scholarly journals Genetic diversity among cultivated beets (Beta vulgaris) assessed via population-based whole genome sequences

2019 ◽  
Author(s):  
Paul J. Galewski ◽  
J. Mitchell McGrath
Keyword(s):  
Genetic Variation ◽  
Sugar Beet ◽  
Beta Vulgaris ◽  
Demographic History ◽  
Crop Improvement ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Crop Type ◽  
Crop Types ◽  
Well Differentiated

Abstract Diversification on the basis of utilization is a hallmark of Beta vulgaris (beet). Crop improvement and management activities are segregated by crop type, preserving unique genome diversity and differentiation, with occasional introgressions between diverged lineages for specific traits. Full interfertility is typically retained in crosses between these groups and more traits may be accessible if the genetic basis of crop type lineage were known, along with available genetic markers to effect efficient transfer (e.g., via backcrossing). Beta vulgaris L. (2n =18) is a species complex composed of diverged lineages (e.g., crop types), including table, leaf (chard), fodder, and sugar beet. Using population genetic and statistical methods with whole genome sequence data from pooled samples of 23 beet cultivars and breeding lines, relationships were determined between populations based on identity-by-state and shared genetic variation among lineages. Distribution of genetic variation within and between crop types showed extensive shared (e.g. non-unique) genetic variation. Lineage specific variation (e.g. apomorphy) within crop types supported a shared demographic history within each crop type, while principal components analysis revealed strong crop type differentiation. Relative contributions of specific chromosomes to genome wide differentiation were ascertained, with each chromosome revealing a different pattern of differentiation with respect to crop type. Inferred population size history inferences for each crop type helped integrate selection history for each lineage, and highlighted potential genetic bottlenecks in the development of cultivated beet lineages. A complex evolutionary history of cultigroups in Beta vulgaris was demonstrated, involving lineage divergence as a result of selection and reproductive isolation. Clear delineation of crop types was obfuscated by historical gene flow and common ancestry (e.g. admixture and introgression, and sorting of ancestral polymorphism) which served to share genome variation between crop types and, likely, important phenotypic characters. Table beet was well differentiated as a crop type, and shared more genetic variation within than among crop types. The sugar beet group was not quite as well differentiated as the table beet group. Fodder and chard groups were intermediate between the table and chard groups, perhaps the result of less intensive selection for their end use.

scholarly journals Genetic diversity among cultivated beets (Beta vulgaris) assessed via population-based whole genome sequences

2020 ◽  
Author(s):  
Paul J. Galewski(New Corresponding Author) ◽  
J. Mitchell McGrath(Former Corresponding Author)
Keyword(s):  
Genetic Variation ◽  
Sugar Beet ◽  
Beta Vulgaris ◽  
Demographic History ◽  
Crop Improvement ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Crop Type ◽  
Crop Types ◽  
Well Differentiated

Abstract Background: Diversification on the basis of utilization is a hallmark of Beta vulgaris (beet), as well as other crop species. Often, crop improvement and management activities are segregated by crop type, thus preserving unique genome diversity and organization. Full interfertility is typically retained in crosses between these groups and more traits may be accessible if the genetic basis of crop type lineage were known, along with available genetic markers to effect efficient transfer (e.g., via backcrossing). Beta vulgaris L. (2n =18) is a species complex composed of diverged lineages (e.g., crop types), including the familiar table, leaf (chard), fodder, and sugar beet crop types. Using population genetic and statistical methods with whole genome sequence data from pooled samples of 23 beet cultivars and breeding lines, relationships were determined between accessions based on identity-by-state metrics and shared genetic variation among lineages. Results: Distribution of genetic variation within and between crop types showed extensive shared (e.g. non-unique) genetic variation. Lineage specific variation (e.g. apomorphy) within crop types supported a shared demographic history within each crop type, while principal components analysis revealed strong crop type differentiation. Relative contributions of specific chromosomes to genome wide differentiation were ascertained, with each chromosome revealing a different pattern of differentiation with respect to crop type. Inferred population size history for each crop type helped integrate selection history for each lineage, and highlighted potential genetic bottlenecks in the development of cultivated beet lineages. Conclusions: A complex evolutionary history of cultigroups in Beta vulgaris was demonstrated, involving lineage divergence as a result of selection and reproductive isolation. Clear delineation of crop types was obfuscated by historical gene flow and common ancestry (e.g. admixture and introgression, and sorting of ancestral polymorphism) which served to share genome variation between crop types and, likely, important phenotypic characters. Table beet was well differentiated as a crop type, and shared more genetic variation within than among crop types. The sugar beet group was not quite as well differentiated as the table beet group. Fodder and chard groups were intermediate between table and sugar groups, perhaps the result of less intensive selection for end use.

