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https://www.readbyqxmd.com/read/28819820/genome-wide-characterization-of-the-wrky-gene-family-in-radish-raphanus-sativus-l-reveals-its-critical-functions-under-different-abiotic-stresses
#1
Bernard Kinuthia Karanja, Lianxue Fan, Liang Xu, Yan Wang, Xianwen Zhu, Mingjia Tang, Ronghua Wang, Fei Zhang, Everlyne M'mbone Muleke, Liwang Liu
The radish WRKY gene family was genome-widely identified and played critical roles in response to multiple abiotic stresses. The WRKY is among the largest transcription factors (TFs) associated with multiple biological activities for plant survival, including control response mechanisms against abiotic stresses such as heat, salinity, and heavy metals. Radish is an important root vegetable crop and therefore characterization and expression pattern investigation of WRKY transcription factors in radish is imperative...
August 17, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28818345/mobile-group-ii-introns-as-ancestral-eukaryotic-elements
#2
REVIEW
Olga Novikova, Marlene Belfort
The duality of group II introns, capable of carrying out both self-splicing and retromobility reactions, is hypothesized to have played a profound role in the evolution of eukaryotes. These introns likely provided the framework for the emergence of eukaryotic retroelements, spliceosomal introns and other key components of the spliceosome. Group II introns are found in all three domains of life and are therefore considered to be exceptionally successful mobile genetic elements. Initially identified in organellar genomes, group II introns are found in bacteria, chloroplasts, and mitochondria of plants and fungi, but not in nuclear genomes...
August 14, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28813471/mitochondrial-genome-evolution-in-the-saccharomyces-sensu-stricto-complex
#3
Jiangxing Ruan, Jian Cheng, Tongcun Zhang, Huifeng Jiang
Exploring the evolutionary patterns of mitochondrial genomes is important for our understanding of the Saccharomyces sensu stricto (SSS) group, which is a model system for genomic evolution and ecological analysis. In this study, we first obtained the complete mitochondrial sequences of two important species, Saccharomyces mikatae and Saccharomyces kudriavzevii. We then compared the mitochondrial genomes in the SSS group with those of close relatives, and found that the non-coding regions evolved rapidly, including dramatic expansion of intergenic regions, fast evolution of introns and almost 20-fold higher rearrangement rates than those of the nuclear genomes...
2017: PloS One
https://www.readbyqxmd.com/read/28800729/accd-nuclear-transfer-of-platycodon-grandiflorum-and-the-plastid-of-early-campanulaceae
#4
Chang Pyo Hong, Jihye Park, Yi Lee, Minjee Lee, Sin Gi Park, Yurry Uhm, Jungho Lee, Chang-Kug Kim
BACKGROUND: Campanulaceae species are known to have highly rearranged plastid genomes lacking the acetyl-CoA carboxylase (ACC) subunit D gene (accD), and instead have a nuclear (nr)-accD. Plastid genome information has been thought to depend on studies concerning Trachelium caeruleum and genome announcements for Adenophora remotiflora, Campanula takesimana, and Hanabusaya asiatica. RNA editing information for plastid genes is currently unavailable for Campanulaceae. To understand plastid genome evolution in Campanulaceae, we have sequenced and characterized the chloroplast (cp) genome and nr-accD of Platycodon grandiflorum, a basal member of Campanulaceae...
August 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28796293/il7ra-polymorphisms-are-not-associated-with-aids-progression
#5
Luz María Medrano, José Luis Jiménez, María A Jiménez-Sousa, Amanda Fernández-Rodíguez, Mónica Gutiérrez-Rivas, José María Bellón, José Ramón Blanco, Alexy Inciarte, Mª Ángeles Muñoz-Fernández, Salvador Resino
BACKGROUND: Our aim was to determine whether α-chain of the IL-7 Receptor (IL7RA) polymorphisms (rs10491434, rs6897932, and rs987106) are associated with the clinical pattern of AIDS progression in ART-naïve HIV-infected patients. METHODS: We carried out a cross-sectional study in 673 HIV-infected patients who were classified into three groups according to the clinical pattern of AIDS progression (188 long-term non-progressors (LTNPs), 334 moderate progressors (MPs), and 151 rapid progressors (RPs))...
