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Intron evolution

Raphaël Méheust, Debashish Bhattacharya, Jananan S Pathmanathan, James O McInerney, Philippe Lopez, Eric Bapteste
BACKGROUND: Eukaryotes evolved from the symbiotic association of at least two prokaryotic partners, and a good deal is known about the timings, mechanisms, and dynamics of these evolutionary steps. Recently, it was shown that a new class of nuclear genes, symbiogenetic genes (S-genes), was formed concomitant with endosymbiosis and the subsequent evolution of eukaryotic photosynthetic lineages. Understanding their origins and contributions to eukaryogenesis would provide insights into the ways in which cellular complexity has evolved...
March 13, 2018: BMC Biology
Kelly Louise Bennett, Martha Kaddumukasa, Fortunate Shija, Rousseau Djouaka, Gerald Misinzo, Julius Lutwama, Yvonne Marie Linton, Catherine Walton
The study of demographic processes involved in species diversification and evolution ultimately provides explanations for the complex distribution of biodiversity on earth, indicates regions important for the maintenance and generation of biodiversity, and identifies biological units important for conservation or medical consequence. African and forest biota have both received relatively little attention with regard to understanding their diversification, although one possible mechanism is that this has been driven by historical climate change...
March 2018: Ecology and Evolution
Kyuha Choi, Xiaohui Zhao, Andrew J Tock, Christophe Lambing, Charles J Underwood, Thomas J Hardcastle, Heïdi Serra, Juhyun Kim, Hyun Seob Cho, Jaeil Kim, Piotr A Ziolkowski, Nataliya E Yelina, Ildoo Hwang, Robert A Martienssen, Ian R Henderson
Meiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Meiotic DSB frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis thaliana SPO11-1-oligonucleotides. SPO11-1-oligos are elevated in gene promoters, terminators, and introns, which is driven by AT-sequence richness that excludes nucleosomes and allows SPO11-1 access...
March 12, 2018: Genome Research
Wan-Lin Dong, Ruo-Nan Wang, Na-Yao Zhang, Wei-Bing Fan, Min-Feng Fang, Zhong-Hu Li
Orchidaceae is the 3rd largest family of angiosperms, an evolved young branch of monocotyledons. This family contains a number of economically-important horticulture and flowering plants. However, the limited availability of genomic information largely hindered the study of molecular evolution and phylogeny of Orchidaceae. In this study, we determined the evolutionary characteristics of whole chloroplast (cp) genomes and the phylogenetic relationships of the family Orchidaceae. We firstly characterized the cp genomes of four orchid species: Cremastra appendiculata , Calanthe davidii , Epipactis mairei , and Platanthera japonica ...
March 2, 2018: International Journal of Molecular Sciences
Jônatas Abrahão, Lorena Silva, Ludmila Santos Silva, Jacques Yaacoub Bou Khalil, Rodrigo Rodrigues, Thalita Arantes, Felipe Assis, Paulo Boratto, Miguel Andrade, Erna Geessien Kroon, Bergmann Ribeiro, Ivan Bergier, Herve Seligmann, Eric Ghigo, Philippe Colson, Anthony Levasseur, Guido Kroemer, Didier Raoult, Bernard La Scola
Here we report the discovery of two Tupanvirus strains, the longest tailed Mimiviridae members isolated in amoebae. Their genomes are 1.44-1.51 Mb linear double-strand DNA coding for 1276-1425 predicted proteins. Tupanviruses share the same ancestors with mimivirus lineages and these giant viruses present the largest translational apparatus within the known virosphere, with up to 70 tRNA, 20 aaRS, 11 factors for all translation steps, and factors related to tRNA/mRNA maturation and ribosome protein modification...
