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Intron evolution

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https://www.readbyqxmd.com/read/27910910/genome-wide-characterisation-and-expression-profile-of-the-grapevine-atl-ubiquitin-ligase-family-reveal-biotic-and-abiotic-stress-responsive-and-development-related-members
#1
Pietro Ariani, Alice Regaiolo, Arianna Lovato, Alejandro Giorgetti, Andrea Porceddu, Salvatore Camiolo, Darren Wong, Simone Castellarin, Elodie Vandelle, Annalisa Polverari
The Arabidopsis Tóxicos en Levadura (ATL) protein family is a class of E3 ubiquitin ligases with a characteristic RING-H2 Zn-finger structure that mediates diverse physiological processes and stress responses in plants. We carried out a genome-wide survey of grapevine (Vitis vinifera L.) ATL genes and retrieved 96 sequences containing the canonical ATL RING-H2 domain. We analysed their genomic organisation, gene structure and evolution, protein domains and phylogenetic relationships. Clustering revealed several clades, as already reported in Arabidopsis thaliana and rice (Oryza sativa), with an expanded subgroup of grapevine-specific genes...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27871309/draft-genome-of-the-living-fossil-ginkgo-biloba
#2
Rui Guan, Yunpeng Zhao, He Zhang, Guangyi Fan, Xin Liu, Wenbin Zhou, Chengcheng Shi, Jiahao Wang, Weiqing Liu, Xinming Liang, Yuanyuan Fu, Kailong Ma, Lijun Zhao, Fumin Zhang, Zuhong Lu, Simon Ming-Yuen Lee, Xun Xu, Jian Wang, Huanming Yang, Chengxin Fu, Song Ge, Wenbin Chen
BACKGROUND: Ginkgo biloba L. (Ginkgoaceae) is one of the most distinctive plants. It possesses a suite of fascinating characteristics including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies. However, the lack of a high-quality genome sequence has been an impediment to our understanding of its biology and evolution. FINDINGS: The 10.61 Gb genome sequence containing 41,840 annotated genes was assembled in the present study...
November 21, 2016: GigaScience
https://www.readbyqxmd.com/read/27867769/comparative-analysis-of-the-complete-chloroplast-genome-sequences-in-psammophytic-haloxylon-species-amaranthaceae
#3
Wenpan Dong, Chao Xu, Delu Li, Xiaobai Jin, Ruili Li, Qi Lu, Zhili Suo
The Haloxylon genus belongs to the Amaranthaceae (formerly Chenopodiaceae) family. The small trees or shrubs in this genus are referred to as the King of psammophytic plants, and perform important functions in environmental protection, including wind control and sand fixation in deserts. To better understand these beneficial plants, we sequenced the chloroplast (cp) genomes of Haloxylon ammodendron (HA) and Haloxylon persicum (HP) and conducted comparative genomic analyses on these and two other representative Amaranthaceae species...
2016: PeerJ
https://www.readbyqxmd.com/read/27864009/evolutionary-dynamics-of-triosephosphate-isomerase-gene-intron-location-pattern-in-metazoa-a-new-perspective-on-intron-evolution-in-animals
#4
Bing Chen, Jingru Shao, Huifu Zhuang, Jianfan Wen
Intron evolution, including its dynamics in the evolutionary transitions and diversification of eukaryotes, remains elusive. Inadequate taxon sampling due to data shortage, unclear phylogenetic framework, and inappropriate outgroup application might be among the causes. Besides, the integrity of all the introns within a gene was often neglected previously. Taking advantage of the ancient conserved triosephosphate isomerase gene (tim), the relatively robust phylogeny of Metazoa, and choanoflagellates as outgroup, the evolutionary dynamics of tim intron location pattern (ILP) in Metazoa was investigated...
November 15, 2016: Gene
https://www.readbyqxmd.com/read/27861119/splicing-repression-allows-the-gradual-emergence-of-new-alu-exons-in-primate-evolution
#5
Jan Attig, Igor Ruiz de Los Mozos, Nejc Haberman, Zhen Wang, Warren Emmett, Kathi Zarnack, Julian König, Jernej Ule
Alu elements are retrotransposons that frequently form new exons during primate evolution. Here, we assess the interplay of splicing repression by hnRNPC and nonsense-mediated mRNA decay (NMD) in the quality control and evolution of new Alu-exons. We identify 3100 new Alu-exons and show that NMD more efficiently recognises transcripts with Alu-exons compared to other exons with premature termination codons. However, some Alu-exons escape NMD, especially when an adjacent intron is retained, highlighting the importance of concerted repression by splicing and NMD...
