scholarly journals Genomic analysis reveals selection signatures of Yucatan miniature pig on its X chromosome during domestication

2019 ◽  
Author(s):  
Wei Zhang ◽  
Yuanlang Wang ◽  
Min Yang ◽  
Xudong Wu ◽  
Xiaodong Zhang ◽  
...  
Keyword(s):  
X Chromosome ◽  
Genetic Relationships ◽  
Genomic Analysis ◽  
Fixation Index ◽  
Sweat Glands ◽  
Whole Genome Sequencing Data ◽  
Miniature Pig ◽  
Sequencing Data ◽  
Selection Signatures ◽  
Long Time

AbstractYucatan miniature pig (YMP), a naturally small breed, has been domesticated in the hot and arid Yucatan Peninsula for a long time. However, its selection signatures on the X chromosome remain poorly understood. In this study, we focused on elucidating the selection signatures of YMP on the X chromosome during its domestication and breeding, using the whole-genome sequencing data. We performed population admixture analyses to determine its genetic relationships with other domesticated breeds and wild boars. Subsequently, we used two approaches, the fixation index (Fst) and π ratios, to identify the selection signatures with 100 kb windows sliding in 10 kb steps. As a result, we found that the ectodysplasin A (EDA) gene was related with hypoplasia or absence of hair and sweat glands. This could uncover the relative lack of odor in YMP and the presence of hypoplasia or absence of hair in pigs. Furthermore, we found several genes under selection in other animals. A bioinformatics analysis of the genes in selection regions showed that they were associated with growth, lipid metabolism, reproduction, and immune system. Our findings will lead to a better understanding of the unique genetic and phenotypic characteristics of YMP and offer a plausible method for their utilization as an animal model for hair and odor disease research.

scholarly journals Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding

2020 ◽  
Vol 33 (5) ◽  
pp. 712-721
Author(s):  
Wei Zhang ◽  
Min Yang ◽  
Yuanlang Wang ◽  
Xudong Wu ◽  
Xiaodong Zhang ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Genomic Analysis ◽  
Fixation Index ◽  
High Fertility ◽  
Selection Signatures ◽  
Single Nucleotide Variants ◽  
Genetic Characteristics ◽  
Genome Variation ◽  
Wild Boars ◽  
Pig Breeds

Objective: The Wannan Black pig is a typical Chinese indigenous, disease-resistant pig breed with high fertility, and a crude-feed tolerance that has been bred by artificial selection in the south of Anhui province for a long time. However, genome variation, genetic relationships with other pig breeds, and domestication, remain poorly understood. Here, we focus on elucidating the genetic characteristics of the Wannan Black pig and identifying selection signatures during domestication and breeding.Methods: We identified the whole-genome variation in the Wannan Black pig and performed population admixture analyses to determine genetic relationships with other domesticated pig breeds and wild boars. Then, we identified the selection signatures between the Wannan Black pig and Asian wild boars in 100-kb windows sliding in 10 kb steps by using two approaches: the fixation index (FST) and π ratios.Results: Resequencing the Wannan Black pig genome yielded 501.52 G of raw data. After calling single-nucleotide variants (SNVs) and insertions/deletions (InDels), we identified 21,316,754 SNVs and 5,067,206 InDels (2,898,582 inserts and 2,168,624 deletions). Additionally, we found genes associated with growth, immunity, and digestive functions.Conclusion: Our findings help in explaining the unique genetic and phenotypic characteristics of Wannan Black pigs, which in turn can be informative for future breeding programs of Wannan Black pigs.

scholarly journals The LCORL Locus Is under Selection in Large-Sized Pakistani Goat Breeds

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 168
Author(s):  
Rashid Saif ◽  
Jan Henkel ◽  
Vidhya Jagannathan ◽  
Cord Drögemüller ◽  
Christine Flury ◽  
...  
Keyword(s):  
Mammalian Species ◽  
Causal Variant ◽  
Whole Genome Sequencing Data ◽  
Potential Candidate ◽  
Sequencing Data ◽  
Selection Signatures ◽  
Selection Signature ◽  
Replication Studies ◽  
Independent Replication ◽  
Selection For

Goat domestication and human selection for valued traits have formed diverse breeds with characteristic phenotypes. This process led to the fixation of causative genetic variants controlling breed-specific traits within regions of reduced genetic diversity—so-called “selection signatures”. We previously reported an analysis of selection signatures based on pooled whole-genome sequencing data of 20 goat breeds and bezoar goats. In the present study, we reanalyzed the data and focused on a subset of eight Pakistani goat breeds (Angora, Barbari, Beetal, Dera Din Panah, Kamori, Nachi, Pahari, Teddy). We identified 749 selection signatures based on reduced heterozygosity in these breeds. A search for signatures that are shared across large-sized goat breeds revealed that five medium-to-large-sized Pakistani goat breeds had a common selection signature on chromosome 6 in a region harboring the LCORL gene, which has been shown to modulate height or body size in several mammalian species. Fine-mapping of the region confirmed that all five goat breeds with the selection signature were nearly fixed for the same haplotype in a ~191 kb region spanning positions 37,747,447–37,938,449. From the pool sequencing data, we identified a frame-shifting single base insertion into an isoform-specific exon of LCORL as a potential candidate causal variant mediating the size-increasing effect. If this preliminary result can be confirmed in independent replication studies, genotyping of this variant might be used to improve breeding programs and the selection for stature in goats.