scholarly journals Genetic diversity among cultivated beets (Beta vulgaris) assessed via population-based whole genome sequences

2019 ◽  
Author(s):  
J. Mitchell McGrath ◽  
Paul J. Galewski
Keyword(s):  
Genetic Variation ◽  
Sugar Beet ◽  
Beta Vulgaris ◽  
Demographic History ◽  
Crop Improvement ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Crop Type ◽  
Crop Types ◽  
Well Differentiated

Abstract Diversification on the basis of utilization is a hallmark of Beta vulgaris (beet). Crop improvement and management activities are segregated by crop type, preserving unique genome diversity and differentiation, with occasional introgressions between diverged lineages for specific traits. Full interfertility is typically retained in crosses between these groups and more traits may be accessible if the genetic basis of crop type lineage were known, along with available genetic markers to effect efficient transfer (e.g., via backcrossing). Beta vulgaris L. (2n =18) is a species complex composed of diverged lineages (e.g., crop types), including table, leaf (chard), fodder, and sugar beet. Using population genetic and statistical methods with whole genome sequence data from pooled samples of 23 beet cultivars and breeding lines, relationships were determined between populations based on identity-by-state and shared genetic variation among lineages. Distribution of genetic variation within and between crop types showed extensive shared (e.g. non-unique) genetic variation. Lineage specific variation (e.g. apomorphy) within crop types supported a shared demographic history within each crop type, while principal components analysis revealed strong crop type differentiation. Relative contributions of specific chromosomes to genome wide differentiation were ascertained, with each chromosome revealing a different pattern of differentiation with respect to crop type. Inferred population size history inferences for each crop type helped integrate selection history for each lineage, and highlighted potential genetic bottlenecks in the development of cultivated beet lineages. A complex evolutionary history of cultigroups in Beta vulgaris was demonstrated, involving lineage divergence as a result of selection and reproductive isolation. Clear delineation of crop types was obfuscated by historical gene flow and common ancestry (e.g. admixture and introgression, and sorting of ancestral polymorphism) which served to share genome variation between crop types and, likely, important phenotypic characters. Table beet was well differentiated as a crop type, and shared more genetic variation within than among crop types. The sugar beet group was not quite as well differentiated as the table beet group. Fodder and chard groups were intermediate between the table and chard groups, perhaps the result of less intensive selection for their end use.

scholarly journals Aquila: diploid personal genome assembly and comprehensive variant detection based on linked reads

2019 ◽  
Author(s):  
Xin Zhou ◽  
Lu Zhang ◽  
Ziming Weng ◽  
David L. Dill ◽  
Arend Sidow
Keyword(s):  
Genetic Variation ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Sequence Data ◽  
Association Studies ◽  
Cost Effective ◽  
Whole Genome Sequence ◽  
Personal Genome ◽  
Whole Genome ◽  
Nucleotide Polymorphisms

AbstractVariant discovery in personal, whole genome sequence data is critical for uncovering the genetic contributions to health and disease. We introduce a new approach, Aquila, that uses linked-read data for generating a high quality diploid genome assembly, from which it then comprehensively detects and phases personal genetic variation. Assemblies cover >95% of the human reference genome, with over 98% in a diploid state. Thus, the assemblies support detection and accurate genotyping of the most prevalent types of human genetic variation, including single nucleotide polymorphisms (SNPs), small insertions and deletions (small indels), and structural variants (SVs), in all but the most difficult regions. All heterozygous variants are phased in blocks that can approach arm-level length. The final output of Aquila is a diploid and phased personal genome sequence, and a phased VCF file that also contains homozygous and a few unphased heterozygous variants. Aquila represents a cost-effective evolution of whole-genome reconstruction that can be applied to cohorts for variation discovery or association studies, or to single individuals with rare phenotypes that could be caused by SVs or compound heterozygosity.

scholarly journals Whole genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

