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Intron evolution

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https://www.readbyqxmd.com/read/29351555/omega-3-fatty-acid-desaturase-gene-family-from-two-%C3%AF-3-sources-salvia-hispanica-and-perilla-frutescens-cloning-characterization-and-expression
#1
Yufei Xue, Baojun Chen, Aung Naing Win, Chun Fu, Jianping Lian, Xue Liu, Rui Wang, Xingcui Zhang, Yourong Chai
Omega-3 fatty acid desaturase (ω-3 FAD, D15D) is a key enzyme for α-linolenic acid (ALA) biosynthesis. Both chia (Salvia hispanica) and perilla (Perilla frutescens) contain high levels of ALA in seeds. In this study, the ω-3 FAD gene family was systematically and comparatively cloned from chia and perilla. Perilla FAD3, FAD7, FAD8 and chia FAD7 are encoded by single-copy (but heterozygous) genes, while chia FAD3 is encoded by 2 distinct genes. Only 1 chia FAD8 sequence was isolated. In these genes, there are 1 to 6 transcription start sites, 1 to 8 poly(A) tailing sites, and 7 introns...
2018: PloS One
https://www.readbyqxmd.com/read/29340223/yabby3-orthologous-genes-in-wild-tomato-species-structure-variability-and-expression
#2
M A Filyushin, M A Slugina, A V Shchennikova, E Z Kochieva
Evolution of the genes encoding YABBY transcription factors is believed to be one of the key reasons for flat leaf emergence from the radially symmetrical stem and gynoecium diversity. YABBY genes determine the identity of the abaxial surface of all aboveground lateral organs in seed plants. In the present study, complete sequences of YABBY3-orthologous genes were identified and characterized in 13 accessions of cultivated and wild tomato species with diverse morphophysiology of leaves, flowers, and fruits...
October 2017: Acta Naturae
https://www.readbyqxmd.com/read/29324689/characterization-of-translationally-controlled-tumour-protein-from-the-sea-anemone-anemonia-viridis-and-transcriptome-wide-identification-of-cnidarian-homologues
#3
Aldo Nicosia, Carmelo Bennici, Girolama Biondo, Salvatore Costa, Marilena Di Natale, Tiziana Masullo, Calogera Monastero, Maria Antonietta Ragusa, Marcello Tagliavia, Angela Cuttitta
Gene family encoding translationally controlled tumour protein (TCTP) is defined as highly conserved among organisms; however, there is limited knowledge of non-bilateria. In this study, the first TCTP homologue from anthozoan was characterised in the Mediterranean Sea anemone, Anemonia viridis. The release of the genome sequence of Acropora digitifera, Exaiptasia pallida, Nematostella vectensis and Hydra vulgaris enabled a comprehensive study of the molecular evolution of TCTP family among cnidarians. A comparison among TCTP members from Cnidaria and Bilateria showed conserved intron exon organization, evolutionary conserved TCTP signatures and 3D protein structure...
January 11, 2018: Genes
https://www.readbyqxmd.com/read/29304483/genome-wide-identification-of-phd-finger-genes-and-expression-pattern-analysis-under-various-treatments-in-moso-bamboo-phyllostachys-edulis
#4
Yameng Gao, Huanlong Liu, Yujiao Wang, Fei Li, Yan Xiang
Plant homeodomain (PHD)-finger proteins are a class of important zinc-finger transcription factors responsible for regulating transcription and the chromatin state and responsive to various stresses. The family genes have been reported in many plants, but there is little information about PHD-finger genes in moso bamboo. In this study, 60 PHD-finger genes (PePHD1-60) were identified in moso bamboo and classified into 11 subfamilies (A-K) based on phylogenetic analysis. Gene structure and conserved motif analysis showed that these genes contained different numbers of introns but had similar motif organizations within each subfamily...
