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https://www.readbyqxmd.com/read/28533181/comparative-genome-analysis-of-lactobacillus-plantarum-gb-lp3-provides-candidates-of-survival-related-genetic-factors
#1
Soomin Jeon, Jaehoon Jung, Kwondo Kim, DongAhn Yoo, Chanho Lee, Jungsun Kang, Kyungjin Cho, Dae-Kyung Kang, Woori Kwak, Sook Hee Yoon, Heebal Kim, Seoae Cho
Lactobacillus plantarum is found in various environmental niches such as in the gastrointestinal tract of an animal host or a fermented food. This species isolated from a certain environment is known to possess a variety of properties according to inhabited environment's adaptation. However, a causal relationship of a genetic factor and phenotype affected by a specific environment has not been systematically comprehended. L. plantarum GB-LP3 strain was isolated from Korean traditional fermented vegetable and the whole genome of GB-LP3 was sequenced...
May 19, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28529468/contrasting-patterns-of-nucleotide-polymorphism-suggest-different-selective-regimes-within-different-parts-of-the-pgic1-gene-in-festuca-ovina-l
#2
Yuan Li, Bengt Hansson, Lena Ghatnekar, Honor C Prentice
BACKGROUND: Phosphoglucose isomerase (PGI, EC 5.3.1.9) is an essential metabolic enzyme in all eukaryotes. An earlier study of the PgiC1 gene, which encodes cytosolic PGI in the grass Festuca ovina L., revealed a marked difference in the levels of nucleotide polymorphism between the 5' and 3' portions of the gene. METHODS: In the present study, we characterized the sequence polymorphism in F. ovina PgiC1 in more detail and examined possible explanations for the non-uniform pattern of nucleotide polymorphism across the gene...
2017: Hereditas
https://www.readbyqxmd.com/read/28484686/impact-of-pe_pgrs33-gene-polymorphisms-on-mycobacterium-tuberculosis-infection-and-pathogenesis
#3
Serena Camassa, Ivana Palucci, Raffaella Iantomasi, Tiziana Cubeddu, Mariachiara Minerva, Flavio De Maio, Samuel Jouny, Elisa Petruccioli, Delia Goletti, Francesco Ria, Michela Sali, Maurizio Sanguinetti, Riccardo Manganelli, Stefano Rocca, Priscille Brodin, Giovanni Delogu
PE_PGRS33 is a surface-exposed protein of Mycobacterium tuberculosis (Mtb) which exerts its role in macrophages entry and immunomodulation. In this study, we aimed to investigate the polymorphisms in the pe_pgrs33 gene of Mtb clinical isolates and evaluate their impact on protein functions. We sequenced pe_pgrs33 in a collection of 135 clinical strains, genotyped by 15-loci MIRU-VNTR and spoligotyping and belonging to the Mtb complex (MTBC). Overall, an association between pe_pgrs33 alleles and MTBC genotypes was observed and a dN/dS ratio of 0...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28466060/population-genetic-analysis-of-potato-virus-x-based-on-the-cp-gene-sequence
#4
Mohammad Hajizadeh, Nemat Sokhandan-Bashir
To investigate the genetic variation and molecular evolution of potato virus X (PVX), 87 coat protein (CP) gene sequences were retrieved from GenBank and analyzed. Of the PVX isolates studied, one recombinant isolate (X3) was detected from South America population of the virus. The other isolates belonged to two lineages, Eurasia and America, with the significant FST value (0.60). Non-synonymous nucleotide diversity to synonymous nucleotide diversity (ω = dN/dS) was less than 1 indicating that the CP gene has been under negative selection or neutral evolution...
March 2017: Virusdisease
https://www.readbyqxmd.com/read/28454644/genetic-diversity-of-immune-related-antigens-in-region-of-difference-2-of-mycobacterium-tuberculosis-strains
#5
Yi Jiang, Haican Liu, Xuezhi Wang, Shiqi Xiao, Machao Li, Guilian Li, Lili Zhao, Xiuqin Zhao, Xiangfeng Dou, Kanglin Wan
Region of Difference 2 (RD2) was lost during the ongoing propagation of BCG between 1927 and 1931, a time that coincides with reports of the ongoing attenuation of the vaccine. Some data demonstrate that RD2 plays a role in mycobacterial virulence, and that its deletion from Mycobacterium tuberculosis leads to a decrease in bacterial growth in both a macrophage and a murine model. Human T-cell epitopes of M. tuberculosis are evolutionarily hyperconserved and thus it was deduced that M. tuberculosis lacks antigenic variation and immune evasion...