February 27, 2018: Nature Communications
Zhaoen Yang, Qian Gong, Lingling Wang, Yuying Jin, Jianping Xi, Zhi Li, Wenqiang Qin, Zuoren Yang, Lili Lu, Quanjia Chen, Fuguang Li
Members of the YABBY gene family, a small plant-specific family of genes, have been proposed to function in specifying abaxial cell fate. Although to date little has been learned about cotton YABBY genes, completion of the cotton genome enables a comprehensive genome-wide analysis of YABBY genes in cotton. Here, a total of 12, 12, and 23 YABBY genes were identified in Gossypium arboreum (2n = 26, A2 ), G. raimondii (2n = 26, D5 ), and G. hirsutum (2n = 4x = 52, [AD]t ), respectively. Sequence analysis showed that the N-terminal zinc-finger and C-terminal YABBY domains in YABBY proteins are highly conserved among cotton, Arabidopsis , and rice...
2018: Frontiers in Genetics
Geoffrey Guittard, Pierre Pontarotti, Samuel Granjeaud, Magda Rodrigues, Laurent Abi-Rached, Jacques A Nunès
Downstream of Kinase (DOK) proteins represent a multigenic family of adaptors that includes negative regulators of immune cell signaling. Using phylogenetics and intron/exon structure data, we show here that the seven human DOK genes (DOK1 to DOK7) form three highly divergent groups that emerged before the protostome-deuterostome split: DOK1/2/3, DOK4/5/6, and DOK7. For two of these three groups (DOK1/2/3 and DOK4/5/6), further gene duplications occurred in vertebrates and so while chordates only have three DOK genes, vertebrates have seven DOK genes over the three groups...
February 14, 2018: Developmental and Comparative Immunology
Vydianathan Ravi, Byrappa Venkatesh
Boasting nearly 30,000 species, teleosts account for half of all extant vertebrates and approximately 98% of all ray-finned fish species (Actinopterygii). Teleosts are also the largest and most diverse group of vertebrates, exhibiting an astonishing level of morphological, physiological, and behavioral diversity. Previous studies had indicated that the teleost lineage has experienced an additional whole-genome duplication event. Recent comparative genomic analyses of teleosts and other bony vertebrates using spotted gar (a nonteleost ray-finned fish) and elephant shark (a cartilaginous fish) as outgroups have revealed several divergent features of teleost genomes...
February 15, 2018: Annual Review of Animal Biosciences
Jun Aruga, Minoru Hatayama
Zic family genes encode five C2H2-type zinc finger domain-containing proteins that have many roles in animal development and maintenance. Recent phylogenetic analyses showed that Zic family genes are distributed in metazoans (multicellular animals), except Porifera (sponges) and Ctenophora (comb jellies). The sequence comparisons revealed that the zinc finger domains were absolutely conserved among the Zic family genes. Zic zinc finger domains are similar to, but distinct from those of the Gli, Glis, and Nkl gene family, and these zinc finger protein families are proposed to have been derived from a common ancestor gene...
2018: Advances in Experimental Medicine and Biology
Shao-Yao Ying, Donald C Chang, Shi-Lung Lin
MicroRNAs (miRNAs), widely distributed, small regulatory RNA genes, target both messenger RNA (mRNA) degradation and suppression of protein translation based on sequence complementarity between the miRNA and its targeted mRNA. Different names have been used to describe various types of miRNA. During evolution, RNA retroviruses or transgenes invaded the eukaryotic genome and were inserted itself in the noncoding regions of DNA, conceivably acting as transposon-like jumping genes, providing defense from viral invasion and fine-tuning of gene expression as a secondary level of gene modulation in eukaryotes...
2018: Methods in Molecular Biology
Yanli Chen, Zhaoen Yang, Yanqing Xiao, Peng Wang, Ye Wang, Xiaoyang Ge, Chaojun Zhang, Xianlong Zhang, Fuguang Li
Members of the NF-YB transcription factor gene family play important roles in diverse processes related to plant growth and development, such as seed development, drought tolerance, and flowering time. However, the function of NF-YB genes in cotton remains unclear. A total of 23, 24, and 50 NF-YB genes were identified in Gossypium arboreum (G. arboreum), Gossypium raimondii (G. raimondii), and G. hirsutum, respectively. A systematic phylogenetic analysis was carried out in G. arboretum, G. raimondii, G. hirsutum, Arabidopsis thaliana, cacao, rice and, sorghum, where the 150 NF-YB genes were divided into five groups (α-ε)...