August 10, 2017: European Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28776210/the-hnrnp-q-like-gene-is-retroinserted-into-the-b-chromosomes-of-the-cichlid-fish-astatotilapia-latifasciata
#6
Bianca O Carmello, Rafael L B Coan, Adauto L Cardoso, Erica Ramos, Bruno E A Fantinatti, Diego F Marques, Rogério A Oliveira, Guilherme T Valente, Cesar Martins
B chromosomes are dispensable elements observed in many eukaryotic species, including the African cichlid Astatotilapia latifasciata, which might have one or two B chromosomes. Although there have been many studies focused on the biology of these chromosomes, questions about the evolution, maintenance, and potential effects of these chromosomes remain. Here, we identified a variant form of the hnRNP Q-like gene inserted into the B chromosome of A. latifasciata that is characterized by a high copy number and intron-less structure...
August 3, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28743642/intercontinental-and-intracontinental-biogeography-of-the-eastern-asian-eastern-north-american-disjunct-panax-the-ginseng-genus-araliaceae-emphasizing-its-diversification-processes-in-eastern-asia
#7
Yun-Juan Zuo, Jun Wen, Shi-Liang Zhou
The intercontinental biogeography between eastern Asia and eastern North America has attracted much attention from evolutionary biologists. Further insights into understanding the evolution of the intercontinental disjunctions have been hampered by the lack of studies on the intracontinental biogeography in eastern Asia, a region with complex geology, geography, climates and habitats. Herein we studied the biogeographic history of the eastern Asian-eastern North American disjunct genus Panax with special emphasis on the investigation of its uneven diversification in Asia...
July 22, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28726632/dynamics-of-genomic-innovation-in-the-unicellular-ancestry-of-animals
#8
Xavier Grau-Bové, Guifré Torruella, Stuart Donachie, Hiroshi Suga, Guy Leonard, Thomas A Richards, Iñaki Ruiz-Trillo
Which genomic innovations underpinned the origin of multicellular animals is still an open debate. Here, we investigate this question by reconstructing the genome architecture and gene family diversity of ancestral premetazoans, aiming to date the emergence of animal-like traits. Our comparative analysis involves genomes from animals and their closest unicellular relatives (the Holozoa), including four new genomes: three Ichthyosporea and Corallochytrium limacisporum. Here we show that the earliest animals were shaped by dynamic changes in genome architecture before the emergence of multicellularity: an early burst of gene diversity in the ancestor of Holozoa, enriched in transcription factors and cell adhesion machinery, was followed by multiple and differently-timed episodes of synteny disruption, intron gain and genome expansions...
July 20, 2017: ELife
https://www.readbyqxmd.com/read/28723946/the-mitochondrial-genome-of-the-terrestrial-carnivorous-plant-utricularia-reniformis-lentibulariaceae-structure-comparative-analysis-and-evolutionary-landmarks
#9
Saura R Silva, Danillo O Alvarenga, Yani Aranguren, Helen A Penha, Camila C Fernandes, Daniel G Pinheiro, Marcos T Oliveira, Todd P Michael, Vitor F O Miranda, Alessandro M Varani
The carnivorous plants of the family Lentibulariaceae have attained recent attention not only because of their interesting lifestyle, but also because of their dynamic nuclear genome size. Lentibulariaceae genomes span an order of magnitude and include species with the smallest genomes in angiosperms, making them a powerful system to study the mechanisms of genome expansion and contraction. However, little is known about mitochondrial DNA (mtDNA) sequences of this family, and the evolutionary forces that shape this organellar genome...
2017: PloS One
https://www.readbyqxmd.com/read/28713393/the-complete-chloroplast-genome-of-chinese-bayberry-morella-rubra-myricaceae-implications-for-understanding-the-evolution-of-fagales
#10
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
#11
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
#12
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
#13
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
#14
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...
September 5, 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
#15
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
#16
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
#17
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
#18
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 two ribosomal RNAs (rRNAs), 28 transfer RNAs (tRNAs), 29 protein-coding genes, and 12 open reading frames. The 4.7 kb difference in size was attributed to variation in intron content and tandem repeat regions. A total of six introns were present in the smaller U...
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
#19
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
#20
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
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