scholarly journals Predicting Insect Invasiveness With Whole-genome Sequencing Data

2020 ◽  
Author(s):  
Cong Huang ◽  
Nianwan Yang ◽  
Shuping Wang ◽  
Xiaodan Fan ◽  
Cong Pian ◽  
...  
Keyword(s):  
Insect Pest ◽  
Genomic Analysis ◽  
Gene Families ◽  
Insect Species ◽  
Whole Genome Sequencing Data ◽  
Comparative Genomic ◽  
Nucleic Acid Metabolism ◽  
Sequencing Data ◽  
Invasive Insects ◽  
Invasive Insect

Abstract Background Invasive alien insects threaten agriculture, biodiversity, and human livelihoods globally. Unfortunately, insect invasiveness still cannot be reliably predicted. Empirical policies of insect pest quarantine and inspection are mainly designed against species that are already problematic. Results We conducted a comparative genomic analysis of 37 invasive insect species and six non-invasive insect species, showing that the gene families associated with defense, protein and nucleic acid metabolism, chemosensory function, and transcriptional regulation were significantly expanded in invasive insects, suggesting that enhanced abilities in self-protection, nutrition exploitation, and locating food or mates are intrinsic features conferring invasiveness in insects. By using these intrinsic genome features, we proposed an invasiveness index and estimated the invasiveness of 99 other insect species with genome data, classifying them as highly, moderately, or minimally invasive. Insects possessing all these aforementioned enhanced abilities are predicted to be highly invasive, and vice versa. Next, a logistic-regression classifier was trained to predict insect invasiveness, achieving 93.2% accuracy. Conclusions We present evidence that several traits may confer invasiveness in insects and these features can be used to predict insect invasiveness accurately, and we quantify insect invasiveness with an invasiveness index.

scholarly journals Clin.iobio: A Collaborative Diagnostic Workflow to Enable Team-Based Precision Genomics

2022 ◽  
Vol 12 (1) ◽  
pp. 73
Author(s):  
Alistair Ward ◽  
Matt Velinder ◽  
Tonya Di Sera ◽  
Aditya Ekawade ◽  
Sabrina Malone Jenkins ◽  
...  
Keyword(s):  
Clinical Practice ◽  
Genomic Analysis ◽  
Knowledge Bases ◽  
Diagnostic Process ◽  
Whole Genome Sequencing Data ◽  
Specific Gene ◽  
Sequencing Data ◽  
Team Members ◽  
Variant Information ◽  
Allele Segregation

The primary goal of precision genomics is the identification of causative genetic variants in targeted or whole-genome sequencing data. The ultimate clinical hope is that these findings lead to an efficacious change in treatment for the patient. In current clinical practice, these findings are typically returned by expert analysts as static, text-based reports. Ideally, these reports summarize the quality of the data obtained, integrate known gene–phenotype associations, follow allele segregation and affected status within the sequenced samples, and weigh computational evidence of pathogenicity. These findings are used to prioritize the variant(s) most likely to cause the given patient’s phenotypes. In most diagnostic settings, a team of experts contribute to these reports, including bioinformaticians, clinicians, and genetic counselors, among others. However, these experts often do not have the necessary tools to review genomic findings, test genetic hypotheses, or query specific gene and variant information. Additionally, team members often rely on different tools and methods based on their given expertise, resulting in further difficulties in communicating and discussing genomic findings. Here, we present clin.iobio—a web-based solution to collaborative genomic analysis that enables diagnostic team members to focus on their area of expertise within the diagnostic process, while allowing them to easily review and contribute to all steps of the diagnostic process. Clin.iobio integrates tools from the popular iobio genomic visualization suite into a comprehensive diagnostic workflow, encompassing (1) genomic data quality review, (2) dynamic phenotype-driven gene prioritization, (3) variant prioritization using a comprehensive set of knowledge bases and annotations, (4) and an exportable findings summary. In conclusion, clin.iobio is a comprehensive solution to team-based precision genomics, the findings of which stand to inform genomic considerations in clinical practice.

scholarly journals Predicting Insect Invasiveness with Whole-Genome Sequencing Data

2020 ◽  
Author(s):  
Cong Huang ◽  
Nianwan Yang ◽  
Shuping Wang ◽  
Xiaodan Fan ◽  
Cong Pian ◽  
...  
Keyword(s):  
Insect Pest ◽  
Genomic Analysis ◽  
Gene Families ◽  
Insect Species ◽  
Whole Genome Sequencing Data ◽  
Comparative Genomic ◽  
Nucleic Acid Metabolism ◽  
Sequencing Data ◽  
Invasive Insects ◽  
Invasive Insect

