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Intron evolution

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https://www.readbyqxmd.com/read/28322435/genomic-changes-following-the-reversal-of-a-y-chromosome-to-an-autosome-in-drosophila-pseudoobscura
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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...
March 3, 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
#7
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-to-porto-pulmonary-hypertension-an-analysis-of-6-cases
#8
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...
February 25, 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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/28222695/evolution-and-expression-of-the-fructokinase-gene-family-in-saccharum
#12
Yihong Chen, Qing Zhang, Weichang Hu, Xingtan Zhang, Liming Wang, Xiuting Hua, Qingyi Yu, Ray Ming, Jisen Zhang
BACKGROUND: Sugarcane is an important sugar crop contributing up to about 80% of the world sugar production. Efforts to characterize the genes involved in sugar metabolism at the molecular level are growing since increasing sugar content is a major goal in the breeding of new sugarcane varieties. Fructokinases (FRK) are the main fructose phosphorylating enzymes with high substrate specificity and affinity. RESULTS: In this study, by combining comparative genomics approaches with BAC resources, seven fructokinase genes were identified in S...
February 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28218276/natural-and-laboratory-mutations-in-kuzbanian-are-associated-with-zinc-stress-phenotypes-in-drosophila-melanogaster
#13
Hung Le Manh, Lain Guio, Miriam Merenciano, Quirze Rovira, Maite G Barrón, Josefa González
Organisms must cope with altered environmental conditions such as high concentrations of heavy metals. Stress response to heavy metals is mediated by the metal-responsive transcription factor 1 (MTF-1), which is conserved from Drosophila to humans. MTF-1 binds to metal response elements (MREs) and changes the expression of target genes. kuzbanian (kuz), a metalloendopeptidase that activates the evolutionary conserved Notch signaling pathway, has been identified as an MTF-1 target gene. We have previously identified a putatively adaptive transposable element in the Drosophila melanogaster genome, named FBti0019170, inserted in a kuz intron...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28209125/the-mitochondrial-genome-sequences-of-the-round-goby-and-the-sand-goby-reveal-patterns-of-recent-evolution-in-gobiid-fish
#14
Irene Adrian-Kalchhauser, Ola Svensson, Verena E Kutschera, Magnus Alm Rosenblad, Martin Pippel, Sylke Winkler, Siegfried Schloissnig, Anders Blomberg, Patricia Burkhardt-Holm
BACKGROUND: Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic sequences. Usually, vertebrate mitochondrial genomes measure between 16.5 and 17 kilobases (kb). RESULTS: During genome sequencing projects for two novel vertebrate models, the invasive round goby and the sand goby, we found that the sand goby genome is exceptionally small (16...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28201983/comparative-analysis-of-the-mitochondrial-genomes-of-colletotrichum-gloeosporioides-sensu-lato-insights-into-the-evolution-of-a-fungal-species-complex-interacting-with-diverse-plants
#15
Xiaofei Liang, Xianglin Tian, Wenkui Liu, Tingyu Wei, Wei Wang, Qiuyue Dong, Bo Wang, Yanan Meng, Rong Zhang, Mark L Gleason, Guangyu Sun
BACKGROUND: The fungal species complex Colletotrichum gloeosporioides sensu lato contains over 20 plant-interacting species. These species exhibit different life styles (e.g., endophytes, foliar and fruit pathogens) and show considerable variation in host and tissue adaptation strategies. Accurate species delimitation in C. gloeosporioides s.l. is very challenging due to nascent lineage boundaries and phenotypic plasticity, which strongly impedes studies of the complex's host-interaction biology...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28196413/alu-derived-alternative-splicing-events-specific-to-macaca-lineages-in-ctsf-gene
#16
Ja-Rang Lee, Sang-Je Park, Young-Hyun Kim, Se-Hee Choe, Hyeon-Mu Cho, Sang-Rae Lee, Sun-Uk Kim, Ji-Su Kim, Bo-Woong Sim, Bong-Seok Song, Kang-Jin Jeong, Youngjeon Lee, Yeung Bae Jin, Philyong Kang, Jae-Won Huh, Kyu-Tae Chang
Cathepsin F, which is encoded by CTSF, is a cysteine proteinase ubiquitously expressed in several tissues. In a previous study, novel transcripts of the CTSF gene were identified in the crab-eating monkey deriving from the integration of an Alu element-AluYRa1. The occurrence of AluYRa1-derived alternative transcripts and the mechanism of exonization events in the CTSF gene of human, rhesus monkey, and crab-eating monkey were investigated using PCR and reverse transcription PCR on the genomic DNA and cDNA isolated from several tissues...