December 26, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29304093/the-genomes-of-crithidia-bombi-and-c-expoeki-common-parasites-of-bumblebees
#5
Paul Schmid-Hempel, Markus Aebi, Seth Barribeau, Toshihiko Kitajima, Louis du Plessis, Regula Schmid-Hempel, Stefan Zoller
Trypanosomatids (Trypanosomatidae, Kinetoplastida) are flagellated protozoa containing many parasites of medical or agricultural importance. Among those, Crithidia bombi and C. expoeki, are common parasites in bumble bees around the world, and phylogenetically close to Leishmania and Leptomonas. They have a simple and direct life cycle with one host, and partially castrate the founding queens greatly reducing their fitness. Here, we report the nuclear genome sequences of one clone of each species, extracted from a field-collected infection...
2018: PloS One
https://www.readbyqxmd.com/read/29247163/conserved-molecular-structure-of-the-centromeric-histone-cenh3-in-secale-and-its-phylogenetic-relationships
#6
E V Evtushenko, E A Elisafenko, S S Gatzkaya, Y A Lipikhina, A Houben, A V Vershinin
It has been repeatedly demonstrated that the centromere-specific histone H3 (CENH3), a key component of the centromere, shows considerable variability between species within taxa. We determined the molecular structure and phylogenetic relationships of CENH3 in 11 Secale species and subspecies that possess distinct pollination systems and are adapted to a wide range of abiotic and biotic stresses. The rye (Secale cereale) genome encodes two paralogous CENH3 genes, which differ in intron-exon structure and are transcribed into two main forms of the protein, αCENH3 and βCENH3...
December 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29228267/the-effects-of-sex-biased-gene-expression-and-x-linkage-on-rates-of-sequence-evolution-in-drosophila
#7
José Luis Campos, Keira Johnston, Brian Charlesworth
A faster rate of adaptive evolution of X-linked genes compared with autosomal genes (the faster-X effect) can be caused by the fixation of recessive or partially recessive advantageous mutations. This effect should be largest for advantageous mutations that affect only male fitness, and least for mutations that affect only female fitness. We tested these predictions in Drosophila melanogaster by using coding and functionally significant non-coding sequences of genes with different levels of sex-biased expression...
December 8, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29216330/genome-wide-analysis-of-the-brachypodium-distachyon-l-p-beauv-hsp90-gene-family-reveals-molecular-evolution-and-expression-profiling-under-drought-and-salt-stresses
#8
Ming Zhang, Zhiwei Shen, Guoqing Meng, Yu Lu, Yilei Wang
The structure, evolution, and function of heat shock proteins 90 (Hsp90s) have been investigated in great detail in fungi and animals. However, studies on the Hsp90 genes in plants are generally limited. Brachypodium distachyon (L.) P. Beauv., as a model plant for cereal crops, has become a potential biofuel grass. During its long evolution, the Hsp90 gene family in Brachypodium has developed some strategies to cope with adverse environments. How the Hsp90 gene family in Brachypodium evolved in different plant lineages and what its role is in plant responses to drought and salt stresses remains to be elucidated...
2017: PloS One
https://www.readbyqxmd.com/read/29215000/the-evolution-of-the-macrophage-specific-enhancer-fms-intronic-regulatory-element-within-the-csf1r-locus-of-vertebrates
#9
David A Hume, Evi Wollscheid-Lengeling, Rocio Rojo, Clare Pridans
The Csf1r locus encodes the receptor for macrophage colony-stimulating factor, which controls the proliferation, differentiation and survival of macrophages. The 300 bp Fms intronic regulatory element (FIRE), within the second intron of Csf1r, is necessary and sufficient to direct macrophage-specific transcription. We have analysed the conservation and divergence of the FIRE DNA sequence in vertebrates. FIRE is present in the same location in the Csf1r locus in reptile, avian and mammalian genomes. Nearest neighbor analysis based upon this element alone largely recapitulates phylogenies inferred from much larger genomic sequence datasets...
December 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29211708/selective-silencing-of-euchromatic-l1s-revealed-by-genome-wide-screens-for-l1-regulators
#10
Nian Liu, Cameron H Lee, Tomek Swigut, Edward Grow, Bo Gu, Michael Bassik, Joanna Wysocka
Transposable elements (TEs) are now recognized not only as parasitic DNA, whose spread in the genome must be controlled by the host, but also as major players in genome evolution and regulation1-6. Long INterspersed Element-1 (LINE-1 or L1), the only currently autonomous mobile transposon in humans, occupies 17% of the genome and continues to generate inter- and intra-individual genetic variation, in some cases resulting in disease1-7. Nonetheless, how L1 activity is controlled and what function L1s play in host gene regulation remain incompletely understood...
