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https://www.readbyqxmd.com/read/28438387/structural-insights-into-the-mechanism-of-group-ii-intron-splicing
#1
REVIEW
Chen Zhao, Anna Marie Pyle
While the major architectural features and active-site components of group II introns have been known for almost a decade, information on the individual stages of splicing has been lacking. Recent advances in crystallography and cryo-electron microscopy (cryo-EM) have provided major new insights into the structure of intact lariat introns. Conformational changes that mediate the steps of splicing and retrotransposition are being elucidated, revealing the dynamic, highly coordinated motions that are required for group II intron activity...
April 21, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28419974/prediction-and-feature-analysis-of-intron-retention-events-in-plant-genome
#2
Ying Cui, Chao Zhang, Meng Cai
Alternative splicing (AS) is a major contributor to increase the potential informational content of eukaryotic genomes by creating multiple mRNA species and proteins from a single gene. In plants, up to 60% genes are alternatively spliced and the most common type of AS is intron retention (IR). Genomic analyses of IR have illuminated its crucial role in shaping the evolution of genomes, in the control of developmental processes, and in the dynamic regulation of the transcriptome to influence phenotype. To explore the relationship between the sequence feature and the formation mechanism of IR, we statistically analyzed the retained introns and proposed an improved random forest-based hybrid method to predict intron retention events in plant genome...
April 13, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28412535/complex-biogeographic-scenarios-revealed-in-the-diversification-of-the-largest-woodpecker-radiation-in-the-new-world
#3
Adolfo G Navarro-Sigüenza, Hernán Vázquez-Miranda, Germán Hernández-Alonso, Erick A García-Trejo, Luis A Sánchez-González
Phylogenetic relationships and patterns of evolution within Melanerpes, one of the most diverse groups of New World woodpeckers (22-23 lineages), have been complicated due to complex plumages and morphological adaptations. In an attempt to resolve these issues, we obtained sequence data from four nuclear introns and two mitochondrial protein-coding genes for 22 of the 24 currently recognized species in the genus. We performed phylogenetic analyses involving Maximum Likelihood and Bayesian Inference, species-tree divergence dating, and biogeographic reconstructions...
April 12, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28411162/insights-into-evolution-in-andean-polystichum-dryopteridaceae-from-expanded-understanding-of-the-cytosolic-phosphoglucose-isomerase-gene
#4
Brendan M Lyons, Monique A McHenry, David S Barrington
Cytosolic phosphoglucose isomerase (pgiC) is an enzyme essential to glycolysis found universally in eukaryotes, but broad understanding of variation in the gene coding for pgiC is lacking for ferns. We used a substantially expanded representation of the gene for Andean species of the fern genus Polystichum to characterize pgiC in ferns relative to angiosperms, insects, and an amoebozoan; assess the impact of selection versus neutral evolutionary processes on pgiC; and explore evolutionary relationships of selected Andean species...
April 11, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28389432/topological-and-thermodynamic-factors-that-influence-the-evolution-of-small-networks-of-catalytic-rna-species
#5
Jessica A M Yeates, Philippe Nghe, Niles Lehman
RNA-directed recombination reaction can result in a network of interacting RNA species. It is now becoming increasingly apparent that such networks would have been an important feature of the RNA world during the nascent evolution of life on the Earth. But the means by which such small RNA networks assimilate other available genotypes in the environment to grow and evolve into the more complex networks that are thought to have existed in the prebiotic milieu are not known. Here, we used the ability of fragments of the Azoarcus group I intron ribozyme to covalently self assemble via genotype-selfish and genotype-cooperative interactions into full-length ribozymes to investigate the dynamics of small (3- and 4-membered) networks...
