38 that is strongly associated with a mottled coat pattern (roaning) by genome-wide association study. We identified a putative causal variant in this region, an 11-kb tandem duplication (11,131,835–11,143,237) characterized by sequence read coverage and discordant reads of whole-genome sequence data, microarray probe intensity data, and a duplication-specific PCR assay. The tandem duplication is in an intronic region of usherin gene (USH2A), which was perfectly associated with roaning but absent in non-roaned dogs. We detected strong selection signals in this region characterized by reduced nucleotide diversity (π), increased runs of homozygosity, and extended haplotype homozygosity in Wirehaired Pointing Griffons and Australian Cattle Dogs (typically roaned breeds), as well as elevated genetic difference (FST) between Wirehaired Pointing Griffon (roaned) and Labrador Retriever (non-roaned). Surprisingly, all Dalmatians (N = 262) carried the duplication embedded in identical or similar haplotypes with roaned dogs, indicating this region as a shared target of selection during the breed’s formation. We propose that the Dalmatian’s unique spots were a derived coat pattern by establishing a novel epistatic interaction between roaning “R-locus” on chromosome 38 and an uncharacterized modifier locus. These results highlight the utility of consumer-oriented genotype and phenotype data in the discovery of genomic regions contributing to phenotypic diversity in dogs.

scholarly journals Development of EST-SSR Markers to Assess Genetic Diversity in Elettaria Cardamomum Maton

2015 ◽  
Vol 3 (2) ◽  
pp. 188-192 ◽  
Author(s):  
N Anjali ◽  
Sowmya S Dharan ◽  
F Nadiya ◽  
K K Sabu
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Curcuma Longa ◽  
Whole Genome Sequence ◽  
Limited Information ◽  
Elettaria Cardamomum ◽  
In The Wild ◽  
Pesticide Usage ◽  
Simple Sequence

Elettaria cardamomum Maton is one of the most ancient and valuable spice crops. Cardamom is cultivated following intensive pesticide usage where alleles present in the wild cardamom genotypes could positively contribute towards genetic improvement of the cultivars. However, the genetic map or whole-genome sequence of E. cardamomum is not available and very limited information on simple sequence repeat (SSR) markers are publicly available. We have tested whether SSRs from Curcuma longa can be used to analyze genetic diversity E. cardamomum.Int J Appl Sci Biotechnol, Vol 3(2): 188-192 DOI: http://dx.doi.org/10.3126/ijasbt.v3i2.12380   

scholarly journals Paenibacillus odorifer, the Predominant Paenibacillus Species Isolated from Milk in the United States, Demonstrates Genetic and Phenotypic Conservation of Psychrotolerance but Clade-Associated Differences in Nitrogen Metabolic Pathways

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Sarah M. Beno ◽  
Rachel A. Cheng ◽  
Renato H. Orsi ◽  
Diana R. Duncan ◽  
Xiaodong Guo ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Nitrogen Fixation ◽  
Cold Shock ◽  
Phenotypic Diversity ◽  
The United States ◽  
Nitrite Reduction ◽  
Phenotypic Data ◽  
Content Type ◽  
Fluid Milk

