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https://www.readbyqxmd.com/read/28713393/the-complete-chloroplast-genome-of-chinese-bayberry-morella-rubra-myricaceae-implications-for-understanding-the-evolution-of-fagales
#1
Lu-Xian Liu, Rui Li, James R P Worth, Xian Li, Pan Li, Kenneth M Cameron, Cheng-Xin Fu
Morella rubra (Myricaceae), also known as Chinese bayberry, is an economically important, subtropical, evergreen fruit tree. The phylogenetic placement of Myricaceae within Fagales and the origin of Chinese bayberry's domestication are still unresolved. In this study, we report the chloroplast (cp) genome of M. rubra and take advantage of several previously reported chloroplast genomes from related taxa to examine patterns of evolution in Fagales. The cp genomes of three M. rubra individuals were 159,478, 159,568, and 159...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28711668/genome-wide-characterization-and-expression-analysis-of-the-aldehyde-dehydrogenase-aldh-gene-superfamily-under-abiotic-stresses-in-cotton
#2
Xinlei Guo, Yuanyuan Wang, Hejun Lu, Xiaoyan Cai, Xingxing Wang, Zhongli Zhou, Chunying Wang, Yuhong Wang, Zhenmei Zhang, Kunbo Wang, Fang Liu
In plants, aldehyde dehydrogenases (ALDHs) function as 'aldehyde scavengers' by removing reactive aldehydes and thus play important roles in stress responses. To date, 30 ALDHs have been identified in Gossypium raimondii, whereas ALDHs have not been studied in Gossypium arboreum or in tetraploid cotton. In this study, we identified 30, 59 and 59 aldehyde dehydrogenase (ALDH) genes from G. arboreum, G. hirsutum and G. barbadense, respectively. Gene structure analysis revealed that members of the same family exhibit similar exon-intron structures and structural domains, and all members of the ALDH18 family possess a distinct AA-kinase domain...
July 12, 2017: Gene
https://www.readbyqxmd.com/read/28710127/floral-evolution-and-phylogeny-of-the-dialioideae-a-diverse-subfamily-of-tropical-legumes
#3
Erin Zimmerman, Patrick S Herendeen, Gwilym P Lewis, Anne Bruneau
PREMISE OF THE STUDY: The Dialioideae is an early diverging clade of caesalpinioid legumes containing approximately 85 species in 17 genera. Dialioideae floral morphology is highly variable and may provide clues to caesalpinioid evolution, but a well-resolved phylogeny is needed. Here, we have carried out a comprehensive morphological study of 78 Dialioideae and four outgroup species. METHODS: For all available Dialioideae DNA samples, the plastid rpS16 and trnL introns were sequenced...
July 14, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28706224/postglacial-range-expansion-and-the-role-of-ecological-factors-in-driving-adaptive-evolution-of-musa-basjoo-var-formosana
#4
Jui-Hung Chen, Chun-Lin Huang, Yu-Long Lai, Chung-Te Chang, Pei-Chun Liao, Shih-Ying Hwang, Chih-Wen Sun
Genetic variation evolves during postglacial range expansion of a species and is important for adapting to varied environmental conditions. It is crucial for the future survival of a species. We investigate the nuclear DNA sequence variation to provide evidence of postglacial range expansion of Musa basjoo var. formosana, a wild banana species, and test for adaptive evolution of amplified fragment length polymorphic (AFLP) loci underlying local adaptation in association with environmental variables. Postglacial range expansion was suggested by phylogeographical analyses based on sequence variation of the second intron of copper zinc superoxide dismutase 2 gene...
July 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28694209/genome-wide-identification-and-expression-profiling-of-the-sox-gene-family-in-a-bivalve-mollusc-patinopecten-yessoensis
#5
Jiachen Yu, Lingling Zhang, Yangping Li, Ruojiao Li, Meiwei Zhang, Wanru Li, Xinran Xie, Shi Wang, Xiaoli Hu, Zhenmin Bao
SOX family is composed of transcription factors that play vital roles in various developmental processes. Comprehensive understanding on evolution of the SOX family requires full characterization of SOX genes in different phyla. Mollusca is the second largest metazoan phylum, but till now, systematic investigation on the SOX family is still lacking in this phylum. In this study, we conducted genome-wide identification of the SOX family in Yesso scallop Patinopecten yessoensis and profiled their tissue distribution and temporal expression patterns in the ovaries and testes during gametogenesis...