April 7, 2017: RNA
https://www.readbyqxmd.com/read/28367378/assembly-and-comparative-analysis-of-complete-mitochondrial-genome-sequence-of-an-economic-plant-salix-suchowensis
#6
Ning Ye, Xuelin Wang, Juan Li, Changwei Bi, Yiqing Xu, Dongyang Wu, Qiaolin Ye
Willow is a widely used dioecious woody plant of Salicaceae family in China. Due to their high biomass yields, willows are promising sources for bioenergy crops. In this study, we assembled the complete mitochondrial (mt) genome sequence of S. suchowensis with the length of 644,437 bp using Roche-454 GS FLX Titanium sequencing technologies. Base composition of the S. suchowensis mt genome is A (27.43%), T (27.59%), C (22.34%), and G (22.64%), which shows a prevalent GC content with that of other angiosperms...
2017: PeerJ
https://www.readbyqxmd.com/read/28367152/genome-wide-identification-evolution-and-expression-analysis-of-the-atp-binding-cassette-transporter-gene-family-in-brassica-rapa
#7
Chao Yan, Weike Duan, Shanwu Lyu, Ying Li, Xilin Hou
ATP-binding cassette (ABC) proteins can act as transporters of different substrates across biological membranes by hydrolyzing ATP. However, little information is available about ABC transporters in Brassica rapa, an important leafy vegetable. In the present study, we carried out genome-wide identification, characterization and molecular evolution analyses of ABC gene family in B. rapa and 9 other plant species. A total of 179 B. rapa ABC genes (BraABCs) were identified. Among them, 173 BraABCs were identified on 10 chromosomes...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28344992/mechanism-of-deletion-removing-all-dystrophin-exons-in-a-canine-model-for-dmd-implicates-concerted-evolution-of-x-chromosome-pseudogenes
#8
D Jake VanBelzen, Alock S Malik, Paula S Henthorn, Joe N Kornegay, Hansell H Stedman
Duchenne muscular dystrophy (DMD) is a lethal, X-linked, muscle-wasting disorder caused by mutations in the large, 2.4-Mb dystrophin gene. The majority of DMD-causing mutations are sporadic, multi-exon, frameshifting deletions, with the potential for variable immunological tolerance to the dystrophin protein from patient to patient. While systemic gene therapy holds promise in the treatment of DMD, immune responses to vectors and transgenes must first be rigorously evaluated in informative preclinical models to ensure patient safety...
March 17, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28341884/mitochondrial-genome-of-the-nematode-endoparasitic-fungus-hirsutella-vermicola-reveals-a-high-level-of-synteny-in-the-family-ophiocordycipitaceae
#9
Yong-Jie Zhang, Hong-Yue Zhang, Xing-Zhong Liu, Shu Zhang
Ophiocordycipitaceae is a diverse fungal family comprising multiple ecologically, economically, medicinally, and culturally important fungal species; however, only four species of the family have available mitochondrial genomes (mitogenomes). In this study, the complete mitogenome of the nematode endoparasitic fungus Hirsutella vermicola in Ophiocordycipitaceae was sequenced, and a comparative mitogenomic analysis of Ophiocordycipitaceae was performed. We found that the 53,793-bp circular mitogenome of H. vermicola, except for standard fungal mitochondrial genes, harbors seven introns acquired possibly through lateral transfer from other fungi and three free-standing open reading frames (ORFs) coding for hypothetical proteins...
April 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28322435/genomic-changes-following-the-reversal-of-a-y-chromosome-to-an-autosome-in-drosophila-pseudoobscura
#10
Ching-Ho Chang, Amanda M Larracuente
Robertsonian translocations resulting in fusions between sex chromosomes and autosomes shape karyotype evolution by creating new sex chromosomes from autosomes. These translocations can also reverse sex chromosomes back into autosomes, which is especially intriguing given the dramatic differences between autosomes and sex chromosomes. To study the genomic events following a Y chromosome reversal, we investigated an autosome-Y translocation in Drosophila pseudoobscura. The ancestral Y chromosome fused to a small autosome (the dot chromosome) approximately 10-15 Mya...
