scholarly journals Genome-wide protein phylogenies for four African cichlid species

2017 ◽  
Author(s):  
Ajay Ramakrishnan Varadarajan ◽  
Rohini Mopuri ◽  
J. Todd Streelman ◽  
Patrick T. McGrath
Keyword(s):  
Protein Function ◽  
Evolutionary Relationship ◽  
Trait Variation ◽  
Cichlid Species ◽  
Genome Wide ◽  
A Genome ◽  
History Of ◽  
Astatotilapia Burtoni ◽  
African Cichlids ◽  
Relationship Of

ABSTRACTBackgroundThe thousands of species of closely related cichlid fishes in the great lakes of East Africa are a powerful model for understanding speciation and the genetic basis of trait variation. Recently, the genomes of five species of African cichlids representing five distinct lineages were sequenced and used to predict protein products at a genome-wide level. Here we characterize the evolutionary relationship of each cichlid protein to previously sequenced animal species.ResultsWe used the Treefam database, a set of preexisting protein phylogenies built using 109 previously sequenced genomes, to identify Treefam families for each protein annotated from four cichlid species: Metriaclima zebra, Astatotilapia burtoni, Pundamilia nyererei and Neolamporologus brichardi. For each of these Treefam families, we built new protein phylogenies containing each of the cichlid protein hits. Using these new phylogenies we identified the evolutionary relationship of each cichlid protein to its nearest human and zebrafish protein. This data is available either through download or through a webserver we have implemented.ConclusionThese phylogenies will be useful for any cichlid researchers trying to predict biological and protein function for a given cichlid gene, understanding the evolutionary history of a given cichlid gene, identifying recently duplicated cichlid genes, or performing genome-wide analysis in cichlids that relies on using databases generated from other species.

scholarly journals Genome-wide variations of SARS-CoV-2 infer evolution relationship and transmission route

2020 ◽  
Author(s):  
Lehai Zhang ◽  
Shifu Wang ◽  
Qian Ren ◽  
Junjie Yang ◽  
Yanqin Lu ◽  
...  
Keyword(s):  
Molecular Detection ◽  
Detection Efficiency ◽  
Evolutionary Relationship ◽  
Clinical Manifestations ◽  
Coding Region ◽  
Gene Coding ◽  
Genome Wide ◽  
Group A ◽  
Group B ◽  
Relationship Of

AbstractIn the epidemic evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the issues of mutation, origin, typing and the effect of mutation on molecular detection remain to be unrevealed. In order to identify the evolutionary relationship of SARS-CoV-2 and evaluate the detection efficiency of primers that are currently used in different countries, we retrieved genomic sequences of 373 SARS-CoV-2 strains from multiple databases and performed genome-wide variation analysis. According to the nucleotide C28144T variation, the SARS-CoV-2 can be divided into group A (117 strains) and group B (256 strains). The spike protein gene (S gene) coding region 1841 (total 23403) A1841G, formed a B1 subgroup (40 strains) in group B, of which 30 strains were from European and American countries in March (especially Washington, USA). These mutations are likely to be influenced by the environment or the immunization selection pressure of different populations. Although the mutation is not in the receptor binding region (RBD) and alkaline cleavage region, it may also affect the ability of transmission and pathogenicity; however, the significance is not yet clear. As the ratio of A / B strains in the epidemic months showed an increasing trend (0.35: 1 in January, 0.62: 1 in February and 0.76: 1 in March), it seems that the transmissibility of group A strains becomes stronger with time. Based on the variation of 11 nucleotide sites during the epidemic process, it is speculated that the Washington strain is more like an ancestor type, and the Wuhan strain is the offspring of the group A virus strain. By comparing the detection capabilities of primers in different countries, the SARS-CoV-2 nucleotide variation may only affect molecular detection of very few strains. The differences in the transmissibility, pathogenicity and clinical manifestations of different types of strains require further investigations.

scholarly journals Each of 3,323 metabolic innovations in the evolution ofE. coliarose through the horizontal transfer of a single DNA segment

2018 ◽  
Vol 116 (1) ◽  
pp. 187-192 ◽  
Author(s):  
Tin Yau Pang ◽  
Martin J. Lercher
Keyword(s):  
E Coli ◽  
New Genes ◽  
Metabolic Adaptations ◽  
Genome Wide ◽  
A Genome ◽  
Individual Strain ◽  
History Of ◽  
Phenotype Space ◽  
Genome Content ◽  
Metabolic Models

