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Intron evolution

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https://www.readbyqxmd.com/read/28105956/vrn1-genes-variability-in-tetraploid-wheat-species-with-a-spring-growth-habit
#1
Irina Konopatskaia, Valeriya Vavilova, Elena Ya Kondratenko, Alexandr Blinov, Nikolay P Goncharov
BACKGROUND: Vernalization genes VRN1 play a major role in the transition from vegetative to reproductive growth in wheat. In di-, tetra- and hexaploid wheats the presence of a dominant allele of at least one VRN1 gene homologue (Vrn-A1, Vrn-B1, Vrn-G1 or Vrn-D1) determines the spring growth habit. Allelic variation between the Vrn-1 and vrn-1 alleles relies on mutations in the promoter region or the first intron. The origin and variability of the dominant VRN1 alleles, determining the spring growth habit in tetraploid wheat species have been poorly studied...
November 16, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/28103252/comparative-and-evolutionary-analysis-of-grass-pollen-allergens-using-brachypodium-distachyon-as-a-model-system
#2
Akanksha Sharma, Niharika Sharma, Prem Bhalla, Mohan Singh
Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses...
2017: PloS One
https://www.readbyqxmd.com/read/28097404/complete-mitochondrial-genome-of-the-endophytic-fungus-pestalotiopsis-fici-features-and-evolution
#3
Shu Zhang, Xiu-Na Wang, Xiao-Ling Zhang, Xing-Zhong Liu, Yong-Jie Zhang
Endophytic fungi (EF) live within plants and have profound impacts on plant communities. They are astonishingly diverse but poorly studied at the genome level. Herein, we assembled the mitochondrial genome (mitogenome) of the EF Pestalotiopsis fici, annotated and compared it with those of other relatives to better understand the evolution of the EF lineage. Except for standard fungal mitochondrial genes, the 69,529-bp circular mitogenome of P. fici harbors 18 introns acquired possibly through lateral transfer from other fungi and nine free-standing open reading frames with some scarcely seen in fungal mitogenomes...
January 17, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28092027/classification-and-lineage-tracing-of-sh2-domains-throughout-eukaryotes
#4
Bernard A Liu
Today there exists a rapidly expanding number of sequenced genomes. Cataloging protein interaction domains such as the Src Homology 2 (SH2) domain across these various genomes can be accomplished with ease due to existing algorithms and predictions models. An evolutionary analysis of SH2 domains provides a step towards understanding how SH2 proteins integrated with existing signaling networks to position phosphotyrosine signaling as a crucial driver of robust cellular communication networks in metazoans. However organizing and tracing SH2 domain across organisms and understanding their evolutionary trajectory remains a challenge...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28081145/probing-the-association-between-early-evolutionary-markers-and-schizophrenia
#5
Saurabh Srinivasan, Francesco Bettella, Sahar Hassani, Yunpeng Wang, Aree Witoelar, Andrew J Schork, Wesley K Thompson, David A Collier, Rahul S Desikan, Ingrid Melle, Anders M Dale, Srdjan Djurovic, Ole A Andreassen
Schizophrenia is suggested to be a by-product of the evolution in humans, a compromise for our language, creative thinking and cognitive abilities, and thus, essentially, a human disorder. The time of its origin during the course of human evolution remains unclear. Here we investigate several markers of early human evolution and their relationship to the genetic risk of schizophrenia. We tested the schizophrenia evolutionary hypothesis by analyzing genome-wide association studies of schizophrenia and other human phenotypes in a statistical framework suited for polygenic architectures...
2017: PloS One
https://www.readbyqxmd.com/read/28057052/an-evaluation-of-the-evolution-of-the-gene-structure-of-dystroglycan
#6
Andrea Brancaccio, Josephine C Adams
BACKGROUND: Dystroglycan (DG) is an adhesion receptor complex composed of two non-covalently associated subunits, transcribed from a single gene. The extracellular α-DG is highly and heterogeneously glycosylated and binds with high affinity to laminins, and the transmembrane β-DG binds intracellular dystrophin. Multiple cellular functions have been proposed for DG, notwithstanding that its role in skeletal muscle appears central as demonstrated by both primary and secondary severe muscular dystrophic phenotypes collectively known as dystroglycanopathies...