2015 ◽  
Author(s):  
PingHsun Hsieh ◽  
Krishna R Veeramah ◽  
Joseph Lachance ◽  
Sarah A Tishkoff ◽  
Jeffrey D Wall ◽  
...  
Keyword(s):  
Gene Flow ◽  
Natural Selection ◽  
Muscle Development ◽  
Demographic History ◽  
Single Pulse ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Anatomically Modern Humans ◽  
History Of ◽  
African Pygmies

African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 years ago. We also find that bi-directional asymmetric gene-flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.

scholarly journals The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenic position of Lobotiformes and biological conservation

2019 ◽  
Author(s):  
Shuai Sun ◽  
Yue Wang ◽  
Xiao Du ◽  
Lei Li ◽  
Xiaoning Hong ◽  
...  
Keyword(s):  
Demographic History ◽  
Whole Genome Sequence ◽  
Biological Conservation ◽  
Whole Genome ◽  
Effective Population ◽  
Phylogenetic Tree Analysis ◽  
Pigment Synthesis ◽  
Long Time ◽  
History Of ◽  
Immune Related Genes

AbstractMekong tiger perch (Datnioides undecimradiatus) is one ornamental fish and a vulnerable species, which belongs to order Lobotiformes. Here, we report a ∼595 Mb D. undecimradiatus genome, which is the first whole genome sequence in the order Lobotiformes. Based on this genome, the phylogenetic tree analysis suggested that Lobotiformes and Sciaenidae are closer than Tetraodontiformes, resolving a long-time dispute. We depicted the pigment synthesis pathway in Mekong tiger perch and result confirmed that this pathway had evolved from the shared whole genome duplication. We also estimated the demographic history of Mekong tiger perch, showing the effective population size suffered a continuous reduction possibly related to the contraction of immune-related genes. Our study provided a reference genome resource for the Lobotiformes, as well as insights into the phylogeny of Eupercaria and biological conservation.

scholarly journals Whole-genome sequences shed light onto demographic history and contemporaneous genetic erosion of free-ranging jaguar (Panthera onca) populations

2021 ◽  
Author(s):  
Gustavo Lorenzana ◽  
Henrique Figueiró ◽  
Christopher Kaelin ◽  
Greg Barsh ◽  
Jeremy Johnson ◽  
...  
Keyword(s):  
Large Scale ◽  
Environmental Changes ◽  
Demographic History ◽  
Genetic Erosion ◽  
Border Region ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Population Bottlenecks ◽  
Panthera Onca ◽  
Anthropogenic Habitat

The vast amount of data contained in a single genome represents a detailed record of past events in that lineage and may forecast its evolutionary potential in the face of environmental changes. Here we employed whole-genome sequence (WGS) data to infer the demographic history and assess signals of recent inbreeding in jaguar (Panthera onca) populations. We analyzed whole genomes from 13 individuals (nine of which are reported here for the first time) sampled in seven different biomes across the species’ range, including its northernmost extreme in the Mexico/USA border region. We modelled demographic history using the PSMC method, and analyzed long runs of homozygosity (ROH) to assess signals of population bottlenecks and inbreeding. PSMC plots were very consistent among individuals, indicating that the jaguar lineage had an effective population size of up 100,000 individuals ca. 1 million years ago, then sharply declined and rebounded during the Late Pleistocene, followed by a more gradual decline in the last 40,000 years. This decline was more pronounced in the North/Central American genomes, likely reflecting population bottlenecks during the south-north colonization towards the edge of the species’ current range. The ROH analysis revealed a relatively small burden for most jaguars, indicating a recent history of outbreeding and large-scale connectivity among regional populations. However, northern range-edge individuals and those from severely fragmented populations showed signals of recent bottlenecks and, in the latter case, inbreeding. Our results illustrate the power of WGS data to survey and monitor the genetic erosion triggered by anthropogenic habitat fragmentation.

scholarly journals Whole-genome sequence analyses of Glaesserella parasuis isolates reveals extensive genomic variation and diverse antibiotic resistance determinants

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9293
Author(s):  
Xiulin Wan ◽  
Xinhui Li ◽  
Todd Osmundson ◽  
Chunling Li ◽  
He Yan
Keyword(s):  
Antibiotic Resistance ◽  
Genetic Variation ◽  
Genome Sequence ◽  
Resistance Genes ◽  
Genomic Variation ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Broad Host Range ◽  
Whole Genome ◽  
Resistance Determinants