Even closely related prokaryotes often show an astounding diversity in their ability to grow in different nutritional environments. It has been hypothesized that complex metabolic adaptations—those requiring the independent acquisition of multiple new genes—can evolve via selectively neutral intermediates. However, it is unclear whether this neutral exploration of phenotype space occurs in nature, or what fraction of metabolic adaptations is indeed complex. Here, we reconstruct metabolic models for the ancestors of a phylogeny of 53Escherichia colistrains, linking genotypes to phenotypes on a genome-wide, macroevolutionary scale. Based on the ancestral and extant metabolic models, we identify 3,323 phenotypic innovations in the history of theE. coliclade that arose through changes in accessory genome content. Of these innovations, 1,998 allow growth in previously inaccessible environments, while 1,325 increase biomass yield. Strikingly, every observed innovation arose through the horizontal acquisition of a single DNA segment less than 30 kb long. Although we found no evidence for the contribution of selectively neutral processes, 10.6% of metabolic innovations were facilitated by horizontal gene transfers on earlier phylogenetic branches, consistent with a stepwise adaptation to successive environments. Ninety-eight percent of metabolic phenotypes accessible to the combinedE. colipangenome can be bestowed on any individual strain by transferring a single DNA segment from one of the extant strains. These results demonstrate an amazing ability of theE. colilineage to adapt to novel environments through single horizontal gene transfers (followed by regulatory adaptations), an ability likely mirrored in other clades of generalist bacteria.

scholarly journals Genome-wide analysis of the aquaporin genes in melon (Cucumis melo L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Alvaro Lopez-Zaplana ◽  
Juan Nicolas-Espinosa ◽  
Micaela Carvajal ◽  
Gloria Bárzana
Keyword(s):  
Cucumis Melo ◽  
Evolutionary Relationship ◽  
Physiological Importance ◽  
Genome Wide ◽  
Related Plant ◽  
Complete Set ◽  
The Individual ◽  
Almost All ◽  
Relationship Of ◽  
Cucumis Melo L

AbstractMelon (Cucumis melo L.) is a very important crop throughout the world and has great economic importance, in part due to its nutritional properties. It prefers well-drained soil with low acidity and has a strong demand for water during fruit set. Therefore, a correct water balance—involving aquaporins—is necessary to maintain the plants in optimal condition. This manuscript describes the identification and comparative analysis of the complete set of aquaporins in melon. 31 aquaporin genes were identified, classified and analysed according to the evolutionary relationship of melon with related plant species. The individual role of each aquaporin in the transport of water, ions and small molecules was discussed. Finally, qPCR revealed that almost all melon aquaporins in roots and leaves were constitutively expressed. However, the high variations in expression among them point to different roles in water and solute transport, providing important features as that CmPIP1;1 is the predominant isoform and CmTIP1;1 is revealed as the most important osmoregulator in the tonoplast under optimal conditions. The results of this work pointing to the physiological importance of each individual aquaporin of melon opening a field of knowledge that deserves to be investigated.

scholarly journals Genome-wide Study of SBT Genes in Eight Plant Species: Evolution and Expression Outlines for Development and Stress

2020 ◽  
Author(s):  
Sulin Wen ◽  
Guanqun Chen ◽  
Tingting Huang ◽  
Xiaohui Shen
Keyword(s):  
Expression Pattern ◽  
Plant Species ◽  
Protein Function ◽  
Evolutionary Relationship ◽  
Evolutionary Trend ◽  
Classification Feature ◽  
Genome Wide ◽  
Species Evolution ◽  
Genome Wide Study ◽  
Diverse Plant

Abstract Background: Subtilisin-like proteases (or subtilases, SBT), a specific family of serine peptidases, are a very big family in plants. Previous studies showed association of SBTs with environment response and development. However, it is still unclear about the function and features of SBTs. Also, there is little information about SBTs classification or protein function research.Results: The characters of SBTs in eight plant species including Arabidopsis, rice, wheat etc. were analyzed. The analysis mainly contained evolutionary relationship, gene structure, chromosomal location, gene synteny and expression pattern. In short, the evolutionary trend of SBTs in the eight plant species was revealed. The expression pattern showed a scattered distribution of SBTs in diverse plant organs.Conclusions: Our results reveal classification, feature and expression pattern of SBT. Then the results might offer clues for future studies about SBTs and additionally related to their possible function in plants against stress and development.

scholarly journals Investigation of clinical characteristics and genome associations in the UK Lipoedema cohort

2021 ◽  
Author(s):  
Dionysios Grigoriadis ◽  
Ege Sackey ◽  
Katie Riches ◽  
Malou van Zanten ◽  
Glen Brice ◽  
...  
Keyword(s):  
Clinical Characteristics ◽  
Genome Wide Association Study ◽  
Subcutaneous Fat ◽  
Lower Limbs ◽  
Genome Wide ◽  
A Genome ◽  
History Of ◽  
Different Populations ◽  
The Uk