March 21, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28320321/evolution-of-group-i-introns-in-porifera-new-evidence-for-intron-mobility-and-implications-for-dna-barcoding
#11
Astrid Schuster, Jose V Lopez, Leontine E Becking, Michelle Kelly, Shirley A Pomponi, Gert Wörheide, Dirk Erpenbeck, Paco Cárdenas
BACKGROUND: Mitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarians, placozoans and one annelid species. Within demosponges, group I and group II introns are present in six families. Based on different insertion sites within the cox1 gene and secondary structures, four types of group I and two types of group II introns are known, which can harbor up to three encoding homing endonuclease genes (HEG) of the LAGLIDADG family (group I) and/or reverse transcriptase (group II)...
March 20, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28288944/evolutionary-and-domestication-history-of-cucurbita-pumpkin-and-squash-species-inferred-from-44-nuclear-loci
#12
Heather R Kates, Pamela S Soltis, Douglas E Soltis
Phylogenetics can facilitate the study of plant domestication by resolving sister relationships between crops and their wild relatives, thereby identifying the ancestors of cultivated plants. Previous phylogenetic studies of the six Cucurbita crop lineages (pumpkins and squashes) and their wild relatives suggest histories of deep coalescence that complicate uncovering the genetic origins of the six crop taxa. We investigated the evolution of wild and domesticated Cucurbita using the most comprehensive and robust molecular-based phylogeny for Cucurbita to date based on 44 loci derived from introns of single-copy nuclear genes...
March 10, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28261921/divergence-of-annual-and-perennial-species-in-the-brassicaceae-and-the-contribution-of-cis-acting-variation-at-flc-orthologues
#13
C Kiefer, E Severing, R Karl, S Bergonzi, M Koch, A Tresch, G Coupland
Variation in life history contributes to reproductive success in different environments. Divergence of annual and perennial angiosperm species is an extreme example that has occurred frequently. Perennials survive for several years and restrict the duration of reproduction by cycling between vegetative growth and flowering, whereas annuals live for one year and flower once. We used the tribe Arabideae (Brassicaceae) to study the divergence of seasonal flowering behavior among annual and perennial species. In perennial Brassicaceae, orthologues of FLOWERING LOCUS C (FLC), a floral inhibitor in Arabidopsis thaliana, are repressed by winter cold and reactivated in spring conferring seasonal flowering patterns, whereas in annuals they are stably repressed by cold...
March 6, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28261262/the-evolutionary-relationship-between-alternative-splicing-and-gene-duplication
#14
REVIEW
Luis P Iñiguez, Georgina Hernández
The protein diversity that exists today has resulted from various evolutionary processes. It is well known that gene duplication (GD) along with the accumulation of mutations are responsible, among other factors, for an increase in the number of different proteins. The gene structure in eukaryotes requires the removal of non-coding sequences, introns, to produce mature mRNAs. This process, known as cis-splicing, referred to here as splicing, is regulated by several factors which can lead to numerous splicing arrangements, commonly designated as alternative splicing (AS)...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28258369/the-alternative-splicing-of-eam8-contributes-to-early-flowering-and-short-season-adaptation-in-a-landrace-barley-from-the-qinghai-tibetan-plateau
#15
Tengfei Xia, Lianquan Zhang, Jinqing Xu, Lei Wang, Baolong Liu, Ming Hao, Xi Chang, Tangwei Zhang, Shiming Li, Huaigang Zhang, Dengcai Liu, Yuhu Shen
The early flowering of Lalu was determined to be due to a novel spontaneous eam8 mutation, which resulted in intron retention and the formation of a putative truncated protein. Barley is a staple crop grown over an extensive area in the Qinghai-Tibetan Plateau. Understanding the genetic mechanism for its success in a high altitude is important for crop improvement in marginal environments. Early flowering is a critical adaptive trait that strongly influences reproductive fitness in a short growing season. Loss-of-function mutations at the circadian clock gene EARLY MATURITY 8 (EAM8) promote rapid flowering...