May 2017: Tuberculosis
https://www.readbyqxmd.com/read/28424354/less-effective-selection-leads-to-larger-genomes
#6
Tristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen, Michèle Weiss-Gayet, Andaine Seguin-Orlando, Luca Ermini, Clio Der Sarkissian, N Pierre Charrier, David Eme, Florian Mermillod-Blondin, Laurent Duret, Cristina Vieira, Ludovic Orlando, Christophe Jean Douady
The evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. However, this hypothesis has proved difficult to investigate using empirical data sets. Here, we tested this hypothesis using 22 de novo transcriptomes and low-coverage genomes of asellid isopods, which represent 11 independent habitat shifts from surface water to resource-poor groundwater...
April 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28423875/adaptive-selection-at-agouti-gene-inferred-breed-specific-selection-signature-within-the-indigenous-goat-populations
#7
Hafiz Ishfaq Ahmad, Guiqiong Liu, Xunping Jiang, Chenhui Liu, Xu Fangzheng, Yuqing Chong, Nabeel Ijaz, Huang Huarong
Objective: The aim of this study was to calculate selection signatures at possible loci leading to population differentiation, as well as pattern of selection of agouti gene within the local goat breeds and its correlation among other animal species to reveal molecular evolution. Methods: The high Fst outlier method corresponding to Fst distribution was used to identify the loci subject to positive selection. According to the empirical distribution of Fst estimates, we selected the SNPs having high Fst outlier corresponded to the upper 1% of the distribution as the loci under selection...
April 19, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28397003/plastome-wide-nucleotide-substitution-rates-reveal-accelerated-rates-in-papilionoideae-and-correlations-with-genome-features-across-legume-subfamilies
#8
Erika N Schwarz, Tracey A Ruhlman, Mao-Lun Weng, Mohammad A Khiyami, Jamal S M Sabir, Nahid H Hajarah, Njud S Alharbi, Samar O Rabah, Robert K Jansen
This study represents the most comprehensive plastome-wide comparison of nucleotide substitution rates across the three subfamilies of Fabaceae: Caesalpinioideae, Mimosoideae, and Papilionoideae. Caesalpinioid and mimosoid legumes have large, unrearranged plastomes compared with papilionoids, which exhibit varying levels of rearrangement including the loss of the inverted repeat (IR) in the IR-lacking clade (IRLC). Using 71 genes common to 39 legume taxa representing all the three subfamilies, we show that papilionoids consistently have higher nucleotide substitution rates than caesalpinioids and mimosoids, and rates in the IRLC papilionoids are generally higher than those in the IR-containing papilionoids...
April 10, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28387863/neutral-genetic-processes-influence-mhc-evolution-in-threatened-gopher-tortoises-gopherus-polyphemus
#9
Jean P Elbers, Rachel W Clostio, Sabrina S Taylor
Levels of adaptive genetic variation influence how species deal with environmental and ecological change, but these levels are frequently inferred using neutral genetic markers. Major histocompatibility complex (MHC) genes play a key role in the adaptive branch of the immune system and have been used extensively to estimate levels of adaptive genetic variation. Parts of the peptide binding region, sites where MHC molecules directly interact with pathogen and self-proteins, were sequenced from a MHC class I (95/441 tortoises) and class II (245/441 tortoises) gene in threatened and non-threatened populations of gopher tortoises (Gopherus polyphemus), and adaptive genetic variation at MHC genes was compared to neutral genetic variation derived from 10 microsatellite loci (441 tortoises)...
April 6, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28386078/evolution-of-full-length-genomes-of-hbv-quasispecies-in-sera-of-patients-with-a-coexistence-of-hbsag-and-anti-hbs-antibodies
#10
Tai-Cheng Zhou, Xiao Li, Long Li, Xiao-Fei Li, Liang Zhang, Jia Wei
Although the evolutionary changes of viral quasispecies are correlated to the pathological status of a disease, little is known in the coexistence of hepatitis B surface antigen (HBsAg) and antibodies to these antigens (anti-HBs). To examine evolutionary changes in hepatitis B virus (HBV) and their relationship to the coexistence of HBsAg and anti-HBs antibodies, HBV genomes in patients with a coexistence of HBsAg and anti-HBs antibodies (experimental group) and HBsAg positive without anti-HBs (control group) were assessed...