July 7, 2017: Gene
https://www.readbyqxmd.com/read/28690821/the-mitochondrial-genome-of-a-sea-anemone-bolocera-sp-exhibits-novel-genetic-structures-potentially-involved-in-adaptation-to-the-deep-sea-environment
#6
Bo Zhang, Yan-Hong Zhang, Xin Wang, Hui-Xian Zhang, Qiang Lin
The deep sea is one of the most extensive ecosystems on earth. Organisms living there survive in an extremely harsh environment, and their mitochondrial energy metabolism might be a result of evolution. As one of the most important organelles, mitochondria generate energy through energy metabolism and play an important role in almost all biological activities. In this study, the mitogenome of a deep-sea sea anemone (Bolocera sp.) was sequenced and characterized. Like other metazoans, it contained 13 energy pathway protein-coding genes and two ribosomal RNAs...
July 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28683816/uncovering-missing-pieces-duplication-and-deletion-history-of-arrestins-in-deuterostomes
#7
Henrike Indrischek, Sonja J Prohaska, Vsevolod V Gurevich, Eugenia V Gurevich, Peter F Stadler
BACKGROUND: The cytosolic arrestin proteins mediate desensitization of activated G protein-coupled receptors (GPCRs) via competition with G proteins for the active phosphorylated receptors. Arrestins in active, including receptor-bound, conformation are also transducers of signaling. Therefore, this protein family is an attractive therapeutic target. The signaling outcome is believed to be a result of structural and sequence-dependent interactions of arrestins with GPCRs and other protein partners...
July 6, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28683794/genome-wide-analysis-of-wox-genes-in-upland-cotton-and-their-expression-pattern-under-different-stresses
#8
Zhaoen Yang, Qian Gong, Wenqiang Qin, Zuoren Yang, Yuan Cheng, Lili Lu, Xiaoyang Ge, Chaojun Zhang, Zhixia Wu, Fuguang Li
BACKGROUND: WUSCHEL-related homeobox (WOX) family members play significant roles in plant growth and development, such as in embryo patterning, stem-cell maintenance, and lateral organ formation. The recently published cotton genome sequences allow us to perform comprehensive genome-wide analysis and characterization of WOX genes in cotton. RESULTS: In this study, we identified 21, 20, and 38 WOX genes in Gossypium arboreum (2n = 26, A2), G. raimondii (2n = 26, D5), and G...
July 6, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28677163/mitochondrial-genomes-of-the-green-macroalga-ulva-pertusa-ulvophyceae-chlorophyta-novel-insights-into-the-evolution-of-mitogenomes-in-the-ulvophyceae
#9
Feng Liu, James T Melton, Yuping Bi
To further understand the trends in the evolution of mitochondrial genomes (mitogenomes or mtDNAs) in the Ulvophyceae, the mitogenomes of two separate thalli of Ulva pertusa were sequenced. Two U. pertusa mitogenomes (Up1 and Up2) were 69,333 bp and 64,602 bp in length. These mitogenomes shared 2 ribosomal RNAs (rRNAs), 28 transfer RNAs (tRNAs), 29 protein-coding genes (PCGs), and 12 open reading frames (ORFs). The 4.7 kb difference in size was attributed to variation in intron content and tandem repeat regions...
July 4, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28673893/from-intronization-to-intron-loss-how-the-interplay-between-mrna-associated-processes-can-shape-the-architecture-and-the-expression-of-eukaryotic-genes
#10
Francesco Catania
Transcription-coupled processes such as capping, splicing, and cleavage/polyadenylation participate in the journey from genes to proteins. Although they are traditionally thought to serve only as steps in the generation of mature mRNAs, a synthesis of available data indicates that these processes could also act as a driving force for the evolution of eukaryotic genes. A theoretical framework for how mRNA-associated processes may shape gene structure and expression has recently been proposed. Factors that promote splicing and cleavage/polyadenylation in this framework compete for access to overlapping or neighboring signals throughout the transcription cycle...