February 6, 2018: International Journal of Molecular Sciences
George Talal Abboud, Abdullah Zubaer, Alvan Wai, Georg Hausner
Ophiostoma novo-ulmi, a member of the Ophiostomatales (Ascomycota) is the causal agents of the current Dutch elm disease pandemic in Europe and North America. The complete mitochondrial genome (mtDNA) of Ophiostoma novo-ulmi subsp. novo-ulmi, the European component of O. novo-ulmi, has been sequenced and annotated. Gene order (synteny) among the currently available members of the Ophiostomatales was examined and appears to be conserved and mtDNA size variability among the Ophiostomatales in part is due the presence of introns and their encoded open reading frames...
February 5, 2018: Canadian Journal of Microbiology
Hafiz Mamoon Rehman, Muhammad Amjad Nawaz, Zahid Hussain Shah, Jutta Ludwig-Müller, Gyuhwa Chung, Muhammad Qadir Ahmad, Seung Hwan Yang, Soo In Lee
In plants, UGTs (UDP-glycosyltransferases) glycosylate various phytohormones and metabolites in response to biotic and abiotic stresses. Little is known about stress-responsive glycosyltransferases in plants. Therefore, it is important to understand the genomic and transcriptomic portfolio of plants with regard to biotic and abiotic stresses. Here, we identified 140, 154, and 251 putative UGTs in Brassica rapa, Brassica oleracea, and Brassica napus, respectively, and clustered them into 14 major phylogenetic groups (A-N)...
January 30, 2018: Scientific Reports
Tao Wan, Zhi-Ming Liu, Ling-Fei Li, Andrew R Leitch, Ilia J Leitch, Rolf Lohaus, Zhong-Jian Liu, Hai-Ping Xin, Yan-Bing Gong, Yang Liu, Wen-Cai Wang, Ling-Yun Chen, Yong Yang, Laura J Kelly, Ji Yang, Jin-Ling Huang, Zhen Li, Ping Liu, Li Zhang, Hong-Mei Liu, Hui Wang, Shu-Han Deng, Meng Liu, Ji Li, Lu Ma, Yan Liu, Yang Lei, Wei Xu, Ling-Qing Wu, Fan Liu, Qian Ma, Xin-Ran Yu, Zhi Jiang, Guo-Qiang Zhang, Shao-Hua Li, Rui-Qiang Li, Shou-Zhou Zhang, Qing-Feng Wang, Yves Van de Peer, Jin-Bo Zhang, Xiao-Ming Wang
Gnetophytes are an enigmatic gymnosperm lineage comprising three genera, Gnetum, Welwitschia and Ephedra, which are morphologically distinct from all other seed plants. Their distinctiveness has triggered much debate as to their origin, evolution and phylogenetic placement among seed plants. To increase our understanding of the evolution of gnetophytes, and their relation to other seed plants, we report here a high-quality draft genome sequence for Gnetum montanum, the first for any gnetophyte. By using a novel genome assembly strategy to deal with high levels of heterozygosity, we assembled >4 Gb of sequence encoding 27,491 protein-coding genes...
January 29, 2018: Nature Plants
Wojciech P Galej, Navtej Toor, Andrew J Newman, Kiyoshi Nagai
Nuclear pre-mRNA splicing and group II intron self-splicing both proceed by two-step transesterification reactions via a lariat intron intermediate. Recently determined cryo-electron microscopy (cryo-EM) structures of catalytically active spliceosomes revealed the RNA-based catalytic core and showed how pre-mRNA substrates and reaction products are positioned in the active site. These findings highlight a strong structural similarity to the group II intron active site, strengthening the notion that group II introns and spliceosomes evolved from a common ancestor...
