<i>VCF2PopTree</i>: a client-side software to construct population phylogeny from genome-wide SNPs

Subramanian, Sankar; Ramasamy, Umayal; Chen, David

doi:10.7717/peerj.8213

Cited by 32 publications

(20 citation statements)

References 20 publications

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“…The graphical representation of PCA was depicted using plot function in R 3.6.1 ( ) [ 19 ]. A neighbor-joining (N-J) tree was constructed using VCF 4.2 and tassel 4.3 ( ) [ 20 ]. The N-J tree was illuminated and visualized by iTOLv4 ( ) [ 21 ].…”

Section: Methodsmentioning

confidence: 99%

Genetic Signatures of Selection for Cashmere Traits in Chinese Goats

Jin

Lü

Fei

et al. 2020

Animals

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Inner Mongolia and Liaoning cashmere goats in China are well-known for their cashmere quality and yield. Thus, they are great models for identifying genomic regions associated with cashmere traits. Herein, 53 Inner Mongolia cashmere goats, Liaoning cashmere goats and Huanghuai goats were genotyped, and 53,347 single-nucleotide polymorphisms (SNPs) were produced using the Illumina Caprine 50K SNP chip. Additionally, we identified some positively selected SNPs by analyzing Fst and XP-EHH. The top 5% of SNPs had selection signatures. After gene annotation, 222 and 173 candidate genes were identified in Inner Mongolia and Liaoning cashmere goats, respectively. Several genes were related to hair follicle development, such as TRPS1, WDR74, LRRC14, SPTLC3, IGF1R, PADI2, FOXP1, WNT10A and CSN3. Gene enrichment analysis of these cashmere trait-associated genes related 67 enriched signaling pathways that mainly participate in hair follicle development and stem cell pluripotency regulation. Furthermore, we identified 20 overlapping genes that were selected in both cashmere goat breeds. Among these overlapping genes, WNT10A and CSN3, which are associated with hair follicle development, are potentially involved in cashmere production. These findings may improve molecular breeding of cashmere goats in the future.

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Section: Methodsmentioning

confidence: 99%

Genetic Signatures of Selection for Cashmere Traits in Chinese Goats

Jin

Lü

Fei

et al. 2020

Animals

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“…To test for significant population differentiation, we conducted an analysis of molecular variance (AMOVA). For this, we generated a pairwise distance matrix (based on p‐distances) between all 28 samples using VCF2PopTree (Subramanian et al., 2019) and performed the AMOVA on this matrix using GenAlEx 6.503 (Peakall & Smouse, 2006). Subsequently, we used vcftools 0.1.17 (Danecek et al., 2011) to calculate fixation index ( F ST ) for every position between samples from the Azores and mainland Europe, following the method of Weir and Cockerham (1984), and averaged all values for a genome‐wide estimate of F ST .…”

Section: Methodsmentioning

confidence: 99%

Selection underlies phenotypic divergence in the insular Azores woodpigeon

et al. 2020

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The study of phenotypic evolution in island birds following colonization is a classic topic in island biogeography. However, few studies explicitly test for the role of selection in shaping trait evolution in these taxa. Here, we studied the Azores woodpigeon (Columba palumbus azorica) to investigate differences between island and mainland populations, between females and males, and interactions between geographical origin and sex, by using spectrophotometry to quantify plumage colour and linear measurements to examine external and skeletal morphology. We further tested if selection explains the observed patterns by comparing phenotypic differentiation to genome‐wide neutral differentiation. Our findings are consistent with several predictions of morphological evolution in island birds, namely differences in bill, flight and leg morphology and coloration differences between island and mainland birds. Interestingly, some plumage and morphological traits that differ between females and males respond differently according to geographical origin. Sexual dimorphism in colour saturation is more pronounced in the mainland, but this is driven by selection on female plumage coloration. Differences in flight morphology between females and males are also more pronounced in the mainland, possibly to accommodate contrasting pressures between migration and flight displays. Overall, our results suggest that phenotypic differentiation between mainland and island populations leading to divergent sexual dimorphism patterns can arise from selection acting on both females and males on traits that are likely under the influence of natural and sexual selection.

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“…Multiple sequence alignment (MSA) of all nucleotide sequences were carried out in the EMBL-EBI Clustal Omega server to investigate sequence conservation [23,24]. The Newick format for the multiple align sequence was used to generate phylogeny [25]. The phylogenetic tree was constructed in the Interactive Tree of Life (iTOL) online tool [26].…”

Section: Multiple Sequence Alignment and Phylogenetic Tree Constructionmentioning

confidence: 99%

Evolving geographic diversity in SARS-CoV2 and in silico analysis of replicating enzyme 3CLpro targeting repurposed drug candidates

et al. 2020

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Background Severe acute respiratory syndrome (SARS) has been initiating pandemics since the beginning of the century. In December 2019, the world was hit again by a devastating SARS episode that has so far infected almost four million individuals worldwide, with over 200,000 fatalities having already occurred by mid-April 2020, and the infection rate continues to grow exponentially. SARS coronavirus 2 (SARS-CoV-2) is a single stranded RNA pathogen which is characterised by a high mutation rate. It is vital to explore the mutagenic capability of the viral genome that enables SARS-CoV-2 to rapidly jump from one host immunity to another and adapt to the genetic pool of local populations. Methods For this study, we analysed 2301 complete viral sequences reported from SARS-CoV-2 infected patients. SARS-CoV-2 host genomes were collected from The Global Initiative on Sharing All Influenza Data (GISAID) database containing 9 genomes from pangolin-CoV origin and 3 genomes from bat-CoV origin, Wuhan SARS-CoV2 reference genome was collected from GeneBank database. The Multiple sequence alignment tool, Clustal Omega was used for genomic sequence alignment. The viral replicating enzyme, 3-chymotrypsin-like cysteine protease (3CLpro) that plays a key role in its pathogenicity was used to assess its affinity with pharmacological inhibitors and repurposed drugs such as anti-viral flavones, biflavanoids, anti-malarial drugs and vitamin supplements. Results Our results demonstrate that bat-CoV shares > 96% similar identity, while pangolin-CoV shares 85.98% identity with Wuhan SARS-CoV-2 genome. This in-depth analysis has identified 12 novel recurrent mutations in South American and African viral genomes out of which 3 were unique in South America, 4 unique in Africa and 5 were present in-patient isolates from both populations. Using state of the art in silico approaches, this study further investigates the interaction of repurposed drugs with the SARS-CoV-2 3CLpro enzyme, which regulates viral replication machinery. Conclusions Overall, this study provides insights into the evolving mutations, with implications to understand viral pathogenicity and possible new strategies for repurposing compounds to combat the nCovid-19 pandemic.

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VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs

Cited by 32 publications

References 20 publications

Genetic Signatures of Selection for Cashmere Traits in Chinese Goats

Genetic Signatures of Selection for Cashmere Traits in Chinese Goats

Selection underlies phenotypic divergence in the insular Azores woodpigeon

Evolving geographic diversity in SARS-CoV2 and in silico analysis of replicating enzyme 3CLpro targeting repurposed drug candidates

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