April 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28384231/the-mitochondrial-genome-of-pin-tailed-snipe-gallinago-stenura-and-its-implications-for-the-phylogeny-of-charadriiformes
#11
Chaochao Hu, Chenling Zhang, Lei Sun, Yi Zhang, Wenli Xie, Baowei Zhang, Qing Chang
The Charadriiformes, among the most diverse orders of bird, is a good source to research on evolution. The mitochondrial genome sequencing database has rapidly increased in recent years, while Charadriiformes mitogenome has not been well studied. In this research, we determined the complete mitogenome sequence of Gallinago stenura, and comparatively analysed 20 mitogenomes of Charadriiformes. The mitogenomes display moderate size variation, and most of variation due to mutations in the control region. In 13 protein-coding genes, we found: 1...
2017: PloS One
https://www.readbyqxmd.com/read/28379613/signals-of-selection-in-conditionally-expressed-genes-in-the-diversification-of-three-horned-beetle-species
#12
Melissa H Pespeni, Jason T Ladner, Armin P Moczek
Species radiations may be facilitated by phenotypic differentiation already present within populations, such as those arising through sex-specific development or developmental processes biased toward particular reproductive or trophic morphs. We sought to test this hypothesis by utilizing a comparative transcriptomic approach to contrast among and within-species differentiation using three horned beetle species in the genus Onthophagus. These three species exhibit differences along three phenotypic axes reflective of much of the interspecific diversity present within the genus: horn location, polarity of sexual dimorphism, and degree of nutritional sensitivity...
April 5, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28363794/adaptive-evolution-of-insect-selective-excitatory-%C3%AE-type-sodium-channel-neurotoxins-from-scorpion-venom
#13
Wenlan Wu, Zhongjie Li, Yibao Ma
Insect selective excitatory β-type sodium channel neurotoxins from scorpion venom (β-NaScTxs) are composed of about 70-76 amino acid residues and share a common scaffold stabilized by four unique disulfide bonds. The phylogenetic analysis of these toxins was hindered by limited sequence data. In our recent study, two new insect selective excitatory β-NaScTxs, LmIT and ImIT, were isolated from Lychas mucronatus and Isometrus maculatus, respectively. With the sequences previously reported, we examined the adaptive molecular evolution of insect selective excitatory β-NaScTxs by estimating the nonsynonymous-to-synonymous rate ratio (ω=dN/dS)...
March 29, 2017: Peptides
https://www.readbyqxmd.com/read/28360388/transiently-expressed-pattern-during-myogenesis-and-candidate-mirnas-of-tmem8c-in-goose
#14
Ke He, Ting Ren, Songhui Zhu, Shiri Liang, Ayong Zhao
Transmembrane protein 8C (Tmem8C) is a muscle-specific membrane protein that controls myoblast fusion, which is essential for the formation of multinucleated muscle fibres. As most of the birds can fly, they have enormous requirement for the muscle, but there are only a few studies of Tmem8C in birds. In this study, we obtained the coding sequence (CDS) of Tmem8C in goose, predicted miRNAs that can act on the 3'UTR, analysed expression profiles of this gene in breast and leg muscles (BM and LM) during the embryonic period and neonatal stages, and identified miRNAs that might affect the targeted gene...
March 2017: Journal of Genetics
https://www.readbyqxmd.com/read/28359808/asymmetrically-reduced-expression-of-hand1-homeologs-involving-a-single-nucleotide-substitution-in-a-cis-regulatory-element
#15
Haruki Ochi, Nanoka Suzuki, Akane Kawaguchi, Hajime Ogino
During vertebrate evolution, whole genome duplications resulted in a number of duplicated genes, some of which eventually changed their expression patterns and/or levels via alteration of cis-regulatory sequences. However, the initial process involved in such cis-regulatory changes remains unclear. Therefore, we investigated this process by analyzing the duplicated hand1 genes of Xenopus laevis (hand1.L and hand1.S), which were generated by allotetraploidization 17-18 million years ago, and compared these with their single ortholog in the ancestral-type diploid species X...