January 29, 2018: Chemical Reviews
Lijiao Gu, Libei Li, Hengling Wei, Hantao Wang, Junji Su, Yaning Guo, Shuxun Yu
WRKY transcription factors play important roles in plant defense, stress response, leaf senescence, and plant growth and development. Previous studies have revealed the important roles of the group IIa GhWRKY genes in cotton. To comprehensively analyze the group IIa GhWRKY genes in upland cotton, we identified 15 candidate group IIa GhWRKY genes in the Gossypium hirsutum genome. The phylogenetic tree, intron-exon structure, motif prediction and Ka/Ks analyses indicated that most group IIa GhWRKY genes shared high similarity and conservation and underwent purifying selection during evolution...
2018: PloS One
Sergej Nowoshilow, Siegfried Schloissnig, Ji-Feng Fei, Andreas Dahl, Andy W C Pang, Martin Pippel, Sylke Winkler, Alex R Hastie, George Young, Juliana G Roscito, Francisco Falcon, Dunja Knapp, Sean Powell, Alfredo Cruz, Han Cao, Bianca Habermann, Michael Hiller, Elly M Tanaka, Eugene W Myers
Salamanders serve as important tetrapod models for developmental, regeneration and evolutionary studies. An extensive molecular toolkit makes the Mexican axolotl (Ambystoma mexicanum) a key representative salamander for molecular investigations. Here we report the sequencing and assembly of the 32-gigabase-pair axolotl genome using an approach that combined long-read sequencing, optical mapping and development of a new genome assembler (MARVEL). We observed a size expansion of introns and intergenic regions, largely attributable to multiplication of long terminal repeat retroelements...
February 1, 2018: Nature
Pavel V Mazin, Xi Jiang, Ning Fu, Dingding Han, Meng Guo, Mikhail S Gelfand, Philipp Khaitovich
Changes in splicing are known to affect the function and regulation of genes. We analyzed splicing events that take place during the postnatal development of the prefrontal cortex in humans, chimpanzees, and rhesus macaques based on data obtained from 168 individuals. Our study revealed that among the 38,822 quantified alternative exons, 15% are differentially spliced among species, and more than 6% splice differently at different age. Mutations in splicing acceptor and/or donor sites might explain more than 14% of all splicing differences among species and up to 64% of high-amplitude differences...
January 23, 2018: RNA
Minghui Yan, Peter W Fritsch, Michael J Moore, Tao Feng, Aiping Meng, Jing Yang, Tao Deng, Congxiao Zhao, Xiaohong Yao, Hang Sun, Hengchang Wang
Relationships among the genera of the small, woody family Styracaceae and among families of the large, diverse order Ericales have resisted complete resolution with sequences from one or a few genes. We used plastome sequencing to attempt to resolve the backbone relationships of Styracaceae and Ericales and to explore plastome structural evolution. Complete plastomes for 23 species are newly reported here, including 18 taxa of Styracaceae and five of Ericales (including species of Sapotaceae, Clethraceae, Symplocaceae, and Diapensiaceae)...
January 19, 2018: Molecular Phylogenetics and Evolution
Ángel García-Gutiérrez, Francisco M Cánovas, Concepción Ávila
BACKGROUND: Plants synthesize glutamate from ammonium by the combined activity of the enzymes glutamine synthetase (GS) and glutamate synthase (GOGAT) through the glutamate synthase cycle. In plants, there are two forms of glutamate synthases that differ in their electron donors, NADH-GOGAT (EC and Fd-GOGAT (EC, which have differential roles either in primary ammonia assimilation or in the reassimilation of ammonium from different catabolic processes. Glutamate synthases are complex iron-sulfur flavoproteins containing functional domains involved in the control and coordination of their catalytic activities in annual plants...
January 19, 2018: BMC Genomics
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