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Intron evolution

Xiaoxu Li, Madiha Hamyat, Cheng Liu, Ahmad Salman, Xiaoming Gao, Cun Guo, Yuanying Wang, Yongfeng Guo
Members of the plant-specific WOX (WUSCHEL-related homeobox) transcription factor family have been reported to play important roles in peptide signaling that regulates stem cell maintenance and cell fate specification in various developmental processes. Even though remarkable advances have been made in studying WOX genes in Arabidopsis , little is known about this family in Solanaceae species. A total of 45 WOX members from five Solanaceae species were identified, including eight members from Solanum tuberosum , eight from Nicotiana tomentosiformis , 10 from Solanum lycopersicum , 10 from Nicotiana sylvestris and nine from Nicotiana tabacum ...
May 17, 2018: Genes
Shuhuan Zhang, Qiaoqing Xu, Hao Du, Zhitao Qi, Youshen Li, Jun Huang, Jun Di, Qiwei Wei
Liver-expressed antimicrobial peptide 2 (leap-2) is an evolutionarily ancient molecule that acts as the key component in vertebrate innate immunity against invading pathogens. Leap-2 has been identified and characterised in several teleosts, but not yet in chondrosteans. Herein, the complete coding sequences of leap-2b and leap-2c were identified from expressed sequence tags (ESTs) isolated from Dabry's sturgeon (Acipenser dabryanus) and Chinese sturgeon (A. sinensis), designated as adleap-2b, adleap-2c, asleap-2b, and asleap-2c, respectively...
May 14, 2018: Fish & Shellfish Immunology
Jun Yan, Guilin Li, Xingqi Guo, Yang Li, Xuecheng Cao
The protein kinase (PK, kinome) family is one of the largest families in plants and regulates almost all aspects of plant processes, including plant development and stress responses. Despite their important functions, comprehensive functional classification, evolutionary analysis and expression patterns of the cotton PK gene family has yet to be performed on PK genes. In this study, we identified the cotton kinomes in the Gossypium raimondii, Gossypium arboretum, Gossypium hirsutum and Gossypium barbadense genomes and classified them into 7 groups and 122-24 subfamilies using software HMMER v3...
2018: PloS One
Artemis G Korovesi, Maria Ntertilis, Vassili N Kouvelis
The nuclear ribosomal protein S3 (Rps3) is implicated in the assembly of the ribosomal small subunit. Fungi and plants present a gene copy in their mitochondrial (mt) genomes. An analysis of 303 complete fungal mt genomes showed that, when rps3 is found, it is either a free-standing gene or an anchored gene within the omega intron of the rnl gene. Early divergent fungi, Basidiomycota and all yeasts but the CTG group belong to the first case, and Pezizomycotina to the second. Its position, size and genetic code employed are conserved within species of the same Order...
May 12, 2018: Molecular Phylogenetics and Evolution
C Li, J Jiang, Q Zhang, X Wang
The major histocompatibility complex (MHC) molecule plays an important role in the vertebrate immune system. However, we have a limited understanding of the MHC genomic structure in teleosts. Using gene cloning and family analysis, we isolate the MHC class II genes in the tongue sole (Cynoglossus semilaevis) and find that both class II A and class II B genes are duplicated (named Cyse-DAA and Cyse-DBA, Cyse-DAB and Cyse-DBB, respectively). The class II A genes consist of four exons with a highly conserved genomic structure, but each gene has unique and defining exon 2 and intron 2 sequences...
May 13, 2018: International Journal of Immunogenetics
Bin Zhang, J Liu, Zhao E Yang, Er Y Chen, Chao J Zhang, Xue Y Zhang, Fu G Li
BACKGROUND: Cotton is a major fiber and oil crop worldwide. Cotton production, however, is often threatened by abiotic environmental stresses. GRAS family proteins are among the most abundant transcription factors in plants and play important roles in regulating root and shoot development, which can improve plant resistance to abiotic stresses. However, few studies on the GRAS family have been conducted in cotton. Recently, the G. hirsutum genome sequences have been released, which provide us an opportunity to analyze the GRAS family in G...
May 9, 2018: BMC Genomics
Conghui Liu, Bo Liu, Yan Zhang, Fan Jiang, Yuwei Ren, Shuqu Li, Hengchao Wang, Wei Fan
Horizontal gene transfer (HGT), a mechanism that shares genetic material between the host and donor from separated offspring branches, has been described as a means of producing novel and beneficial phenotypes for the host organisms. However, in molluscs, the second most diverse group, the existence of HGT is still controversial. In the present study, 12 HGT genes were identified from California two-spot octopus Octopus bimaculoides based on a similarity search, phylogenetic construction, gene composition analysis and PCR (Polymerase Chain Reaction) validation...