February 2017: Molecules and Cells
https://www.readbyqxmd.com/read/28179182/chloroplast-and-its-phylogenies-to-understand-the-evolutionary-history-of-southern-south-american-azorella-laretia-and-mulinum-azorelloideae-apiaceae
#17
Martina Fernández, Cecilia Ezcurra, Carolina I Calviño
Azorella, Laretia and Mulinum are taxonomically complex, and good candidates to study evolutionary radiations in the Andes and the importance of hybridizations. Previous phylogenetic studies of subfamily Azorelloideae agree that Azorella and Mulinum as currently conceived are not monophyletic, and hence a revision of their circumscription is necessary. However, these phylogenies were based only on chloroplast DNA sequence data. Here, phylogenetic relationships within Azorelloideae were inferred using sequence data from five chloroplast DNA (rps16 intron, trnQ-rps16, rps16-trnK(UUU) 5' -exon, trnG(GCC)-trnS(GCU) and rpL32-trnL(UAG)), and from nuclear rDNA ITS regions to assess the monophyly of Azorella and Mulinum and discuss generic re-circumscriptions, determine hybridization and radiation events, identify and characterize important lineages, and propose hypotheses on evolution of key morphological characters...
March 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28179101/molecular-phylogenomic-study-and-the-role-of-exogenous-spermidine-in-the-metabolic-adjustment-of-endogenous-polyamine-in-two-rice-cultivars-under-salt-stress
#18
Jayita Saha, Kalyan Giri
Compelling evidences anticipated the well acclamation of involvement of exogenous and endogenous polyamines (PAs) in conferring salt tolerance in plants. Intracellular PA's anabolism and catabolism should have contributed to maintain endogenous PAs homeostasis to induce stress signal networks. In this report, the evolutionary study has been conducted to reveal the phylogenetic relationship of genes encoding enzymes of the anabolic and catabolic pathway of PAs among the five plant lineages including green algae, moss, lycophyte, dicot and monocot along with their respective exon-intron structural patterns...
April 20, 2017: Gene
https://www.readbyqxmd.com/read/28178222/complete-chloroplast-genome-of-medicinal-plant-lonicera-japonica-genome-rearrangement-intron-gain-and-loss-and-implications-for-phylogenetic-studies
#19
Liu He, Jun Qian, Xiwen Li, Zhiying Sun, Xiaolan Xu, Shilin Chen
The complete chloroplast (cp) genome of Lonicera japonica, a common ornamental and medicinal plant in North America and East Asia, was sequenced and analyzed. The length of the L. japonica cp genome is 155,078 bp, contains a pair of inverted repeat regions (IRa and IRb), of 23,774 bp each, as well as large (LSC, 88,858 bp) and small (SSC, 18,672 bp) single-copy regions. A total of 129 genes were identified in the cp genome, 16 of which were duplicated within the IR regions. Relative to other plant cp genomes, the L...
February 7, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28174576/comparative-analysis-of-agpase-genes-and-encoded-proteins-in-eight-monocots-and-three-dicots-with-emphasis-on-wheat
#20
Ritu Batra, Gautam Saripalli, Amita Mohan, Saurabh Gupta, Kulvinder S Gill, Pritish K Varadwaj, Harindra S Balyan, Pushpendra K Gupta
ADP-glucose pyrophosphorylase (AGPase) is a heterotetrameric enzyme with two large subunits (LS) and two small subunits (SS). It plays a critical role in starch biosynthesis. We are reporting here detailed structure, function and evolution of the genes encoding the LS and the SS among monocots and dicots. "True" orthologs of maize Sh2 (AGPase LS) and Bt2 (AGPase SS) were identified in seven other monocots and three dicots; structure of the enzyme at protein level was also studied. Novel findings of the current study include the following: (i) at the DNA level, the genes controlling the SS are more conserved than those controlling the LS; the variation in both is mainly due to intron number, intron length and intron phase distribution; (ii) at protein level, the SS genes are more conserved relative to those for LS; (iii) "QTCL" motif present in SS showed evolutionary differences in AGPase belonging to wheat 7BS, T...
2017: Frontiers in Plant Science
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