Genome-wide Identification and Evolutionary Analysis of NBS-LRR Genes From Secale cereale

Secale cereale is an important crop in the Triticeae tribe of the Poaceae family, and it has unique agronomic characteristics and genome properties. It possesses resistance to many diseases and serves as an important resource for the breeding of other Triticeae crops. We performed a genome-wide study on S. cereale to identify the largest group of plant disease resistance genes (R genes), the nucleotide-binding site-leucine-rich repeat receptor (NBS-LRR) genes. In its genome, 582 NBS-LRR genes were identified, including one from the RNL subclass and 581 from the CNL subclass. The NBS-LRR gene number in the S. cereale genome is greater than that in barley and the diploid wheat genomes. S. cereale chromosome 4 contains the largest number of NBS-LRR genes among the seven chromosomes, which is different from the pattern in barley and the genomes B and D of wheat but similar to that in the genome A of wheat. Further synteny analysis suggests that more NBS-LRR genes on chromosome 4 have been inherited from a common ancestor by S. cereale and the wheat genome A than the wheat genomes B and D. Phylogenetic analysis revealed that at least 740 NBS-LRR lineages are present in the common ancestor of S. cereale, Hordeum vulgare and Triticum urartu. However, most of them have only been inherited by one or two species, with only 65 of them preserved in all three species. The S. cereale genome inherited 382 of these ancestral NBS-LRR lineages, but 120 of them have been lost in both H. vulgare and T. urartu. This study provides the full NBS-LRR profile of the S. cereale genome, which is a resource for S. cereale breeding and indicates that S. cereale can be an important material for the molecular breeding of other Triticeae crops.

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Genome-Wide Analysis of NLR Disease Resistance Genes in an Updated Reference Genome of Barley

Frontiers in Genetics ◽

10.3389/fgene.2021.694682 ◽

2021 ◽

Vol 12 ◽

Author(s):

Qian Li ◽

Xing-Mei Jiang ◽

Zhu-Qing Shao

Keyword(s):

Disease Resistance ◽

Plant Disease Resistance ◽

Molecular Breeding ◽

Common Ancestor ◽

Reference Genome ◽

Barley Genome ◽

Genome Wide Analysis ◽

Genome Wide ◽

The Common ◽

Integrated Domains

Barley is one of the top 10 crop plants in the world. During its whole lifespan, barley is frequently infected by various pathogens. In this study, we performed genome-wide analysis of the largest group of plant disease resistance (R) genes, the nucleotide binding site–leucine-rich repeat receptor (NLR) gene, in an updated barley genome. A total of 468 NLR genes were identified from the improved barley genome, including one RNL subclass and 467 CNL subclass genes. Proteins of 43 barley CNL genes were shown to contain 25 different integrated domains, including WRKY and BED. The NLR gene number identified in this study is much larger than previously reported results in earlier versions of barley genomes, and only slightly fewer than that in the diploid wheat Triticum urartu. Barley Chromosome 7 contains the largest number of 112 NLR genes, which equals to seven times of the number of NLR genes on Chromosome 4. The majority of NLR genes (68%) are located in multigene clusters. Phylogenetic analysis revealed that at least 18 ancestral CNL lineages were presented in the common ancestor of barley, T. urartu and Arabidopsis thaliana. Among them fifteen lineages expanded to 533 sub-lineages prior to the divergence of barley and T. urartu. The barley genome inherited 356 of these sub-lineages and duplicated to the 467 CNL genes detected in this study. Overall, our study provides an updated profile of barley NLR genes, which should serve as a fundamental resource for functional gene mining and molecular breeding of barley.

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A Genome-Wide Comparative Evolutionary Analysis of Herpes Simplex Virus Type 1 and Varicella Zoster Virus

PLoS ONE ◽

10.1371/journal.pone.0022527 ◽

2011 ◽

Vol 6 (7) ◽

pp. e22527 ◽

Cited By ~ 44

Author(s):

Peter Norberg ◽

Shaun Tyler ◽

Alberto Severini ◽

Rich Whitley ◽

Jan-Åke Liljeqvist ◽

...