November 18, 2016: ELife
https://www.readbyqxmd.com/read/27852012/analysis-of-ribosome-associated-mrnas-in-rice-reveals-the-importance-of-transcript-size-and-gc-content-in-translation
#6
Dongyan Zhao, John P Hamilton, Michael Hardigan, Dongmei Yin, Tao He, Brieanne Vaillancourt, Mauricio Reynoso, Germain Pauluzzi, Scott Funkhouser, Yuehua Cui, Julia Bailey-Serres, Jiming Jiang, C Robin Buell, Ning Jiang
Gene expression is controlled at transcriptional and post-transcriptional levels including decoding of mRNA into polypeptides via ribosome-mediated translation. Translational regulation has been intensively studied in the model dicot plant Arabidopsis thaliana, and in this study, we assessed the translational status (proportion of steady-state mRNA associated with ribosomes) of mRNAs by Translating Ribosome Affinity Purification followed by mRNA-sequencing (TRAP-seq) in rice (Oryza sativa), a model monocot plant and the most important food crop...
November 14, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27849572/standing-genetic-variation-in-a-tissue-specific-enhancer-underlies-selfing-syndrome-evolution-in-capsella
#7
Adrien Sicard, Christian Kappel, Young Wha Lee, Natalia Joanna Woźniak, Cindy Marona, John R Stinchcombe, Stephen I Wright, Michael Lenhard
Mating system shifts recurrently drive specific changes in organ dimensions. The shift in mating system from out-breeding to selfing is one of the most frequent evolutionary transitions in flowering plants and is often associated with an organ-specific reduction in flower size. However, the evolutionary paths along which polygenic traits, such as size, evolve are poorly understood. In particular, it is unclear how natural selection can specifically modulate the size of one organ despite the pleiotropic action of most known growth regulators...
November 14, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27812423/proliferation-of-group-ii-introns-in-the-chloroplast-genome-of-the-green-alga-oedocladium-carolinianum-chlorophyceae
#8
Jean-Simon Brouard, Monique Turmel, Christian Otis, Claude Lemieux
BACKGROUND: The chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales...
2016: PeerJ
https://www.readbyqxmd.com/read/27791104/horizontal-gene-transfer-is-more-frequent-with-increased-heterotrophy-and-contributes-to-parasite-adaptation
#9
Zhenzhen Yang, Yeting Zhang, Eric K Wafula, Loren A Honaas, Paula E Ralph, Sam Jones, Christopher R Clarke, Siming Liu, Chun Su, Huiting Zhang, Naomi S Altman, Stephan C Schuster, Michael P Timko, John I Yoder, James H Westwood, Claude W dePamphilis
Horizontal gene transfer (HGT) is the transfer of genetic material across species boundaries and has been a driving force in prokaryotic evolution. HGT involving eukaryotes appears to be much less frequent, and the functional implications of HGT in eukaryotes are poorly understood. We test the hypothesis that parasitic plants, because of their intimate feeding contacts with host plant tissues, are especially prone to horizontal gene acquisition. We sought evidence of HGTs in transcriptomes of three parasitic members of Orobanchaceae, a plant family containing species spanning the full spectrum of parasitic capabilities, plus the free-living Lindenbergia Following initial phylogenetic detection and an extensive validation procedure, 52 high-confidence horizontal transfer events were detected, often from lineages of known host plants and with an increasing number of HGT events in species with the greatest parasitic dependence...