June 30, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28673235/comparative-analysis-of-lincrna-in-insect-species
#11
Alberto Lopez-Ezquerra, Mark C Harrison, Erich Bornberg-Bauer
BACKGROUND: The ever increasing availability of genomes makes it possible to investigate and compare not only the genomic complements of genes and proteins, but also of RNAs. One class of RNAs, the long noncoding RNAs (lncRNAs) and, in particular, their subclass of long intergenic noncoding RNAs (lincRNAs) have recently gained much attention because of their roles in regulation of important biological processes such as immune response or cell differentiation and as possible evolutionary precursors for protein coding genes...
July 3, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28660982/biochemical-characteristics-and-gene-expression-profiles-of-two-paralogous-luciferases-from-the-japanese-firefly-pyrocoelia-atripennis-coleoptera-lampyridae-lampyrinae-insight-into-the-evolution-of-firefly-luciferase-genes
#12
Manabu Bessho-Uehara, Kaori Konishi, Yuichi Oba
Two paralogous genes of firefly luciferase, Luc1 and Luc2, have been isolated from the species in two subfamilies, Luciolinae and Photurinae, of the family Lampyridae. The gene expression profiles have previously been examined only in the species of Luciolinae. Here we isolated Luc1 and Luc2 genes from the Japanese firefly Pyrocoelia atripennis. This is the first report of the presence of both Luc1 and Luc2 genes in the species of the subfamily Lampyrinae and of the exon-intron structure of Luc2 in the family Lampyridae...
June 29, 2017: Photochemical & Photobiological Sciences
https://www.readbyqxmd.com/read/28659819/evolutionary-analysis-predicts-sensitive-positions-of-mmp20-and-validates-newly-and-previously-identified-mmp20-mutations-causing-amelogenesis-imperfecta
#13
Barbara Gasse, Megana Prasad, Sidney Delgado, Mathilde Huckert, Marzena Kawczynski, Annelyse Garret-Bernardin, Serena Lopez-Cazaux, Isabelle Bailleul-Forestier, Marie-Cécile Manière, Corinne Stoetzel, Agnès Bloch-Zupan, Jean-Yves Sire
Amelogenesis imperfecta (AI) designates a group of genetic diseases characterized by a large range of enamel disorders causing important social and health problems. These defects can result from mutations in enamel matrix proteins or protease encoding genes. A range of mutations in the enamel cleavage enzyme matrix metalloproteinase-20 gene (MMP20) produce enamel defects of varying severity. To address how various alterations produce a range of AI phenotypes, we performed a targeted analysis to find MMP20 mutations in French patients diagnosed with non-syndromic AI...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28652246/mapk-signaling-and-inflammation-link-melanoma-phenotype-switching-to-induction-of-cd73-during-immunotherapy
#14
Julia Reinhardt, Jennifer Landsberg, Jonathan L Schmid-Burgk, Bartomeu Bibiloni Ramis, Tobias Bald, Nicole Glodde, Dorys Lopez-Ramos, Arabella Young, Shin Foong Ngiow, Daniel Nettersheim, Hubert Schorle, Thomas Quast, Waldemar Kolanus, Dirk Schadendorf, Georgina V Long, Jason Madore, Richard A Scolyer, Antoni Ribas, Mark J Smyth, Paul C Tumeh, Thomas Tuting, Michael Hölzel
Evolution of tumor cell phenotypes promotes heterogeneity and therapy resistance. Here we found that induction of CD73, the enzyme that generates immunosuppressive adenosine, is linked to melanoma phenotype switching. Activating MAPK mutations and growth factors drove CD73 expression, which marked both nascent and full activation of a mesenchymal-like melanoma cell state program. Proinflammatory cytokines like TNF-alpha cooperated with MAPK signaling through the c-Jun/AP-1 transcription factor complex to activate CD73 transcription by binding to an intronic enhancer...