ABSTRACT Paenibacillus is a spore-forming bacterial genus that is frequently isolated from fluid milk and is proposed to play a role in spoilage. To characterize the genetic and phenotypic diversity of Paenibacillus spp., we first used rpoB allelic typing data for a preexisting collection of 1,228 Paenibacillus species isolates collected from raw and processed milk, milk products, and dairy environmental sources. Whole-genome sequencing (WGS) and average nucleotide identity by BLAST (ANIb) analyses performed for a subset of 58 isolates representing unique and overrepresented rpoB allelic types in the collection revealed that these isolates represent 21 different Paenibacillus spp., with P. odorifer being the predominant species. Further genomic characterization of P. odorifer isolates identified two distinct phylogenetic clades, clades A and B, which showed significant overrepresentation of 172 and 164 ortholog clusters and 94 and 52 gene ontology (GO) terms, respectively. While nitrogen fixation genes were found in both clades, multiple genes associated with nitrate and nitrite reduction were overrepresented in clade A isolates; additional phenotypic testing demonstrated that nitrate reduction is specific to isolates in clade A. Hidden Markov models detected 9 to 10 different classes of cold shock-associated genetic elements in all P. odorifer isolates. Phenotypic testing revealed that all isolates tested here can grow in skim milk broth at 6°C, suggesting that psychrotolerance is conserved in P. odorifer. Overall, our data suggest that Paenibacillus spp. isolated from milk in the United States represent broad genetic diversity, which may provide challenges for targeted-control strategies aimed at reducing fluid milk spoilage. IMPORTANCE Although Paenibacillus species isolates are frequently isolated from pasteurized fluid milk, the link between the genetic diversity and phenotypic characteristics of these isolates was not well understood, especially as some Bacillales isolated from milk are unable to grow at refrigeration temperatures. Our data demonstrate that Paenibacillus spp. isolated from fluid milk represent tremendous interspecies diversity, with P. odorifer being the predominant Paenibacillus sp. isolated. Furthermore, genetic and phenotypic data support that P. odorifer is well suited to transition from a soil-dwelling environment, where nitrogen fixation (and other nitrate/nitrite reduction pathways present only in clade A) may facilitate growth, to fluid milk, where its multiple cold shock-associated adaptations enable it to grow at refrigeration temperatures throughout the storage of milk. Therefore, efforts to reduce bacterial contamination of milk will require a systematic approach to reduce P. odorifer contamination of raw milk.

scholarly journals Development of a Maize Molecular Evolutionary Genomic Database

2003 ◽  
Vol 4 (2) ◽  
pp. 246-249 ◽  
Author(s):  
Chunguang Du ◽  
Edward Buckler ◽  
Spencer Muse
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Phenotypic Diversity ◽  
Genome Structure ◽  
Genome Project ◽  
Genomic Diversity ◽  
Plant Genome ◽  
Phenotypic Data ◽  
North Carolina State University ◽  
Dna Sequence Data

PANZEA is the first public database for studying maize genomic diversity. It was initiated as a repository of genomic diversity for an NSF Plant Genome project on ‘Maize Evolutionary Genomics’. PANZEA is hosted at the Bioinformatics Research Center, North Carolina State University, and is open to the public (http://statgen.ncsu.edu/panzea). PANZEA is designed to capture the interrelationships between germplasm, molecular diversity, phenotypic diversity and genome structure. It has the ability to store, integrate and visualize DNA sequence, enzymatic, SSR (simple sequence repeat) marker, germplasm and phenotypic data. The relational data model is selected and implemented in Oracle. An automated DNA sequence data submission tool has been created that allows project researchers to remotely submit their DNA sequence data directly to PANZEA. On-line database search forms and reports have been created to allow users to search or download germplasm, DNA sequence, gene/locus data and much more, directly from the web.

scholarly journals Assessment of molecular and phenotypic diversity among winter wheat cultivars

Genetika ◽  
2017 ◽  
Vol 49 (2) ◽  
pp. 583-598 ◽  
Author(s):  
Sonja Petrovic ◽  
Sonja Maric ◽  
Tihomir Cupic ◽  
A. Rebekic ◽  
Ivana Rukavina
Keyword(s):  
Genetic Diversity ◽  
Winter Wheat ◽  
Agronomic Traits ◽  
Phenotypic Diversity ◽  
Molecular Data ◽  
Wheat Cultivars ◽  
Phenotypic Data ◽  
Winter Wheat Cultivars ◽  
Morphologic Data ◽  
Diversity Estimates

Comparing results of different genetic diversity estimates can be useful in parental selection for plant breeders. Forty winter wheat cultivars, from three Croatian breeding centres and four foreign countries, were used to utilize and compare agronomic, morphologic and molecular based genetic diversity estimates. Ten morphologic descriptors according to UPOV guidelines and eight agronomic traits were used to establish phenotypic data. Molecular data consisted of 26 SSR and four combinations of AFLP markers, covering all three wheat genomes. Agro-morphologic data showed variability especially regarding plant height (CV=18.44%), yield (CV=22.02%), and ear emergence (range=8). Discriminant analysis confirmed grouping among cultivars was mostly influenced by number of days to heading and yield. The four AFLP primer combinations and 26 SSR markers yielded 108 polymorphic bands. The UPGMA based on phenotypic data, arranged cultivars in four clusters, with one distinctive outlier, cultivar U1. The UPGMA based on molecular data also arranged cultivars in four clusters, with one distinctive outlier, cultivar Antonius. The similarities based on all four genetic diversity estimates reflected, on average, the degree of relatedness of cultivars used. No correlations between phenotypic and molecular data were found implying that both types of data should be used for genetic diversity estimates in order to cover wider variability between tested cultivars.