April 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28257744/twenty-year-follow-up-of-a-familial-case-of-pth1r-associated-primary-failure-of-tooth-eruption
#16
Cláudia Misue Kanno, José Américo de Oliveira, José Fernando Garcia, Helmut Roth, Bernhard H F Weber
INTRODUCTION: Nonsyndromic primary failure of eruption (PFE) is a rare autosomal dominant disorder of dental eruption with no obvious dental or soft tissue interference. The purposes of this study were to genetically and clinically characterize a family with many members affected by PFE and to describe the natural evolution of the disorder. METHODS: Three generations of a family with 18 members, 10 of them clinically affected by PFE, were evaluated periodically during 20 years of clinical follow-up...
March 2017: American Journal of Orthodontics and Dentofacial Orthopedics
https://www.readbyqxmd.com/read/28245912/mutational-screening-in-genes-related-with-porto-pulmonary-hypertension-an-analysis-of-6-cases
#17
Guillermo Pousada, Adolfo Baloira, Diana Valverde
INTRODUCTION: Portopulmonary hypertension (PPH) is a rare disease with a low incidence and without a clearly-identified genetic component. The aim of this work was to check genes and genetic modifiers related to pulmonary arterial hypertension in patients with PPH in order to clarify the molecular basis of the pathology. PATIENTS: We selected a total of 6 patients with PPH and amplified the exonic regions and intronic flanking regions of the relevant genes and regions of interest of the genetic modifiers...
April 7, 2017: Medicina Clínica
https://www.readbyqxmd.com/read/28242298/the-alu-neurodegeneration-hypothesis-a-primate-specific-mechanism-for-neuronal-transcription-noise-mitochondrial-dysfunction-and%C3%A2-manifestation-of-neurodegenerative-disease
#18
Peter A Larsen, Michael W Lutz, Kelsie E Hunnicutt, Mirta Mihovilovic, Ann M Saunders, Anne D Yoder, Allen D Roses
It is hypothesized that retrotransposons have played a fundamental role in primate evolution and that enhanced neurologic retrotransposon activity in humans may underlie the origin of higher cognitive function. As a potential consequence of this enhanced activity, it is likely that neurons are susceptible to deleterious retrotransposon pathways that can disrupt mitochondrial function. An example is observed in the TOMM40 gene, encoding a β-barrel protein critical for mitochondrial preprotein transport. Primate-specific Alu retrotransposons have repeatedly inserted into TOMM40 introns, and at least one variant associated with late-onset Alzheimer's disease originated from an Alu insertion event...
February 24, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/28235826/a-new-reference-genome-assembly-for-the-microcrustacean-daphnia-pulex
#19
Zhiqiang Ye, Sen Xu, Ken Spitze, Jana Asselman, Xiaoqian Jiang, Matthew S Ackerman, Jacqueline Lopez, Brent Harker, R Taylor Raborn, W Kelley Thomas, Jordan Ramsdell, Michael E Pfrender, Michael Lynch
Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high-quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino-acid sequence identity of 98...
February 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28231507/the-phytochelatin-synthase-gene-in-date-palm-phoenix-dactylifera-l-phylogeny-evolution-and-expression
#20
Chaâbene Zayneb, Rekik Hakim Imen, Kriaa Walid, C Douglas Grubb, Khemakhem Bassem, Vandenbulcke Franck, Mejdoub Hafedh, Elleuch Amine
We studied date palm phytochelatin synthase type I (PdPCS1), which catalyzes the cytosolic synthesis of phytochelatins (PCs), a heavy metal binding protein, in plant cells. The gene encoding PdPCS1 (Pdpcs) consists of 8 exons and 7 introns and encodes a protein of 528 amino acids. PCs gene history was studied using Notung phylogeny. During evolution, gene loss from several lineages was predicted including Proteobacteria, Bilateria and Brassicaceae. In addition, eleven gene duplication events appeared toward interior nodes of the reconciled tree and four gene duplication events appeared toward the external nodes...
February 20, 2017: Ecotoxicology and Environmental Safety
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