December 6, 2017: Nature
https://www.readbyqxmd.com/read/29202710/parallel-loss-of-introns-in-the-abcb1-gene-in-angiosperms
#11
Rajiv K Parvathaneni, Victoria L DeLeo, John J Spiekerman, Debkanta Chakraborty, Katrien M Devos
BACKGROUND: The presence of non-coding introns is a characteristic feature of most eukaryotic genes. While the size of the introns, number of introns per gene and the number of intron-containing genes can vary greatly between sequenced eukaryotic genomes, the structure of a gene with reference to intron presence and positions is typically conserved in closely related species. Unexpectedly, the ABCB1 (ATP-Binding Cassette Subfamily B Member 1) gene which encodes a P-glycoprotein and underlies dwarfing traits in maize (br2), sorghum (dw3) and pearl millet (d2) displayed considerable variation in intron composition...
December 4, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29196940/evolution-of-intron-poor-clades-and-expression-patterns-of-the-glycosyltransferase-family-47
#12
Junfeng Tan, Zhenyan Miao, Chengzhi Ren, Ruxia Yuan, Yunjia Tang, Xiaorong Zhang, Zhaoxue Han, Chuang Ma
A large-scale bioinformatics analysis revealed the origin and evolution of GT47 gene family, and identified two clades of intron-poor genes with putative functions in drought stress responses and seed development in maize. Glycosyltransferase family 47 (GT47) genes encode β-galactosyltransferases and β-glucuronyltransferases that synthesize pectin, xyloglucans and xylan, which are important components of the plant cell wall. In this study, we performed a systematic and large-scale bioinformatics analysis of GT47 gene family using 352 GT47 proteins from 15 species ranging from cyanobacteria to seed plants...
December 1, 2017: Planta
https://www.readbyqxmd.com/read/29191215/domestication-of-self-splicing-introns-during-eukaryogenesis-the-rise-of-the-complex-spliceosomal-machinery
#13
REVIEW
Julian Vosseberg, Berend Snel
ᅟ: The spliceosome is a eukaryote-specific complex that is essential for the removal of introns from pre-mRNA. It consists of five small nuclear RNAs (snRNAs) and over a hundred proteins, making it one of the most complex molecular machineries. Most of this complexity has emerged during eukaryogenesis, a period that is characterised by a drastic increase in cellular and genomic complexity. Although not fully resolved, recent findings have started to shed some light on how and why the spliceosome originated...
December 1, 2017: Biology Direct
https://www.readbyqxmd.com/read/29165335/integral-phylogenomic-approach-over-ilex-l-species-from-southern-south-america
#14
Jimena Cascales, Mariana Bracco, Mariana J Garberoglio, Lidia Poggio, Alexandra M Gottlieb
The use of molecular markers with inadequate variation levels has resulted in poorly resolved phylogenetic relationships within Ilex. Focusing on southern South American and Asian species, we aimed at contributing informative plastid markers. Also, we intended to gain insights into the nature of morphological and physiological characters used to identify species. We obtained the chloroplast genomes of I.paraguariensis and I. dumosa, and combined these with all the congeneric plastomes currently available to accomplish interspecific comparisons and multilocus analyses...