Lipoedema is a chronic adipose tissue disorder mainly affecting women, causing excess subcutaneous fat deposition on the lower limbs with pain and tenderness. There is often a family history of lipoedema, suggesting a genetic origin, but the contribution of genetics is currently unclear. A tightly phenotyped cohort of 200 lipoedema patients was recruited from two UK specialist clinics. Objective clinical characteristics and measures of quality of life data were obtained. In an attempt to understand the genetic architecture of the disease better, genome-wide single nucleotide polymorphism (SNP) genotype data were obtained, and a genome wide association study (GWAS) performed on 130 of the recruits. The analysis revealed genetic loci suggestively associated with the lipoedema phenotype, with further support provided by an independent cohort taken from the 100,000 Genomes Project. Top SNPs included loci associated with lipoma formation, biosynthesis of hormones and lipid hydroxylation. Exactly how these SNPs relate to a lipoedema disease mechanism is not yet understood but the findings are consistent with existing fat and hormone hypotheses. This first GWAS of a UK lipoedema cohort has identified genetic regions of suggestive association with the disease. Further replication of these findings in different populations is warranted.

scholarly journals The wild species genome ancestry of domestic chickens

2019 ◽  
Author(s):  
Raman Akinyanju Lawal ◽  
Simon H. Martin ◽  
Koen Vanmechelen ◽  
Addie Vereijken ◽  
Pradeepa Silva ◽  
...  
Keyword(s):  
Single Case ◽  
Divergence Time ◽  
Introgressive Hybridization ◽  
Domestic Chicken ◽  
Control Of Gene Expression ◽  
Red Junglefowl ◽  
Genome Wide ◽  
A Genome ◽  
History Of ◽  
Sister Relationships

AbstractHybridization and/or introgression play a key role in the evolutionary history of animal species. It is commonly observed in several orders in wild birds. The domestic chicken Gallus gallus domesticus is the commonest livestock species exploited for the benefit of mankind. The origin of its diversity remains unsettled. Here, we report a genome-wide analyses for signatures of introgression within domestic village chicken. We first established the genome-wide phylogeny and divergence time across the genus Gallus, showing the sister relationships between Grey junglefowl G. sonneratii and Ceylon junglefowl G. lafayettii and that the Green junglefowl is the first diverging lineage within the genus Gallus. Then, by analysing the whole-genome sequences of geographically diverse chicken populations, we reveal extensive bidirectional introgression between Grey junglefowl and domestic chicken and to a much less extent with Ceylon junglefowl. A single case of Green junglefowl G. varius introgression was identified. These introgressed regions include biological functions related to the control of gene expression. Our results show that while the Red junglefowl is the main ancestral species, introgressive hybridization episodes have impacted the genome and contributed to the diversity of domestic chicken, although likely at different level across its geographic range.

scholarly journals A genome‐wide linkage map for the house sparrow ( Passer domesticus ) provides insights into the evolutionary history of the avian genome

2020 ◽  
Vol 20 (2) ◽  
pp. 544-559 ◽  
Author(s):  
Ingerid J. Hagen ◽  
Sigbjørn Lien ◽  
Anna M. Billing ◽  
Tore O. Elgvin ◽  
Cassandra Trier ◽  
...  
Keyword(s):  
Linkage Map ◽  
Evolutionary History ◽  
House Sparrow ◽  
Passer Domesticus ◽  
Genome Wide ◽  
A Genome ◽  
Avian Genome ◽  
History Of

scholarly journals Genome-wide linkage scan for contraction velocity characteristics of knee musculature in the Leuven Genes for Muscular Strength Study

2008 ◽  
Vol 35 (1) ◽  
pp. 36-44 ◽  
Author(s):  
Gunther De Mars ◽  
An Windelinckx ◽  
Wim Huygens ◽  
Maarten W. Peeters ◽  
Gaston P. Beunen ◽  
...  
Keyword(s):  
Velocity Ratio ◽  
Protective Role ◽  
Linkage Study ◽  
Knee Extensors ◽  
Genome Wide ◽  
A Genome ◽  
Extensor Muscles ◽  
Velocity Relationship ◽  
Relationship Of ◽  
Knee Flexors