March 28, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28348852/pan-genomic-perspective-on-the-evolution-of-the-staphylococcus-aureus-usa300-epidemic
#16
Dorota M Jamrozy, Simon R Harris, Naglaa Mohamed, Sharon J Peacock, Charles Y Tan, Julian Parkhill, Annaliesa S Anderson, Matthew T G Holden
Staphylococcus aureus USA300 represents the dominant community-associated methicillin-resistant S. aureus lineage in the USA, where it is a major cause of skin and soft tissue infections. Previous comparative genomic studies have described the population structure and evolution of USA300 based on geographically restricted isolate collections. Here, we investigated the USA300 population by sequencing genomes of a geographically distributed panel of 191 clinical S. aureus isolates belonging to clonal complex 8 (CC8), derived from the Tigecycline Evaluation and Surveillance Trial program...
May 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28338965/burrowers-from-the-past-mitochondrial-signatures-of-ordovician-bivalve-infaunalization
#17
Federico Plazzi, Guglielmo Puccio, Marco Passamonti
Bivalves and gastropods are the two largest classes of extant molluscs. Despite sharing a huge number of features, they do not share a key ecological one: gastropods are essentially epibenthic, while most bivalves are infaunal. However, this is not the ancestral bivalve condition; Cambrian forms were surface crawlers and only during the Ordovician a fundamental infaunalization process took place, leading to bivalves as we currently know them. This major ecological shift is linked to the exposure to a different redox environoments (hypoxic or anoxic) and with the Lower Devonian oxygenation event...
March 9, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28331594/the-first-complete-mitogenome-of-the-south-china-deep-sea-giant-isopod-bathynomus-sp-crustacea-isopoda-cirolanidae-allows-insights-into-the-early-mitogenomic-evolution-of-isopods
#18
Yanjun Shen, Qi Kou, Zaixuan Zhong, Xinzheng Li, Lisheng He, Shunping He, Xiaoni Gan
In this study, the complete mitochondrial (mt) genome sequence of the South China deep-sea giant isopod Bathynomus sp. was determined, and this study is the first to explore in detail the mt genome of a deep-sea member of the order Isopoda. This species belongs to the genus Bathynomus, the members of which are saprophagous residents of the deep-sea benthic environment; based on their large size, Bathynomus is included in the "supergiant group" of isopods. The mt genome of Bathynomus sp. is 14,965 bp in length and consists of 13 protein-coding genes, two ribosomal RNA genes, only 18 transfer RNA genes, and a noncoding control region 362 bp in length, which is the smallest control region discovered in Isopoda to date...
March 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28288365/dexd-h-box-rna-helicase-genes-are-differentially-expressed-between-males-and-females-during-the-critical-period-of-male-sex-differentiation-in-channel-catfish
#19
Changxu Tian, Suxu Tan, Lisui Bao, Qifan Zeng, Shikai Liu, Yujia Yang, Xiaoxiao Zhong, Zhanjiang Liu
DExD/H-box RNA helicases are motor proteins participating in nearly all aspects of cellular processes, especially in RNA metabolism. In this study, a total of 54 DExD/H-box RNA helicase genes including 37 DDX (DEAD-box) and 17 DHX (DEAH-box) genes were characterized in channel catfish (Ictalurus punctatus), and annotated through phylogenetic and syntenic analyses. All the catfish RNA helicases contained conserved helicase signature motifs, demonstrating that the RNA helicase gene family was highly conserved...
March 1, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28209761/genetic-adaptation-of-schizothoracine-fish-to-the-phased-uplifting-of-the-qinghai-tibetan-plateau
#20
Dongsheng Zhang, Mengchao Yu, Peng Hu, Sihua Peng, Yimeng Liu, Weiwen Li, Congcong Wang, Shunping He, Wanying Zhai, Qianghua Xu, Liangbiao Chen
Many species of Schizothoracine, a subfamily of Cyprinidae, are highly endemic to the Qinghai-Tibetan Plateau (QTP). To characterize the adaptive changes associated with the Schizothoracine expansion at high altitudes, we sequenced tissue transcriptomes of two highland and two subhighland Schizothoracines and analyzed gene evolution patterns by comparing with lowland cyprinids. Phylogenetic tree reconstruction and divergence time estimation indicated that the common ancestor of Schizothoracine fish lived ∼32...
April 3, 2017: G3: Genes—Genomes—Genetics
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