May 5, 2018: Gene
Anna Kamlárová, Katarína Chovanová, Marcel Zámocký
Catalase-peroxidases represent one important subfamily of ancestral antioxidant enzymes originally evolved in bacteria for the protection against various forms of oxidative stress. KatG genes coding for these bifunctional catalase-peroxidases were during their peculiar evolution transferred from Bacteroidetes to the fungal phylum Ascomycota via a horizontal gene transfer event. Here we analyse a newly discovered fungal katG gene without introns coding for a thermostable catalase-peroxidase from Chaetomium thermophilum var...
May 5, 2018: Gene
Marjanne D van der Hoek, Ole Madsen, Jaap Keijer, Feike R van der Leij
Carnitine/choline acyltransferases play diverse roles in energy metabolism and neuronal signalling. Our knowledge of their evolutionary relationships, important for functional understanding, is incomplete. Therefore, we aimed to determine the evolutionary relationships of these eukaryotic transferases. We performed extensive phylogenetic and intron position analyses. We found that mammalian intramitochondrial CPT2 is most closely related to cytosolic yeast carnitine transferases (Sc-YAT1 and 2), whereas the other members of the family are related to intraorganellar yeast Sc-CAT2...
May 3, 2018: Biochimica et Biophysica Acta
Jordan E Burke, Adam D Longhurst, Daria Merkurjev, Jade Sales-Lee, Beiduo Rao, James J Moresco, John R Yates, Jingyi Jessica Li, Hiten D Madhani
Tools to understand how the spliceosome functions in vivo have lagged behind advances in the structural biology of the spliceosome. Here, methods are described to globally profile spliceosome-bound pre-mRNA, intermediates, and spliced mRNA at nucleotide resolution. These tools are applied to three yeast species that span 600 million years of evolution. The sensitivity of the approach enables the detection of canonical and non-canonical events, including interrupted, recursive, and nested splicing. This application of statistical modeling uncovers independent roles for the size and position of the intron and the number of introns per transcript in substrate progression through the two catalytic stages...
May 3, 2018: Cell
Ana Llopart
The hemizygosity of the X (Z) chromosome fully exposes the fitness effects of mutations on that chromosome, and has evolutionary consequences on the relative rates of evolution of X and autosomes. Specifically, several population genetics models predict increased rates of evolution in X-linked loci relative to autosomal loci. This prediction of faster-X evolution has been evaluated and confirmed for both protein coding sequences and gene expression. In the case of faster-X evolution for gene expression divergence, it is often assumed that variation in 5' noncoding sequences is associated with variation in transcript abundance between species but a formal, genome-wide test of this hypothesis is still missing...
May 1, 2018: Molecular Ecology
Qin Zhou, Sisi Zhang, Feng Chen, Baojun Liu, Lan Wu, Fei Li, Jiaqi Zhang, Manzhu Bao, Guofeng Liu
BACKGROUND: SQUAMOSA PROMOTER BINDING PROTEIN (SBP)-box genes encode a family of plant-specific transcription factors (TFs) that play important roles in many growth and development processes including phase transition, leaf initiation, shoot and inflorescence branching, fruit development and ripening etc. The SBP-box gene family has been identified and characterized in many species, but has not been well studied in Petunia, an important ornamental genus. RESULTS: We identified 21 putative SPL genes of Petunia axillaris and P...
March 12, 2018: BMC Genomics
Jose V Die, Juan Gil, Teresa Millan
BACKGROUND: Auxin Response Factors act as critical components of the auxin-signaling pathway by regulating the transcription of auxin-responsive genes. The release of the chickpea reference genome provides an opportunity to identify and characterize the ARF gene family in this important legume by a data mining coupled by comparative genomics approaches. RESULTS: We performed a comprehensive characterization and analysis of 24 ARF genes in the chickpea reference genome...