The torque-velocity relationship is known to be affected by ageing, decreasing its protective role in the prevention of falls. Interindividual variability in this torque-velocity relationship is partly determined by genetic factors (h2: 44–67%). As a first attempt, this genome-wide linkage study aimed to identify chromosomal regions linked to the torque-velocity relationship of the knee flexors and extensors. A selection of 283 informative male siblings (17–36 yr), belonging to 105 families, was used to conduct a genome-wide SNP-based (Illumina Linkage IVb panel) multipoint linkage analysis for the torque-velocity relationship of the knee flexors and extensors. The strongest evidence for linkage was found at 15q23 for the torque-velocity slope of the knee extensors (TVSE). Other interesting linkage regions with LOD scores >2 were found at 7p12.3 [logarithm of the odds ratio (LOD) = 2.03, P = 0.0011] for the torque-velocity ratio of the knee flexors (TVRF), at 2q14.3 (LOD = 2.25, P = 0.0006) for TVSE, and at 4p14 and 18q23 for the torque-velocity ratio of the knee extensors TVRE (LOD = 2.23 and 2.08; P = 0.0007 and 0.001, respectively). We conclude that many small contributing genes are involved in causing variation in the torque-velocity relationship of the knee flexor and extensor muscles. Several earlier reported candidate genes for muscle strength and muscle mass and new candidates are harbored within or in close vicinity of the linkage regions reported in the present study.

scholarly journals A Genome-Wide Identification of Genes Undergoing Recombination and Positive Selection inNeisseria

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Dong Yu ◽  
Yuan Jin ◽  
Zhiqiu Yin ◽  
Hongguang Ren ◽  
Wei Zhou ◽  
...  
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Molecular Mechanisms ◽  
Acid Sites ◽  
Gram Negative Bacteria ◽  
Orthologous Genes ◽  
Genome Wide ◽  
A Genome ◽  
History Of ◽  
Functional Analyses

Currently, there is particular interest in the molecular mechanisms of adaptive evolution in bacteria.Neisseriais a genus of gram negative bacteria, and there has recently been considerable focus on its two human pathogenic speciesN. meningitidisandN. gonorrhoeae. Until now, no genome-wide studies have attempted to scan for the genes related to adaptive evolution. For this reason, we selected 18Neisseriagenomes (14N. meningitidis, 3N. gonorrhoeaeand 1 commensalN. lactamics) to conduct a comparative genome analysis to obtain a comprehensive understanding of the roles of natural selection and homologous recombination throughout the history of adaptive evolution. Among the 1012 core orthologous genes, we identified 635 genes with recombination signals and 10 genes that showed significant evidence of positive selection. Further functional analyses revealed that no functional bias was found in the recombined genes. Positively selected genes are prone to DNA processing and iron uptake, which are essential for the fundamental life cycle. Overall, the results indicate that both recombination and positive selection play crucial roles in the adaptive evolution ofNeisseriagenomes. The positively selected genes and the corresponding amino acid sites provide us with valuable targets for further research into the detailed mechanisms of adaptive evolution inNeisseria.

scholarly journals Genetic architecture of Wistar-Kyoto rat and spontaneously hypertensive rat substrains from different sources

2013 ◽  
Vol 45 (13) ◽  
pp. 528-538 ◽  
Author(s):  
Yanli Zhang-James ◽  
Frank A. Middleton ◽  
Stephen V. Faraone
Keyword(s):  
Spontaneously Hypertensive Rat ◽  
Wistar Rat ◽  
Spontaneously Hypertensive ◽  
Hypertensive Rat ◽  
Genome Wide ◽  
Daunting Task ◽  
History Of ◽  
Wistar Kyoto ◽  
Complex Relationships ◽  
Relationship Of

The spontaneously hypertensive rat (SHR) has been widely used as a model for studies of hypertension and attention deficit/hyperactivity disorder. The inbred Wistar-Kyoto (WKY) rat, derived from the same ancestral outbred Wistar rat as the SHR, are normotensive and have been used as the closest genetic control for the SHR, although the WKY has also been used as a model for depression. Notably, however, substantial behavioral and genetic differences among the WKY substrains, usually from the different vendors and breeders, have been observed. These differences have often been overlooked in prior studies, leading to inconsistent and even contradictory findings. The complicated breeding history of the SHR and WKY rats and the lack of a comprehensive understanding of the genetic background of different commercial substrains make the selection of control rats a daunting task, even for researchers who are mindful of their genetic heterogeneity. In this study, we examined the genetic relationship of 16 commonly used WKY and SHR rat substrains using genome-wide SNP genotyping data. Our results confirmed a large genetic divergence and complex relationships among the SHR and WKY substrains. This understanding, although incomplete without the genome sequence, provides useful guidance in selecting substrains and helps to interpret previous reports when the source of the animals was known. Moreover, we found two closely related, yet distinct WKY substrains that may provide novel opportunities in modeling psychiatric disorders.

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