Keyword(s):

Herpes Simplex Virus ◽

Herpes Simplex ◽

Varicella Zoster Virus ◽

Herpes Simplex Virus Type ◽

Evolutionary Analysis ◽

Varicella Zoster ◽

Genome Wide ◽

A Genome ◽

Simplex Virus

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A phylogenomic analysis of the role and timing of molecular adaptation in the aquatic transition of cetartiodactyl mammals

Royal Society Open Science ◽

10.1098/rsos.150156 ◽

2015 ◽

Vol 2 (9) ◽

pp. 150156 ◽

Cited By ~ 19

Author(s):

Georgia Tsagkogeorga ◽

Michael R. McGowen ◽

Kalina T. J. Davies ◽

Simon Jarman ◽

Andrea Polanowski ◽

...

Keyword(s):

Protein Interactions ◽

Dna Sequences ◽

Brain Function ◽

Molecular Adaptation ◽

Phylogenomic Analysis ◽

Protein Protein Interactions ◽

Orthologous Genes ◽

Genome Wide ◽

A Genome ◽

The Common

Recent studies have reported multiple cases of molecular adaptation in cetaceans related to their aquatic abilities. However, none of these has included the hippopotamus, precluding an understanding of whether molecular adaptations in cetaceans occurred before or after they split from their semi-aquatic sister taxa. Here, we obtained new transcriptomes from the hippopotamus and humpback whale, and analysed these together with available data from eight other cetaceans. We identified more than 11 000 orthologous genes and compiled a genome-wide dataset of 6845 coding DNA sequences among 23 mammals, to our knowledge the largest phylogenomic dataset to date for cetaceans. We found positive selection in nine genes on the branch leading to the common ancestor of hippopotamus and whales, and 461 genes in cetaceans compared to 64 in hippopotamus. Functional annotation revealed adaptations in diverse processes, including lipid metabolism, hypoxia, muscle and brain function. By combining these findings with data on protein–protein interactions, we found evidence suggesting clustering among gene products relating to nervous and muscular systems in cetaceans. We found little support for shared ancestral adaptations in the two taxa; most molecular adaptations in extant cetaceans occurred after their split with hippopotamids.

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Genome-wide survey and expression analysis of the SLAC/SLAH gene family in pear (Pyrus bretschneideri) and other members of the Rosaceae

10.1101/288308 ◽

2018 ◽

Author(s):

Guodong Chen ◽

Xiaolong Li ◽

Xin qiao ◽

Jiaming Li ◽

Li Wang ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Prunus Persica ◽

Higher Plants ◽

Chloride Transport ◽

Structural Characteristics ◽

Evolutionary Analysis ◽

Anion Channels ◽

Genome Wide ◽

A Genome

AbstractS-type anion channels (SLAC/SLAHs), which play important roles in plant anion (such as nitrate and chloride) transport, growth and development, abiotic stress responses and hormone signaling. However, there is far less information about this family in Rosaceae species. We performed a genome-wide analysis and identified SLAC/SLAH gene family members in pear (Pyrus bretschneideri) and four other species of Rosaceae (Malus domestica, Prunus persica, Fragaria vesca and Prunus mume). A total of 21 SLAC/SLAH genes were identified from the five Rosaceae species. Based on the structural characteristics and a phylogenetic analysis of these genes, the SLAC/SLAH gene family could be classified into three main groups (I, II and III). The evolutionary analysis showed that the SLAC/SLAH gene family was comparatively conserved during the evolution of Rosaceae species. Transcriptome data demonstrated that PbrSLAC/SLAH genes were detected in all parts of the pear. However, PbrSLAC1 showed a higher expression level in leaf, while PbrSLAH2/3 was mainly expressed in roots. In addition, PbrSLAC/SLAH genes were only located on the plasma membrane in transient expression experiments in Arabidopsis protoplasts cells. These results provide valuable information that increases our understanding of the evolution, expression and functions of the SLAC/SLAH gene family in higher plants.

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Recent Molecular Evolution of Human Metapneumovirus (HMPV): Subdivision of HMPV A2b Strains

Microorganisms ◽

10.3390/microorganisms8091280 ◽

2020 ◽

Vol 8 (9) ◽

pp. 1280

Author(s):

Naganori Nao ◽

Miwako Saikusa ◽

Ko Sato ◽

Tsuyoshi Sekizuka ◽

Shuzo Usuku ◽

...