October 24, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27780747/intronless-and-intron-containing-type-i-ifn-genes-coexist-in-amphibian-xenopus-tropicalis-insights-into-the-origin-and-evolution-of-type-i-ifns-in-vertebrates
#10
Zhen Gan, Shan Nan Chen, Bei Huang, Jing Hou, Pin Nie
Type I IFNs are considered to be the core IFN species in vertebrates because of their predominant antiviral effects. But, a puzzling question remains to be answered, as to how intronless type I IFN genes in amniotes might have evolved from intron-containing type I IFN genes in fish and amphibians. In this study, intronless and intron-containing type I IFNs were found in the amphibian model, Xenopus tropicalis, with a total of sixteen and five genes, respectively. The intronless IFNs can be divided into three subgroups, and the intron-containing ones into two subgroups, implying that a retroposition event might have occurred in amphibians, resulting in the generation of intronless type I IFN genes...
October 22, 2016: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/27777283/parallel-evolution-of-cold-tolerance-within-drosophila-melanogaster
#11
John E Pool, Dylan T Braun, Justin B Lack
Drosophila melanogaster originated in tropical Africa before expanding into strikingly different temperate climates in Eurasia and beyond. Here, we find elevated cold tolerance in three distinct geographic regions: beyond the well-studied non-African case, we show that populations from the highlands of Ethiopia and South Africa have significantly increased cold tolerance as well. We observe greater cold tolerance in outbred versus inbred flies, but only in populations with higher inversion frequencies. Each cold-adapted population shows lower inversion frequencies than a closely-related warm-adapted population, suggesting that inversion frequencies may decrease with altitude in addition to latitude...
October 24, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27766348/conservation-mutation-in-the-splice-sites-of-mitochondrial-solute-carrier-genes-of-vertebrates
#12
Rosa Calvello, Maria A Panaro, Rosaria Salvatore, Vincenzo Mitolo, Antonia Cianciulli
The "canonical" introns begin by the dinucleotide GT and end by the dinucleotide AG. GT, together with a few downstream nucleotides, and AG, with a few of the immediately preceding nucleotides, are thought to be the strongest splicing signals (5'ss and 3'ss, respectively). We examined the composition of the intronic initial and terminal hexanucleotides of the mitochondrial solute carrier genes (SLC25A's) of zebrafish, chicken, mouse, and human. These genes are orthologous and we selected the transcripts in which the arrangement of exons and introns was superimposable in the species considered...
October 20, 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27765015/recent-horizontal-transfer-functional-adaptation-and-dissemination-of-a-bacterial-group-ii-intron
#13
Félix LaRoche-Johnston, Caroline Monat, Benoit Cousineau
BACKGROUND: Group II introns are catalytically active RNA and mobile retroelements present in certain eukaryotic organelles, bacteria and archaea. These ribozymes self-splice from the pre-mRNA of interrupted genes and reinsert within target DNA sequences by retrohoming and retrotransposition. Evolutionary hypotheses place these retromobile elements at the origin of over half the human genome. Nevertheless, the evolution and dissemination of group II introns was found to be quite difficult to infer...
October 20, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27760113/mechanism-for-dna-transposons-to-generate-introns-on-genomic-scales
#14
Jason T Huff, Daniel Zilberman, Scott W Roy
The discovery of introns four decades ago was one of the most unexpected findings in molecular biology. Introns are sequences interrupting genes that must be removed as part of messenger RNA production. Genome sequencing projects have shown that most eukaryotic genes contain at least one intron, and frequently many. Comparison of these genomes reveals a history of long evolutionary periods during which few introns were gained, punctuated by episodes of rapid, extensive gain. However, although several detailed mechanisms for such episodic intron generation have been proposed, none has been empirically supported on a genomic scale...
October 19, 2016: Nature
https://www.readbyqxmd.com/read/27748560/insecticide-resistance-mediated-by-an-exon-skipping-event
#15
Madeleine Berger, Alin Mirel Puinean, Emma Randall, Christoph T Zimmer, Wellington M Silva, Pablo Bielza, Linda M Field, David Hughes, Ian Mellor, Keywan Hassani-Pak, Herbert A A Siqueira, Martin S Williamson, Chris Bass
Many genes increase coding capacity by alternate exon usage. The gene encoding the insect nicotinic acetylcholine receptor (nAChR) α6 subunit, target of the bio-insecticide spinosad, is one example of this and expands protein diversity via alternative splicing of mutually exclusive exons. Here, we show that spinosad resistance in the tomato leaf miner, Tuta absoluta is associated with aberrant regulation of splicing of Taα6 resulting in a novel form of insecticide resistance mediated by exon skipping. Sequencing of the α6 subunit cDNA from spinosad selected and unselected strains of T...