January 3, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28055303/gene-length-as-a-biological-timer-to-establish-temporal-transcriptional-regulation
#7
Killeen S Kirkconnell, Brian Magnuson, Michelle T Paulsen, Brian Lu, Karan Bedi, Mats Ljungman
Transcriptional timing is inherently influenced by gene length, thus providing a mechanism for temporal regulation of gene expression. While gene size has been shown to be important for the expression timing of specific genes during early development, whether it plays a role in the timing of other global gene expression programs has not been extensively explored. Here, we investigate the role of gene length during the early transcriptional response of human fibroblasts to serum stimulation. Using the nascent sequencing techniques Bru-seq and BruUV-seq, we identified immediate genome-wide transcriptional changes following serum stimulation that were linked to rapid activation of enhancer elements...
January 5, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28045452/design-and-experimental-evolution-of-trans-splicing-group-i-intron-ribozymes
#8
REVIEW
Ulrich F Müller
Group I intron ribozymes occur naturally as cis-splicing ribozymes, in the form of introns that do not require the spliceosome for their removal. Instead, they catalyze two consecutive trans-phosphorylation reactions to remove themselves from a primary transcript, and join the two flanking exons. Designed, trans-splicing variants of these ribozymes replace the 3'-portion of a substrate with the ribozyme's 3'-exon, replace the 5'-portion with the ribozyme's 5'-exon, or insert/remove an internal sequence of the substrate...
January 2, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27994610/genome-wide-analysis-of-soybean-jmjc-domain-containing-proteins-suggests-evolutionary-conservation-following-whole-genome-duplication
#9
Yapeng Han, Xiangyong Li, Lin Cheng, Yanchun Liu, Hui Wang, Danxia Ke, Hongyu Yuan, Liangsheng Zhang, Lei Wang
Histone modifications, such as methylation and demethylation, play an important role in regulating chromatin structure and gene expression. The JmjC domain-containing proteins, an important family of histone lysine demethylases (KDMs), play a key role in maintaining homeostasis of histone methylation in vivo. In this study, we performed a comprehensive analysis of the jumonji C (JmjC) gene family in the soybean genome and identified 48 JmjC genes (GmJMJs) distributed unevenly across 18 chromosomes. Phylogenetic analysis showed that these JmjC domain-containing genes can be divided into eight groups...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27982734/increased-complexity-of-circrna-expression-during-species-evolution
#10
Rui Dong, Xu-Kai Ma, Ling-Ling Chen, Li Yang
Circular RNAs (circRNAs) are broadly identified from precursor mRNA (pre-mRNA) back-splicing across various species. Recent studies have suggested a cell-/tissue- specific manner of circRNA expression. However, the distinct expression pattern of circRNAs among species and its underlying mechanism still remain to be explored. Here, we systematically compared circRNA expression from human and mouse, and found that only a small portion of human circRNAs could be determined in parallel mouse samples. The conserved circRNA expression between human and mouse is correlated with the existence of orientation-opposite complementary sequences in introns that flank back-spliced exons in both species, but not the circRNA sequences themselves...
December 16, 2016: RNA Biology
https://www.readbyqxmd.com/read/27977424/a-new-case-series-of-crisponi-syndrome-in-a-turkish-family-and-review-of-the-literature
#11
Bilge Bayraktar-Tanyeri, Mervenur Hepokur, Suleyman Bayraktar, Ivana Persico, Laura Crisponi
Crisponi syndrome/cold-induced sweating syndrome (CS/CISS) is a rare autosomal recessive disorder with a complex phenotype, reported in the neonatal period for CS and in the evolutive one for CISS. The syndrome usually manifests at birth. The aim of this study was to report on three new patients with CS and review the Turkish patients. We report here on three patients from two related families harboring a homozygous mutation in the cytokine receptor-like factor-1 (CRLF1) gene. DNA samples of the three patients and their parents were subjected to a mutational analysis of the CRLF1 gene at the Institute of Biomedical and Genetic Research - National Research Council, Cagliari (Italy)...