Keyword(s):

Respiratory Infections ◽

Epidemiological Studies ◽

Human Metapneumovirus ◽

Evolutionary Relationships ◽

Acute Respiratory Infections ◽

Evolutionary Analysis ◽

The Novel ◽

Genome Wide ◽

A Genome

Human metapneumovirus (HMPV) is a major etiological agent of acute respiratory infections in humans. HMPV has been circulating worldwide for more than six decades and is currently divided into five agreed-upon subtypes: A1, A2a, A2b, B1, and B2. Recently, the novel HMPV subtypes A2c, A2b1, and A2b2 have been proposed. However, the phylogenetic and evolutionary relationships between these recently proposed HMPV subtypes are unclear. Here, we report a genome-wide phylogenetic and evolutionary analysis of 161 HMPV strains, including unique HMPV subtype A2b strains with a 180- or 111-nucleotide duplication in the G gene (nt-dup). Our data demonstrate that the HMPV A2b subtype contains two distinct subtypes, A2b1 and A2b2, and that the HMPV subtypes A2c and A2b2 may be different names for the same subtype. HMPV A2b strains with a nt-dup also belong to subtype A2b2. Molecular evolutionary analyses indicate that subtypes A2b1 and A2b2 diverged from subtype A2b around a decade after the subtype A2 was divided into the subtypes A2a and A2b. These data support the A2b1 and A2b2 subtypes proposed in 2012 and are essential for the unified classification of HMPV subtype A2 strains, which is important for future HMPV surveillance and epidemiological studies.

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A genome-wide association identified the common genetic variants influence disease severity in β0-thalassemia/hemoglobin E

Human Genetics ◽

10.1007/s00439-009-0770-2 ◽

2009 ◽

Vol 127 (3) ◽

pp. 303-314 ◽

Cited By ~ 107

Author(s):

Manit Nuinoon ◽

Wattanan Makarasara ◽

Taisei Mushiroda ◽

Iswari Setianingsih ◽

Pustika Amalia Wahidiyat ◽

...

Keyword(s):

Disease Severity ◽

Genetic Variants ◽

Genome Wide Association ◽

Hemoglobin E ◽

Genome Wide ◽

Common Genetic Variants ◽

A Genome ◽

The Common

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Genetic variants in the SHISA6 gene are associated with delayed cognitive impairment in two family datasets

10.1101/2021.07.02.21259940 ◽

2021 ◽

Author(s):

Jairo Ramos ◽

Laura J Caywood ◽

Michael B. Prough ◽

Jason E. Clouse ◽

Sharlene D. Herington ◽

...

Keyword(s):

Cognitive Impairment ◽

Statistical Significance ◽

Age At Onset ◽

Chromosome 17 ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Genome Wide ◽

Cultural Isolation ◽

A Genome ◽

The Common

Background: Studies of cognitive impairment (CI) in Amish communities have identified sibships containing multiple CI and cognitively unimpaired (CU; unaffected after age 75) individuals. We hypothesize that these CU individuals may carry protective alleles delaying age at onset (AAO) of CI, preserving cognition in older age despite increased genetic risk. As well, the genetic and cultural isolation in the Amish since the early 1800s may have reduced the complexity of the genetic architecture of CI, increasing the power to detect protective alleles in this population. With this in mind we conducted a genome-wide study (GWAS) to identify loci associated with AAO of CI in a sample of Amish adults over age 75. Methods: 1,522 individuals aged 43-99 (mean age 73.1, 42% men) screened at least once for CI using the Modified Mini-Mental State exam (3MS) were genotyped using Illumina chipsets. Genotypes were imputed for 7,815,951 single nucleotide variants (SNV) with minor allele frequency (MAF) > 1%. The outcome studied was age, defined as 1) age at the first 3MS result indicating impairment (AAO; 3MS <87; 362 CI individuals) or 2) age at last normal exam (3MS >=87, 1,160 CU individuals). Cox mixed-effects models examined association between age and each SNV, adjusting for sex and familial relationships. To replicate genome-wide significant findings, SNVs in a 1 Megabase region centered on the peak SNV were examined for association with age using these same methods in the NIA-LOAD family study dataset (1,785 AD cases, 1,565 unaffected controls, mean age 73.5. Results: Three SNV were significantly associated (p<5 x 10-8) with AAO in the Amish, on chromosomes 6 (rs14538074; HR=3.35), 9 (rs534551495; HR=2.82), and 17 (rs146729640; Hazard Ratio (HR)=6.38). Each region found the common allele associated with later AAO. Replication analysis detected association at rs146729640, with nominal statistical significance (HR=1.49, p=0.02). Conclusions: The replicated genome-wide significant association with AAO on chromosome 17 suggest this may be novel locus associated with delayed onset of AD. The associated SNP is located in the SHISA6 gene, which is involved in post-synaptic transmission in the hippocampus and is a biologically plausible candidate gene for AD.