April 27, 2018: BMC Genomics
Xin Pang, Yanping Wei, Yuan Cheng, Luzhao Pan, Qingjing Ye, Rongqing Wang, Meiying Ruan, Guozhi Zhou, Zhuping Yao, Zhimiao Li, Yuejian Yang, Weicheng Liu, Hongjian Wan
Melatonin plays an important role in plant growth, development, and environmental stress. In this study, a systematic analysis of tomato tryptophan decarboxylase (SlTrpDC), which is the first enzyme of melatonin biosynthesis, was conducted by integrating structural features, phylogenetic relationships, an exon/intron feature, and a divergent expression profile. The results determined that the tomato genome encoded five members ( SlTrpDC1 - SlTrpDC5 ). The phylogenetic relationships indicated that gene expansion was proposed as the major mode of evolution of the TrpDC genes from the different plant algae species to the higher plants species...
April 24, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Martin Malmstrøm, Ralf Britz, Michael Matschiner, Ole K Tørresen, Renny Kurnia Hadiaty, Norsham Yaakob, Heok Hui Tan, Kjetill Sigurd Jakobsen, Walter Salzburger, Lukas Rüber
The world's smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype...
April 1, 2018: Genome Biology and Evolution
Jong Im Kim, Hwan Su Yoon, Gangman Yi, Woongghi Shin, John M Archibald
BACKGROUND: Cryptophytes are an ecologically important group of algae comprised of phototrophic, heterotrophic and osmotrophic species. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin. Cryptophytes have a clear phylogenetic affinity to heterotrophic eukaryotes and possess four genomes: host-derived nuclear and mitochondrial genomes, and plastid and nucleomorph genomes of endosymbiotic origin. RESULTS: To gain insight into cryptophyte mitochondrial genome evolution, we sequenced the mitochondrial DNAs of five species and performed a comparative analysis of seven genomes from the following cryptophyte genera: Chroomonas, Cryptomonas, Hemiselmis, Proteomonas, Rhodomonas, Storeatula and Teleaulax...
April 20, 2018: BMC Genomics
Nicolás Toro, Francisco Martínez-Abarca, María D Molina-Sánchez, Fernando M García-Rodríguez, Rafael Nisa-Martínez
Mobile group II introns are ribozymes and retroelements that probably originate from bacteria. Sinorhizobium meliloti , the nitrogen-fixing endosymbiont of legumes of genus Medicago , harbors a large number of these retroelements. One of these elements, RmInt1, has been particularly successful at colonizing this multipartite genome. Many studies have improved our understanding of RmInt1 and phylogenetically related group II introns, their mobility mechanisms, spread and dynamics within S. meliloti and closely related species...
2018: Frontiers in Microbiology
A D Lokits, H Indrischek, J Meiler, H E Hamm, P F Stadler
BACKGROUND: Heterotrimeric G proteins are fundamental signaling proteins composed of three subunits, Gα and a Gβγ dimer. The role of Gα as a molecular switch is critical for transmitting and amplifying intracellular signaling cascades initiated by an activated G protein Coupled Receptor (GPCR). Despite their biochemical and therapeutic importance, the study of G protein evolution has been limited to the scope of a few model organisms. Furthermore, of the five primary Gα subfamilies, the underlying gene structure of only two families has been thoroughly investigated outside of Mammalia evolution...
April 11, 2018: BMC Evolutionary Biology
Lei Lei, Wenguang Cao, Ling Liu, Urmi Das, Yujia Wu, Guodong Liu, Muhammad Sohail, Yangjun Chen, Jiuyong Xie
The pituitary-derived somatolactotrophe GH3 cells secrete both growth hormone (GH) and prolactin (PRL). We have found that the hnRNP L and L-like (LL) paralogs differentially regulate alternative splicing of genes in these cells. Here we show that hnRNP L is essential for PRL only, but LL for both PRL and GH production. Transcriptome-wide RNA-seq analysis indicates that they differentially control groups of hormone or hormone-related genes involved in hormone production/regulation at total transcript and alternative exon levels...
April 2, 2018: Molecular and Cellular Biology
Michael C Campbell, Lunden T Smith, Jayla Harvey
Despite its critical role in the defense against microbial infection and tumor development, little is known about the range of nucleotide and haplotype variation at IFN-γ, or the evolutionary forces that have shaped patterns of diversity at this locus. To address this gap in knowledge, we examined sequence data from the IFN-γ gene in 1461 individuals from 15 worldwide populations. Our analyses uncovered novel patterns of variation in distinct African populations, including an excess of high frequency-derived alleles, unusually long haplotype structure surrounding the IFN-γ gene, and a "star-like" genealogy of African-specific haplotypes carrying variants previously associated with infectious disease...
March 29, 2018: Genes and Immunity
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