Background Glaesserella parasuis (G. parasuis) is a respiratory pathogen of swine and the etiological agent of Glässer’s disease. The structural organization of genetic information, antibiotic resistance genes, potential pathogenicity, and evolutionary relationships among global G. parasuis strains remain unclear. The aim of this study was to better understand patterns of genetic variation, antibiotic resistance factors, and virulence mechanisms of this pathogen. Methods The whole-genome sequence of a ST328 isolate from diseased swine in China was determined using Pacbio RS II and Illumina MiSeq platforms and compared with 54 isolates from China sequenced in this study and 39 strains from China and eigtht other countries sequenced by previously. Patterns of genetic variation, antibiotic resistance, and virulence mechanisms were investigated in relation to the phylogeny of the isolates. Electrotransformation experiments were performed to confirm the ability of pYL1—a plasmid observed in ST328—to confer antibiotic resistance. Results The ST328 genome contained a novel Tn6678 transposon harbouring a unique resistance determinant. It also contained a small broad-host-range plasmid pYL1 carrying aac(6’)-Ie-aph(2”)-Ia and blaROB-1; when transferred to Staphylococcus aureus RN4220 by electroporation, this plasmid was highly stable under kanamycin selection. Most (85.13–91.74%) of the genetic variation between G. parasuis isolates was observed in the accessory genomes. Phylogenetic analysis revealed two major subgroups distinguished by country of origin, serotype, and multilocus sequence type (MLST). Novel virulence factors (gigP, malQ, and gmhA) and drug resistance genes (norA, bacA, ksgA, and bcr) in G. parasuis were identified. Resistance determinants (sul2, aph(3”)-Ib, norA, bacA, ksgA, and bcr) were widespread across isolates, regardless of serovar, isolation source, or geographical location. Conclusions Our comparative genomic analysis of worldwide G. parasuis isolates provides valuable insight into the emergence and transmission of G. parasuis in the swine industry. The result suggests the importance of transposon-related and/or plasmid-related gene variations in the evolution of G. parasuis.

Establishment and Application of Dual TaqMan Fluorescence Quantitative Polymerase Chain Reaction (PCR) for the Detection of Porcine Circovirus Types 2 and 3

2021 ◽  
Author(s):  
Fengyang Cao ◽  
Xiaoning Luan ◽  
Wenwen Wang ◽  
Yuyan Li ◽  
Longzong Guo ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Genetic Variation ◽  
Quantitative Polymerase Chain Reaction ◽  
Shandong Province ◽  
Whole Genome Sequence ◽  
Porcine Circovirus ◽  
Whole Genome ◽  
Chain Reaction ◽  
Positive Rate ◽  
Polymerase Chain

Abstract To establish a rapid method for the simultaneous differential detection of porcine circovirus types 2 (PCV2) and 3 (PCV3), two pairs of primers and two TaqMan probes were designed according to the gene sequences of PCV2 and PCV3, and a dual TaqMan fluorescence quantitative polymerase chain reaction (PCR) method for the simultaneous detection of two virus nucleic acids was established. The results showed that the correlation coefficients (R2) of the standard curves drawn using the recombinant plasmids of PCV2 and PCV3 were greater than 0.99 and had a good linear relationship. The specific detection results of PCV type 1, Porcine parvovirus, and Porcine pseudorabies virus were negative. The detection limits of this experimental method for PCV2 and PCV3 were 10 and 1 copies/μL, respectively, which were more sensitive than those of the common PCR detection methods. The established method was used to detect 76 samples from some pig farms in Shandong Province. 11 of the 76 samples were PCV3 positive (positive rate of 14.47%), 24 were PCV2 positive (positive rate of 34.58%), and PCV3 and PCV2 were mixed in six samples (positive rate of 7.89%). The whole-genome sequence of PCV3 was amplified and sequenced to further understand the molecular biological characteristics and genetic variation of PCV3 in Shandong Province. The genomes of 11 PCV3 strains were all 2000 bp long, and the whole-genome sequence homology between them ranged from 98.4% to 99.9%. There were mutation sites in the amino acid sequences of Cap and Rep proteins, and the strains isolated in this experiment were concentrated in the PCV3a and PCV3c subgroups. This study provides technical support and molecular biological basis for nucleic acid detection, epidemiological characteristics, genetic variation, and control of PCV3 in Shandong Province.

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