November 22, 2017: Life
https://www.readbyqxmd.com/read/29163555/ttt-and-pikk-complex-genes-reverted-to-single-copy-following-polyploidization-and-retain-function-despite-massive-retrotransposition-in-maize
#15
Nelson Garcia, Joachim Messing
The TEL2, TTI1, and TTI2 proteins are co-chaperones for heat shock protein 90 (HSP90) to regulate the protein folding and maturation of phosphatidylinositol 3-kinase-related kinases (PIKKs). Referred to as the TTT complex, the genes that encode them are highly conserved from man to maize. TTT complex and PIKK genes exist mostly as single copy genes in organisms where they have been characterized. Members of this interacting protein network in maize were identified and synteny analyses were performed to study their evolution...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29162666/molecular-characterization-and-expression-analysis-of-cs%C3%AE-%C3%AE-defensin-genes-from-the-scorpion-mesobuthus-martensii
#16
Yange Lang, Xiaohuan Pi, Zhiyong Di, Quian Zhang, Huijuan Wang, Bingzheng Shen, Fangfang Li, Gaomin Liu, Yao Yu, Xuan Li, Yingliang Wu, Wenxin Li, Zhijian Cao
Defensins are important components of innate host defence system against bacteria, fungi, parasites and viruses. Here, we predicted six potential defensin genes from the genome of the scorpion Mesobuthus martensii and then validated four genes of them via the combination of PCR and genomic sequence analysis. These four scorpion defensin genes share the same gene organization and structure of two exons and one phase-I intron with the GT-AG rule. Conserved motif and phylogenetic analysis showed that they belong to the members of the invertebrate CSαβ defensin family...
November 21, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/29157056/the-intron-landscape-of-the-mtdna-cytb-gene-among-the-ascomycota-introns-and-intron-encoded-open-reading-frames
#17
Tuhin K Guha, Alvan Wai, Sahra-Taylor Mullineux, Georg Hausner
Fungal mitochondrial genes are frequently noted for the presence of introns. These introns are self-splicing and can be assigned to either group I or II introns and they can encode open reading frames (ORFs). This study examines the introns present within the cytochrome b (cytb) gene of ascomycetes fungi. Cytochrome b gene sequences were sampled from GenBank and supplemented with our own data for species of Leptographium and Ophiostoma. Group I introns were encountered most frequently, many encoding either LAGLIDADG or GIY-YIG homing endonucleases (HEs)...
November 20, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29154754/functional-divergence-of-paralogous-transcription-factors-supported-the-evolution-of-biomineralization-in-echinoderms
#18
Jian Ming Khor, Charles A Ettensohn
Alx1 is a pivotal transcription factor in a gene regulatory network that controls skeletogenesis throughout the echinoderm phylum. We performed a structure-function analysis of sea urchin Alx1 using a rescue assay and identified a novel, conserved motif (Domain 2) essential for skeletogenic function. The paralogue of Alx1, Alx4, was not functionally interchangeable with Alx1, but insertion of Domain 2 conferred robust skeletogenic function on Alx4. We used cross-species expression experiments to show that Alx1 proteins from distantly related echinoderms are not interchangeable, although the sequence and function of Domain 2 are highly conserved...
November 20, 2017: ELife
https://www.readbyqxmd.com/read/29146998/regulation-of-gene-expression-and-rna-editing-in-drosophila-adapting-to-divergent-microclimates
#19
Arielle L Yablonovitch, Jeremy Fu, Kexin Li, Simpla Mahato, Lin Kang, Eugenia Rashkovetsky, Abraham B Korol, Hua Tang, Pawel Michalak, Andrew C Zelhof, Eviatar Nevo, Jin Billy Li
Determining the mechanisms by which a species adapts to its environment is a key endeavor in the study of evolution. In particular, relatively little is known about how transcriptional processes are fine-tuned to adjust to different environmental conditions. Here we study Drosophila melanogaster from 'Evolution Canyon' in Israel, which consists of two opposing slopes with divergent microclimates. We identify several hundred differentially expressed genes and dozens of differentially edited sites between flies from each slope, correlate these changes with genetic differences, and use CRISPR mutagenesis to validate that an intronic SNP in prominin regulates its editing levels...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29145825/assembling-large-genomes-analysis-of-the-stick-insect-clitarchus-hookeri-genome-reveals-a-high-repeat-content-and-sex-biased-genes-associated-with-reproduction
#20
Chen Wu, Victoria G Twort, Ross N Crowhurst, Richard D Newcomb, Thomas R Buckley
BACKGROUND: Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south...
November 16, 2017: BMC Genomics
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