Abstract Background: Invasive alien insects threaten agriculture, biodiversity, and human livelihoods globally. Unfortunately, insect invasiveness still cannot be reliably predicted. Empirical policies of insect pest quarantine and inspection are mainly designed against species that are already problematic.Results: We conducted a comparative genomic analysis of 37 invasive insect species and six non-invasive insect species, showing that the gene families associated with defense, protein and nucleic acid metabolism, chemosensory function, and transcriptional regulation were significantly expanded in invasive insects, suggesting that enhanced abilities in self-protection, nutrition exploitation, and locating food or mates are intrinsic features conferring invasiveness in insects. By using these intrinsic genome features, we proposed an invasiveness index and estimated the invasiveness of 99 other insect species with genome data, classifying them as highly, moderately, or minimally invasive. Insects possessing all these aforementioned enhanced abilities are predicted to be highly invasive, and vice versa. Next, a logistic-regression classifier was trained to predict insect invasiveness, achieving 93.2% accuracy. Conclusions: We present evidence that several traits may confer invasiveness in insects and these features can be used to predict insect invasiveness accurately, and we quantify insect invasiveness with an invasiveness index.

scholarly journals 1046. Clinical and Microbiological Characteristics of Patients With Septicemia Caused by IMP-1-Producing Enterobacteriaceae in a Tertiary Hospital in Japan

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S312-S313
Author(s):  
Nobuaki Mori ◽  
Narito Kagawa ◽  
Kotaro Aoki ◽  
Yoshikazu Ishii ◽  
Kazuhiro Tateda ◽  
...  
Keyword(s):  
Severe Disease ◽  
Previous History ◽  
Genomic Analysis ◽  
Underlying Disease ◽  
Tertiary Hospital ◽  
Mercaptoacetic Acid ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Microbiological Characteristics

Abstract Background Carbapenemase-producing Enterobacteriaceae (CPE) infection has become a great threat to public health worldwide. Although KPC and OXA-48 infections have mostly described, IMP-1 producing Enterobacteriaceae (IMP1-E) are not well studied. We investigated the clinical and microbiological characteristics of septicemia due to the IMP1-E. Methods This observational study of inpatients who developed IMP-1E septicemia was conducted in a Japanese tertiary hospital from April 2013 to March 2017. IMP1-E was defined as a decreased susceptibility to meropenem (minimum inhibitory concentration, ≥2 mg/L), as well as a positive sodium mercaptoacetic acid test, and polymerase chain reaction for blaIMP genes. Clinical data were collected from medical charts. Antimicrobial susceptibilitly was determined by the MicroScan Walkway. We performed total genomic analysis, plasmid analysis, and multilocus sequence typing (MLST) using whole genome sequencing data. Results In total, six patients were identified (median age: 55 years). All had severe underlying disease on admission, and five were admitted to the intensive care unit. The sources of IMP1-E septicemia were as follows: two catheter-related BSI, one pyelonephritis, one cholangitis, one bacterial peritonitis, and one unknown focus. Four isolates were Enterobacter cloacae and two were Klebsiella pneumoniae. All patients had a previous history of antibiotic treatment and long-term hospitalization. All patients were treated with either levofloxacin (LVFX) only or LVFX and aminoglycoside (AG). Follow-up blood culture was negative for all patients. All-cause 30-day mortality rate was 50%. Although no isolates were resistant to LVFX and AG, they harbored aac(6’)-Ⅱc, sul1, and tet(B) genes.Two isolates harbored the qnrB6 gene. There was a high probability that blaIMP-1 was carried by IncHI2 plasmids. MLST sequence type of E. cloacae isolates comprised three ST78, and one ST997; K. pneumonia isolates comprised ST134, and ST252. Conclusion This study showed that IMP1-E septicemia was isolated in patients with severe disease and long-term hospitalization. Selection of antibiotics therapy based on antimicrobial susceptibility induced microbiological cure, but clinical response was dependent on the underlying diseases. Disclosures All authors: No reported disclosures.

Detecting selection signatures on X chromosome in pig through high density SNPs

2012 ◽  
Vol 34 (10) ◽  
pp. 1251-1260 ◽  
Author(s):  
Yun-Long MA ◽  
Qin ZHANG ◽  
Xiang-Dong DING
Keyword(s):  
X Chromosome ◽  
High Density ◽  
Selection Signatures

scholarly journals Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes

2021 ◽  
Author(s):  
Eric S Tvedte ◽  
Mark Gasser ◽  
Benjamin C Sparklin ◽  
Jane Michalski ◽  
Carl E Hjelmen ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Hybrid Approach ◽  
Cost Effective ◽  
Fruit Fly ◽  
Drosophila Ananassae ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
E Coli ◽  
Hybrid Approaches ◽  
Long Read

Abstract The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.

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