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Genome-wide identification and expression analysis of CYP450 gene family in Cucumis sativus L.

10.21203/rs.3.rs-1196334/v1 ◽

2021 ◽

Author(s):

hongyu wang ◽

Pengfei Li ◽

Yu Wang ◽

Chunyu Chi ◽

Guohua Ding

Keyword(s):

Subcellular Localization ◽

Gene Family ◽

Cucumis Sativus ◽

Expression Profile ◽

Evolutionary Relationship ◽

Evolutionary Analysis ◽

Cucumis Sativus L ◽

P450 Gene ◽

Genome Wide ◽

A Genome

Abstract The cytochrome P450 (CYP450) gene family plays a vital role in basic metabolism and enhances plant resistance to stress and pests. However, little information is available on the genome-wide characterization and evolutionary relationship of the CYP450 gene family in Cucumis sativus L. In the present study, a genome-wide bioinformatics analysis was performed, including gene structure, conserved motif, cis-acting promoter element, evolutionary analysis, collinearity, subcellular localization, and expression profile. The gene expression profile of CYP450 was verified using transcriptome sequencing and quantitative reverse transcription polymerase chain reaction. A total of 165 P450 genes were identified in the cucumber genome. These genes were classified into eight subfamilies and unevenly distributed on seven chromosomes. Subcellular localization predicted that most of P450 genes were located in chloroplasts and a few were located on the plasma membrane. CYP450 genes were differentially expressed in different tissues and in response to salicylic acid (SA) treatment. The sizes of all cucumber P450 proteins ranged from 317 to 1,056 aa, the theoretical isoelectric points ranged from 5.05 to 10.31, and the molecular weights ranged from 36,095 to 121,403 KD. This study provides a theoretical basis for further research on the biological functions of the P450 gene in cucumber plants.

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A genome-wide scan for linkage to human exceptional longevity identifies a locus on chromosome 4

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.181337598 ◽

2001 ◽

Vol 98 (18) ◽

pp. 10505-10508 ◽

Cited By ~ 224

Author(s):

A. A. Puca ◽

M. J. Daly ◽

S. J. Brewster ◽

T. C. Matise ◽

J. Barrett ◽

...

Keyword(s):

Chromosome 4 ◽

Exceptional Longevity ◽

Genome Wide ◽

A Genome ◽

Genome Wide Scan

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Genetic determinants of risk in autoimmune pulmonary alveolar proteinosis

Nature Communications ◽

10.1038/s41467-021-21011-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Saori Sakaue ◽

Etsuro Yamaguchi ◽

Yoshikazu Inoue ◽

Meiko Takahashi ◽

Jun Hirata ◽

...

Keyword(s):

Genome Wide Association Study ◽

Pulmonary Alveolar Proteinosis ◽

Disease Risk ◽

Amino Acid Position ◽

Genetic Determinants ◽

Gm Csf ◽

Genome Wide ◽

A Genome ◽

The Common ◽

Alveolar Proteinosis

AbstractPulmonary alveolar proteinosis (PAP) is a devastating lung disease caused by abnormal surfactant homeostasis, with a prevalence of 6–7 cases per million population worldwide. While mutations causing hereditary PAP have been reported, the genetic basis contributing to autoimmune PAP (aPAP) has not been thoroughly investigated. Here, we conducted a genome-wide association study of aPAP in 198 patients and 395 control participants of Japanese ancestry. The common genetic variant, rs138024423 at 6p21, in the major-histocompatibility-complex (MHC) region was significantly associated with disease risk (Odds ratio [OR] = 5.2; P = 2.4 × 10−12). HLA fine-mapping revealed that the common HLA class II allele, HLA-DRB1*08:03, strongly drove this signal (OR = 4.8; P = 4.8 × 10−12), followed by an additional independent risk allele at HLA-DPβ1 amino acid position 8 (OR = 0.28; P = 3.4 × 10−7). HLA-DRB1*08:03 was also associated with an increased level of anti-GM-CSF antibody, a key driver of the disease (β = 0.32; P = 0.035). Our study demonstrated a heritable component of aPAP, suggesting an underlying genetic predisposition toward an abnormal antibody production.

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