scholarly journals Patterns of population genomic diversity in the invasive Japanese knotweed species complex

2020 ◽  
Author(s):  
Acer VanWallendael ◽  
Mariano Alvarez ◽  
Steven J. Franks
Keyword(s):  
Genetic Diversity ◽  
Invasive Species ◽  
Genetic Structure ◽  
Species Complex ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Genomic Diversity ◽  
Japanese Knotweed ◽  
Reynoutria Japonica ◽  
Giant Knotweed

AbstractPremiseInvasive species are expected to experience a reduction in genetic diversity due to founder effects, which should limit their ability to adapt to new habitats. Still, many invasive species achieve widespread distributions and dense populations. This paradox of invasions could potentially be overcome through multiple introductions or hybridization, both of which increase genetic diversity. We conducted a population genomics study of Japanese knotweed (Reynoutria japonica), which is a polyploid, clonally reproducing invasive species that has been notoriously successful worldwide despite supposedly low genetic diversity.MethodsWe used Genotyping-by-Sequencing to collect 12,912 SNP markers from 88 samples collected at 38 locations across North America for the species complex. We used non-alignment based k-mer hashing analysis in addition to traditional population genetic analyses to account for the challenges of genotyping polyploids.ResultsGenotypes conformed to three genetic clusters, likely representing Japanese knotweed, Giant knotweed, and hybrid Bohemian knotweed. We found that, contrary to previous findings, the Japanese knotweed cluster had substantial genetic diversity, though it had no apparent genetic structure across the landscape. In contrast, Giant knotweed and hybrids showed distinct population groups. We did not find evidence of Isolation-by-Distance in the species complex, likely reflecting the stochastic introduction history of this species complex. Among species, we found no correlations between SNPs and several temperature- and precipitation-based climatic variables.ConclusionsThe results indicate that clonal invasive species can show substantial genetic diversity and can be successful at colonizing a variety of habitats without showing evidence of local adaptation or genetic structure.

scholarly journals The influence of a colonial frugivore on genetic diversity of two tropical trees

2021 ◽  
Author(s):  
Victoria DeLeo ◽  
Yolanda León ◽  
Jackeline Salazar ◽  
Frank Rivera-Milán ◽  
Tomas Carlo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Seed Dispersal ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Fruit Trees ◽  
Common Species ◽  
Population Diversity ◽  
Genomic Diversity ◽  
Ecological Niches ◽  
Population Genomic

Animal seed dispersers may influence plant genetic diversity, though there are few examples linking disperser behavior to population genomic diversity. We hypothesized that breeding colonies of the frugivorous White-Crowned Pigeon (Patagioenas leucocephala) would increase population diversity and decrease population differentiation in fruit trees at nesting sites due to increased seed dispersal from foraging trips. We measured the density and extent of colonies at Parque Nacional Jaragua (Dominican Republic) and used nuclear and plastid SNPs from ddRADseq to examine the spatial genetic structure of two common species: poisonwood (Metopium toxiferum), a key fruit resource during the breeding season, and gumbo limbo (Bursera simaruba). We found that pigeon nesting aggregations in and around Parque Nacional Jaragua occupy areas between 3 and 5 Km2, with an estimated number of active nests for 2016 extrapolated to 3 km2 of 159,144  21,484 s.e., making this one of the largest breeding aggregations for the species across its range. However, colony locations did not determine tree genetic diversity and differentiation. Gumbo limbo (consumed by a diverse community) showed less isolation by distance than poisonwood. Saplings and plastid markers, expected to be more strongly influenced by seed dispersal, did not display geographic structure associated with colony sites, suggesting that patterns were not primarily due to pigeon foraging. Our results highlight the diversity of population genomic patterns among co-occurring species with similar ecological niches and demonstrate the limitations for frugivores to influence genetic differences among plant species.

Sign in / Sign up

Export Citation Format

Share Document