June 26, 2017: Cancer Research
https://www.readbyqxmd.com/read/28646210/identification-of-introns-harboring-functional-sequence-elements-through-positional-conservation
#15
Michal Chorev, Alan Joseph Bekker, Jacob Goldberger, Liran Carmel
Many human introns carry out a function, in the sense that they are critical to maintain normal cellular activity. Their identification is fundamental to understanding cellular processes and disease. However, being noncoding elements, such functional introns are poorly predicted based on traditional approaches of sequence and structure conservation. Here, we generated a dataset of human functional introns that carry out different types of functions. We showed that functional introns share common characteristics, such as higher positional conservation along the coding sequence and reduced loss rates, regardless of their specific function...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634583/circular-rnas-biogenesis-function-and-role-in-human-diseases
#16
REVIEW
John Greene, Anne-Marie Baird, Lauren Brady, Marvin Lim, Steven G Gray, Raymond McDermott, Stephen P Finn
Circular RNAs (circRNAs) are currently classed as non-coding RNA (ncRNA) that, unlike linear RNAs, form covalently closed continuous loops and act as gene regulators in mammals. They were originally thought to represent errors in splicing and considered to be of low abundance, however, there is now an increased appreciation of their important function in gene regulation. circRNAs are differentially generated by backsplicing of exons or from lariat introns. Unlike linear RNA, the 3' and 5' ends normally present in an RNA molecule have been joined together by covalent bonds leading to circularization...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28634029/discovery-of-scors-anciently-derived-highly-conserved-gene-associated-repeats-in-stony-corals
#17
Huan Qiu, Ehud Zelzion, Hollie M Putnam, Ruth D Gates, Nicole E Wagner, Diane K Adams, Debashish Bhattacharya
Stony coral (Scleractinia) genomes are still poorly explored and many questions remain about their evolution and contribution to the success and longevity of reefs. We analyzed transcriptome and genome data from Montipora capitata, Acropora digitifera, and transcriptome data from 20 other coral species. To our surprise, we found highly conserved, anciently derived, Scleractinia COral-specific Repeat families (SCORs) that are abundant in all the studied lineages. SCORs form complex secondary structures and are located in untranslated regions and introns, but most abundant in intergenic DNA...
June 17, 2017: Genomics
https://www.readbyqxmd.com/read/28623893/evolutionary-origin-of-type-iv-classical-cadherins-in-arthropods
#18
Mizuki Sasaki, Yasuko Akiyama-Oda, Hiroki Oda
BACKGROUND: Classical cadherins are a metazoan-specific family of homophilic cell-cell adhesion molecules that regulate morphogenesis. Type I and type IV cadherins in this family function at adherens junctions in the major epithelial tissues of vertebrates and insects, respectively, but they have distinct, relatively simple domain organizations that are thought to have evolved by independent reductive changes from an ancestral type III cadherin, which is larger than derived paralogs and has a complicated domain organization...
June 17, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28594821/dynamics-of-dna-methylomes-underlie-oyster-development
#19
Guillaume Riviere, Yan He, Samuele Tecchio, Elizabeth Crowell, Michaël Gras, Pascal Sourdaine, Ximing Guo, Pascal Favrel
DNA methylation is a critical epigenetic regulator of development in mammals and social insects, but its significance in development outside these groups is not understood. Here we investigated the genome-wide dynamics of DNA methylation in a mollusc model, the oyster Crassostrea gigas, from the egg to the completion of organogenesis. Large-scale methylation maps reveal that the oyster genome displays a succession of methylated and non methylated regions, which persist throughout development. Differentially methylated regions (DMRs) are strongly regulated during cleavage and metamorphosis...
June 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28578201/correlated-evolutionary-rates-across-genomic-compartments-in-annonaceae
#20
Paul H Hoekstra, Jan J Wieringa, Erik Smets, Rita D Brandão, Jenifer de Carvalho Lopes, Roy H J Erkens, Lars W Chatrou
The molecular clock hypothesis is an important concept in biology. Deviations from a constant rate of nucleotide substitution have been found widely among lineages, genomes, genes and individual sites. Phylogenetic research can accommodate for these differences in applying specific models of evolution. Lineage-specific rate heterogeneity however can generate bi- or multimodal distributions of substitution rates across the branches of a tree and this may mislead phylogenetic inferences with currently available models...
May 31, 2017: Molecular Phylogenetics and Evolution
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