scholarly journals Genome-wide Analysis of CNVs in Three Populations of Tibetan Sheep using Whole-genome Resequencing

2021 ◽  
Author(s):  
Linyong Hu ◽  
Qi Li ◽  
Liangzhi Zhang ◽  
Hongjin Liu ◽  
Tianwei Xu ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Average Length ◽  
Wide Distribution ◽  
Phenotypic Traits ◽  
Genomic Structural Variation ◽  
Kegg Pathways ◽  
Genome Wide ◽  
Tibetan Sheep ◽  
Number Variation ◽  
Duplication Events

Abstract Background: Copy number variation (CNV), an important source of genomic structural variation, can disturb genetic structure, dosage, regulation and expression, and is associated with phenotypic diversity and adaptation to local environments in mammals. In the present study, 24 resequencing datasets were used to characterize CNVs in three ecotypic populations of Tibetan sheep and assess CNVs related to domestication and adaptations in the Qinghai-Tibetan Plateau.Results: A total of 87,832 CNV events accounting for 0.3% of the sheep genome were detected in three Tibetan sheep populations. After merging the overlapping CNVs, 2777 CNV regions (CNVRs) were obtained, among which 1098 CNVRs were shared by the three populations. The average length of these CNVRs was more than 3 kb, and duplication events were more frequent than deletions. Functional analysis showed that the shared CNVRs were significantly enriched in 56 GO terms and 18 KEGG pathways that were mainly concerned with ABC transporters, olfactory transduction and oxygen transport. Moreover, 188 CNVRs overlapped with 97 quantitative trait loci (QTLs), such as growth and carcass QTLs, immunoglobulin QTLs, milk yield QTLs and fecal counts QTLs. PCDH15, APP and GRID2 overlapped with body weight QTLs. Furthermore, Vst analysis at each CNVR showed that RUNX1, LOC101104348, LOC105604082 and PAG11 were highly divergent between HTS and VTS, and RUNX1 and LOC101111988 were significantly differentiated between VTS and OTS. Meaningfully, the duplication of RUNX1 may facilitate the hypoxia adaptation of OTS and HTS in QTP, which deserves further research in detail.Conclusions: In this study, we represented the genome-wide distribution characteristics of CNVs in Tibetan sheep and provided a valuable genetic variation resource, which will facilitate the elucidation of the genetic basis underlying the distinct phenotypic traits and local adaptation of Tibetan sheep.

scholarly journals Adaptive radiation and burst speciation of hillstream cyprinid fish Garra in African river

2021 ◽  
Author(s):  
Boris Levin ◽  
Evgeniy Simonov ◽  
Paolo Franchini ◽  
Nikolai Mugue ◽  
Alexander Golubtsov ◽  
...  
Keyword(s):  
Adaptive Radiation ◽  
Phenotypic Diversity ◽  
Wide Distribution ◽  
Hybrid Origin ◽  
Feeding Strategies ◽  
Ecological Opportunity ◽  
Western Africa ◽  
Snp Data ◽  
Genome Wide ◽  
Genome Wide Data

Adaptive radiation of fishes was long thought to be possible only in lacustrine environments. Recently, several studies have shown that also riverine and stream environments provide the ecological opportunity for adaptive radiation. In this study, we report on a riverine adaptive radiation of six ecomorphs of cyprinid hillstream fishes of the genus Garra in a river located in the Ethiopian Highlands in East Africa. Garra are predominantly highly specialized algae-scrapers with a wide distribution ranging from Southeastern Asia to Western Africa. However, adaptive phenotypic diversification in mouth type, sucking disc morphology, gut length and body shape have been found among these new species in a single Ethiopian river. Moreover, we found two novel phenotypes of Garra (‘thick-lipped’ and ‘predatory’) that were not described before in this species-rich genus (>160 species). Mitochondrial and genome-wide data suggest monophyletic, intra-basin evolution of Garra phenotypic diversity with signatures of gene flow from other local populations. Although sympatric ecomorphs are genetically distinct and can be considered to being young species as suggested by genome-wide SNP data, mtDNA was unable to identify any genetic structure suggesting a recent and rapid speciation event. Furthermore, we found evidence for a hybrid origin of the novel ‘thick-lipped’ phenotype, as being the result of the hybridization of two other sympatrically occurring species. Here we highlight how, driven by ecological opportunity, an ancestral trophically highly specialized lineage is likely to have rapidly adaptively radiated in a riverine environment, and that this radiation was promoted by the evolution of novel feeding strategies.

scholarly journals Current analysis platforms and methods for detecting copy number variation