December 13, 2016: Clinical Dysmorphology
https://www.readbyqxmd.com/read/27974049/the-draft-genome-of-whitefly-bemisia-tabaci-meam1-a-global-crop-pest-provides-novel-insights-into-virus-transmission-host-adaptation-and-insecticide-resistance
#12
Wenbo Chen, Daniel K Hasegawa, Navneet Kaur, Adi Kliot, Patricia Valle Pinheiro, Junbo Luan, Marcus C Stensmyr, Yi Zheng, Wenli Liu, Honghe Sun, Yimin Xu, Yuan Luo, Angela Kruse, Xiaowei Yang, Svetlana Kontsedalov, Galina Lebedev, Tonja W Fisher, David R Nelson, Wayne B Hunter, Judith K Brown, Georg Jander, Michelle Cilia, Angela E Douglas, Murad Ghanim, Alvin M Simmons, William M Wintermantel, Kai-Shu Ling, Zhangjun Fei
BACKGROUND: The whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) is among the 100 worst invasive species in the world. As one of the most important crop pests and virus vectors, B. tabaci causes substantial crop losses and poses a serious threat to global food security. RESULTS: We report the 615-Mb high-quality genome sequence of B. tabaci Middle East-Asia Minor 1 (MEAM1), the first genome sequence in the Aleyrodidae family, which contains 15,664 protein-coding genes...
December 14, 2016: BMC Biology
https://www.readbyqxmd.com/read/27965700/genome-wide-analysis-of-the-aquaporin-gene-family-in-chickpea-cicer-arietinum-l
#13
Amit A Deokar, Bunyamin Tar'an
Aquaporins (AQPs) are essential membrane proteins that play critical role in the transport of water and many other solutes across cell membranes. In this study, a comprehensive genome-wide analysis identified 40 AQP genes in chickpea (Cicer arietinum L.). A complete overview of the chickpea AQP (CaAQP) gene family is presented, including their chromosomal locations, gene structure, phylogeny, gene duplication, conserved functional motifs, gene expression, and conserved promoter motifs. To understand AQP's evolution, a comparative analysis of chickpea AQPs with AQP orthologs from soybean, Medicago, common bean, and Arabidopsis was performed...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27955695/exon-intron-structure-and-sequence-variation-of-the-calreticulin-gene-among-rhipicephalus-sanguineus-group-ticks
#14
Daniele Porretta, Maria Stefania Latrofa, Filipe Dantas-Torres, Valentina Mastrantonio, Roberta Iatta, Domenico Otranto, Sandra Urbanelli
BACKGROUND: Calreticulin proteins (CRTs) are important components of tick saliva, which is involved in the blood meal success, pathogen transmission and host allergic responses. The characterization of the genes encoding for salivary proteins, such as CRTs, is pivotal to understand the mechanisms of tick-host interaction during blood meal and to develop tick control strategies based on their inhibition. In hard ticks, crt genes were shown to have only one intron with conserved position among species...
December 12, 2016: Parasites & Vectors
https://www.readbyqxmd.com/read/27927791/molecular-evolution-of-two-distinct-dmrt1-promoters-for-germ-and-somatic-cells-in-vertebrate-gonads
#15
Shuuji Mawaribuchi, Masato Musashijima, Mikako Wada, Yumi Izutsu, Erina Kurakata, Min Kyun Park, Nobuhiko Takamatsu, Michihiko Ito
The transcription factor DMRT1 has important functions in two distinct processes, somatic-cell masculinization and germ-cell development in mammals. However, it is unknown whether the functions are conserevd during evolution, and what mechanism underlies its expression in the two cell lineages. Our analysis of the Xenopus laevis and Silurana tropicalis dmrt1 genes indicated the presence of two distinct promoters: one upstream of the noncoding first exon (ncEx1), and one within the first intron. In contrast, only the ncEx1-upstream promoter was detected in the dmrt1 gene of the agnathan sand lamprey, which expressed dmrt1 exclusively in the germ cells...
December 6, 2016: Molecular Biology and Evolution
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
#16
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
#17
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
#18
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
#19
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...
February 20, 2017: Gene
https://www.readbyqxmd.com/read/27861119/splicing-repression-allows-the-gradual-emergence-of-new-alu-exons-in-primate-evolution
#20
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
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