November 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27746792/genome-wide-identification-and-evolution-analysis-of-trehalose-6-phosphate-synthase-gene-family-in-nelumbo-nucifera
#16
Qijiang Jin, Xin Hu, Xin Li, Bei Wang, Yanjie Wang, Hongwei Jiang, Neil Mattson, Yingchun Xu
Trehalose-6-phosphate synthase (TPS) plays a key role in plant carbohydrate metabolism and the perception of carbohydrate availability. In the present work, the publicly available Nelumbo nucifera (lotus) genome sequence database was analyzed which led to identification of nine lotus TPS genes (NnTPS). It was found that at least two introns are included in the coding sequences of NnTPS genes. When the motif compositions were analyzed we found that NnTPS generally shared the similar motifs, implying that they have similar functions...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27742820/piece-2-0-an-update-for-the-plant-gene-structure-comparison-and-evolution-database
#17
Yi Wang, Ling Xu, Roger Thilmony, Frank M You, Yong Q Gu, Devin Coleman-Derr
PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron-exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recently, we updated PIECE to a new version, PIECE 2.0 (http://probes.pw.usda.gov/piece or http://aegilops.wheat.ucdavis.edu/piece). PIECE 2.0 contains annotated genes from 49 sequenced plant species as compared to 25 species in the previous version...
October 13, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27713749/genomic-dissection-and-expression-profiling-revealed-functional-divergence-in-triticum-aestivum-leucine-rich-repeat-receptor-like-kinases-talrrks
#18
Shumayla, Shailesh Sharma, Rohit Kumar, Venugopal Mendu, Kashmir Singh, Santosh K Upadhyay
The leucine rich repeat receptor like kinases (LRRK) constitute the largest subfamily of receptor like kinases (RLK), which play critical roles in plant development and stress responses. Herein, we identified 531 TaLRRK genes in Triticum aestivum (bread wheat), which were distributed throughout the A, B, and D sub-genomes and chromosomes. These were clustered into 233 homologous groups, which were mostly located on either homeologous chromosomes from various sub-genomes or in proximity on the same chromosome...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27703459/expansion-and-functional-divergence-of-ap2-group-genes-in-spermatophytes-determined-by-molecular-evolution-and-arabidopsis-mutant-analysis
#19
Pengkai Wang, Tielong Cheng, Mengzhu Lu, Guangxin Liu, Meiping Li, Jisen Shi, Ye Lu, Thomas Laux, Jinhui Chen
The APETALA2 (AP2) genes represent the AP2 group within a large group of DNA-binding proteins called AP2/EREBP. The AP2 gene is functional and necessary for flower development, stem cell maintenance, and seed development, whereas the other members of AP2 group redundantly affect flowering time. Here we study the phylogeny of AP2 group genes in spermatophytes. Spermatophyte AP2 group genes can be classified into AP2 and TOE types, six clades, and we found that the AP2 group homologs in gymnosperms belong to the AP2 type, whereas TOE types are absent, which indicates the AP2 type gene are more ancient and TOE type was split out of AP2 type and losing the major function...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27695474/genome-wide-identification-evolution-and-co-expression-network-analysis-of-mitogen-activated-protein-kinase-kinase-kinases-in-brachypodium-distachyon
#20
Kewei Feng, Fuyan Liu, Jinwei Zou, Guangwei Xing, Pingchuan Deng, Weining Song, Wei Tong, Xiaojun Nie
Mitogen-activated protein kinase (MAPK) cascades are the conserved and universal signal transduction modules in all eukaryotes, which play the vital roles in plant growth, development, and in response to multiple stresses. In this study, we used bioinformatics methods to identify 86 MAPKKK protein encoded by 73 MAPKKK genes in Brachypodium. Phylogenetic analysis of MAPKKK family from Arabidopsis, rice, and Brachypodium has classified them into three subfamilies, of which 28 belonged to MEKK, 52 to Raf, and 6 to ZIK subfamily, respectively...
2016: Frontiers in Plant Science
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