2013 ◽  
Vol 45 (1) ◽  
pp. 1-16 ◽  
Author(s):  
Wenli Li ◽  
Michael Olivier
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Genomic Structural Variation ◽  
Disease Phenotypes ◽  
Human Genomes ◽  
Genome Wide ◽  
Number Variation ◽  
Genomic Regions

Copy number variation (CNV), generated through duplication or deletion events that affect one or more loci, is widespread in the human genomes and is often associated with functional consequences that may include changes in gene expression levels or fusion of genes. Genome-wide association studies indicate that some disease phenotypes and physiological pathways might be impacted by CNV in a small number of characterized genomic regions. However, the pervasiveness and full impact of such variation remains unclear. Suitable analytic methods are needed to thoroughly mine human genomes for genomic structural variation, and to explore the interplay between observed CNV and disease phenotypes, but many medical researchers are unfamiliar with the features and nuances of recently developed technologies for detecting CNV. In this article, we evaluate a suite of commonly used and recently developed approaches to uncovering genome-wide CNVs and discuss the relative merits of each.

scholarly journals Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Jaewon Lim ◽  
Hong-Tae Park ◽  
Seyoung Ko ◽  
Hyun-Eui Park ◽  
Gyumin Lee ◽  
...  
Keyword(s):  
Mycobacterium Avium ◽  
Phenotypic Diversity ◽  
Control Strategies ◽  
Genomic Diversity ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Genomic Features ◽  
Phenotypic Differences ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
Type Strains

AbstractMycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits.

scholarly journals Characterization of the Genetic Diversity Present in a Diverse Sesame Landrace Collection Based on Phenotypic Traits and EST-SSR Markers Coupled With an HRM Analysis

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 656
Author(s):  
Evangelia Stavridou ◽  
Georgios Lagiotis ◽  
Parthena Kalaitzidou ◽  
Ioannis Grigoriadis ◽  
Irini Bosmali ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Geographical Origin ◽  
Expressed Sequence Tag ◽  
Phenotypic Diversity ◽  
Molecular Data ◽  
Phenotypic Traits ◽  
Dissimilarity Matrix ◽  
Heterotic Groups ◽  
Hrm Analysis ◽  
Sesame Genotypes

A selection of sesame (Sesamum indicum L.) landraces of different eco-geographical origin and breeding history have been characterized using 28 qualitative morpho-physiological descriptors and seven expressed sequence tag-simple sequence repeat (EST-SSR) markers coupled with a high-resolution melting (HRM) analysis. The most variable qualitative traits that could efficiently discriminate landraces, as revealed by the correlation analyses, were the plant growth type and position of the branches, leaf blade width, stem pubescence, flowering initiation, capsule traits and seed coat texture. The agglomerative hierarchical clustering analysis based on a dissimilarity matrix highlighted three main groups among the sesame landraces. An EST-SSR marker analysis revealed an average polymorphism information content (PIC) value of 0.82, which indicated that the selected markers were highly polymorphic. A principal coordinate analysis and dendrogram reconstruction based on the molecular data classified the sesame genotypes into four major clades. Both the morpho-physiological and molecular analyses showed that landraces from the same geographical origin were not always grouped in the same cluster, forming heterotic groups; however, clustering patterns were observed for the Greek landraces. The selective breeding of such traits could be employed to unlock the bottleneck of local phenotypic diversity and create new cultivars with desirable traits.

scholarly journals Genome-Wide Copy Number Variation Scan Identifies Complement Component C4 as Novel Susceptibility Gene for Crohnʼs Disease

2016 ◽  
Vol 22 (3) ◽  
pp. 505-515 ◽  
Author(s):  
Isabelle Cleynen ◽  
Peter Konings ◽  
Caroline Robberecht ◽  
Debby Laukens ◽  
Leila Amininejad ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Susceptibility Gene ◽  
Complement Component ◽  
Genome Wide ◽  
Number Variation

scholarly journals Genome-wide identification and expression analysis of the GhIQD gene family in upland cotton (Gossypium hirsutum L.)

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Lingling DOU ◽  
Limin LV ◽  
Yangyang KANG ◽  
Ruijie TIAN ◽  
Deqing HUANG ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Gene Family ◽  
Segmental Duplication ◽  
Gene Expression Pattern ◽  
Cell Development ◽  
Fiber Cell ◽  
Fiber Cells ◽  
Genome Wide ◽  
Duplication Events ◽  
Signaling Receptors

