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https://www.readbyqxmd.com/read/28424354/less-effective-selection-leads-to-larger-genomes
#1
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 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 datasets. Here, we tested this hypothesis using twenty-two de novo transcriptomes and low-coverage genomes of asellid isopods, which represent eleven 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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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 28, 2017: Peptides
https://www.readbyqxmd.com/read/28360388/transiently-expressed-pattern-during-myogenesis-and-candidate-mirnas-of-tmem8c-in-goose
#9
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
#10
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 27, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28348852/pan-genomic-perspective-on-the-evolution-of-the-staphylococcus-aureus-usa300-epidemic
#11
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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/28202767/genotype-specific-evolution-of-hepatitis-e-virus
#16
Adam B Brayne, Bethany L Dearlove, James S Lester, Sergei L Kosakovsky Pond, Simon D W Frost
Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis globally. HEV comprises four genotypes with different geographic distributions and host ranges. We utilise this natural case-control study for investigating the evolution of zoonotic viruses compared to single host viruses, using 244 near full length HEV genomes. Genome wide estimates of dN/dS located a region of overlapping reading frames, which is subject to positive selection in genotypes 3 and 4. The open reading frames (ORFs) involved have functions related to host-pathogen interaction, so genotype specific evolution of these regions may reflect their fitness...
February 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28166720/increased-rates-of-protein-evolution-and-asymmetric-deceleration-after-the-whole-genome-duplication-in-yeasts
#17
Diana Ascencio, Soledad Ochoa, Luis Delaye, Alexander DeLuna
BACKGROUND: Whole-genome duplication (WGD) events have shaped the genomes of eukaryotic organisms. Relaxed selection after duplication along with inherent functional constraints are thought to determine the fate of the paralogs and, ultimately, the evolution of gene function. Here, we investigated the rate of protein evolution (as measured by dN/dS ratios) before and after the WGD in the hemiascomycete yeasts, and the way in which changes in such rates relate to molecular and biological function...
February 6, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28159865/comparative-transcriptomics-of-malaria-mosquito-testes-function-evolution-and-linkage
#18
Bryan J Cassone, Raissa G G Kay, Matthew P Daugherty, Bradley J White
Testes-biased genes evolve rapidly and are important in the establishment, solidification, and maintenance of reproductive isolation between incipient species. The Anopheles gambiae complex, a group of at least eight isomorphic mosquito species endemic to Sub-Saharan Africa, is an excellent system to explore the evolution of testes-biased genes. Within this group, the testes are an important tissue in the diversification process because hybridization between species results in sterile hybrid males, but fully fertile females...
April 3, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28120868/evidence-for-positive-selection-and-recombination-hotspots-in-deformed-wing-virus-dwv
#19
A Dalmon, C Desbiez, M Coulon, M Thomasson, Y Le Conte, C Alaux, J Vallon, B Moury
Deformed wing virus (DWV) is considered one of the most damaging pests in honey bees since the spread of its vector, Varroa destructor. In this study, we sequenced the whole genomes of two virus isolates and studied the evolutionary forces that act on DWV genomes. The isolate from a Varroa-tolerant bee colony was characterized by three recombination breakpoints between DWV and the closely related Varroa destructor virus-1 (VDV-1), whereas the variant from the colony using conventional Varroa management was similar to the originally described DWV...
January 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28110273/shifting-balance-on-a-static-mutation-selection-landscape-a-novel-scenario-of-positive-selection
#20
Christopher T Jones, Noor Youssef, Edward Susko, Joseph P Bielawski
A version of the mechanistic mutation-selection (MutSel) model that accounts for temporal dynamics at a site is presented. This is used to show that the rate ratio dN/dS at a site can be transiently >1 even when fitness coefficients are fixed or the fitness landscape is static. This occurs whenever a site drifts away from its fitness peak and is then forced back by selection, a process reminiscent of shifting balance. Shifting balance is strongest when the substitution process is not dominated by selection or drift, but admits interplay between the two...
February 1, 2017: Molecular Biology and Evolution
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