Abstract Background Calmodulin (CaM) is one of the most important Ca2+ signaling receptors because it regulates diverse physiological and biochemical reactions in plants. CaM functions by interacting with CaM-binding proteins (CaMBPs) to modulate Ca2+ signaling. IQ domain (IQD) proteins are plant-specific CaMBPs that bind to CaM by their specific CaM binding sites. Results In this study, we identified 102 GhIQD genes in the Gossypium hirsutum L. genome. The GhIQD gene family was classified into four clusters (I, II, III, and IV), and we then mapped the GhIQD genes to the G. hirsutum L. chromosomes. Moreover, we found that 100 of the 102 GhIQD genes resulted from segmental duplication events, indicating that segmental duplication is the main force driving GhIQD gene expansion. Gene expression pattern analysis showed that a total of 89 GhIQD genes expressed in the elongation stage and second cell wall biosynthesis stage of the fiber cells, suggesting that GhIQD genes may contribute to fiber cell development in cotton. In addition, we found that 20 selected GhIQD genes were highly expressed in various tissues. Exogenous application of MeJA significantly enhanced the expression levels of GhIQD genes. Conclusions Our study shows that GhIQD genes are involved in fiber cell development in cotton and are also widely induced by MeJA. Thw results provide bases to systematically characterize the evolution and biological functions of GhIQD genes, as well as clues to breed better cotton varieties in the future.

scholarly journals Author Correction: Determinants of genome-wide distribution and evolution of uORFs in eukaryotes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hong Zhang ◽  
Yirong Wang ◽  
Xinkai Wu ◽  
Xiaolu Tang ◽  
Changcheng Wu ◽  
...  
Keyword(s):  
Wide Distribution ◽  
Genome Wide

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-22435-2

Weedy Rice Diversity in Southern Brazil

Weed Science ◽  
2021 ◽  
pp. 1-37
Author(s):  
Leonard Bonilla Piveta ◽  
José Alberto Noldin ◽  
Nilda Roma-Burgos ◽  
Vívian Ebeling Viana ◽  
Lariza Benedetti ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Flowering Time ◽  
Weed Management ◽  
Phenotypic Diversity ◽  
Weedy Rice ◽  
Phenotypic Traits ◽  
Southern Brazil ◽  
Variable Response ◽  
Cultivated Rice ◽  
Flowering Synchrony

Abstract Weedy rice (Oryza sativa L.) is one of the most troublesome weeds affecting rice (Oryza sativa L.) production in many countries. Weedy rice control is difficult in rice fields because the weed and crop are phenotypically and morphologically similar. Weedy rice can be a source of genetic diversity to cultivated rice. Thus, this study aimed to characterize the morphological diversity of weedy rice in Southern Brazil. Qualitative and quantitative traits of 249 accessions from eight rice growing mesoregions in Rio Grande do Sul (RS) and Santa Catarina (SC) states were analyzed. For each accession, 24 morphological descriptors (14 qualitative and 10 quantitative) were evaluated. All the 249 accessions from RS and SC are of indica lineage. Considering all the phenotypic traits evaluated, the accessions separated into 14 distinct groups. One of the largest groups consisted of plants that were predominantly tall and with green leaves, intermediate shattering, and variable in flowering time. Distinct subgroups exist within larger clusters, showing discernable phenotypic diversity within the main clusters. The variability in flowering time was high (77 to 110 d after emergence), indicating high potential for flowering synchrony with rice cultivars and, consequently, gene flow. This indicates the need to remove escapes when planting herbicide-resistant rice. Thus, weedy rice populations in Southern Brazil are highly diverse and this diversity could result in variable response to weed management.

scholarly journals Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1510
Author(s):  
Salvatore Mastrangelo ◽  
Rosalia Di Gerlando ◽  
Maria Teresa Sardina ◽  
Anna Maria Sutera ◽  
Angelo Moscarelli ◽  
...  
Keyword(s):  
Conservation Status ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Local Populations ◽  
Genomic Technologies ◽  
Fitness Traits ◽  
Genome Wide ◽  
Breeding Schemes ◽  
Genomic Inbreeding

The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >2 Mb were detected in the whole sample. The Argentata dell’Etna and Messinese were the populations with the lowest mean number of ROH and inbreeding coefficient values, which reflect admixture and gene flow. In the Girgentana, we identified an ROH pattern related with recent inbreeding that can endanger the viability of the breed due to reduced population size. The genomes of Derivata di Siria and Maltese breeds showed the presence of long ROH (>16 Mb) that could seriously impact the overall biological fitness of these breeds. Moreover, the results confirmed that ROH parameters are in agreement with the known demography of these populations and highlighted the different selection histories and breeding schemes of these goat populations. In the analysis of ROH islands, we detected harbored genes involved with important traits, such as for milk yield, reproduction, and immune response, and are consistent with the phenotypic traits of the studied goat populations. Finally, the results of this study can be used for implementing conservation programs for these local populations in order to avoid further loss of genetic diversity and to preserve the production and fitness traits. In view of this, the availability of genomic data is a fundamental resource.

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