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https://www.readbyqxmd.com/read/28717203/genome-wide-identification-and-characterization-of-circular-rnas-by-high-throughput-sequencing-in-soybean
#1
Wei Zhao, Yihui Cheng, Chi Zhang, Qingbo You, Xinjie Shen, Wei Guo, Yongqing Jiao
Circular RNAs (circRNAs) arise during pre-mRNA splicing, in which the 3' and 5' ends are linked to each other by a covalent bond. Soybean is an ancient tetraploid, which underwent two whole genome duplications. Most of soybean genes are paralogous genes with multiple copies. Although many circRNAs have been identified in animals and plants, little is known about soybean circRNAs, especially about circRNAs derived from paralogous genes. Here, we used deep sequencing technology coupled with RNase R enrichment strategy and bioinformatic approach to uncover circRNAs in soybean...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28712501/gene-editing-in-polyploid-crops-wheat-camelina-canola-potato-cotton-peanut-sugar-cane-and-citrus
#2
Donald P Weeks
Polyploid crops make up a significant portion of the major food and fiber crops of the world and include wheat, potato, cotton, apple, peanut, citrus, and brassica oilseeds such as rape, canola, and Camelina. The presence of three sets of chromosomes in triploids, four sets in tetraploids, and six sets in hexaploids present significant challenges to conventional plant breeding and, potentially, to efficient use of rapidly emerging gene and genome-editing systems such as zinc finger nucleases, single-stranded oligonucleotides, TALE effector nucleases, and clustered regularly interspaced short palindromic repeats (CRISPR/Cas9)...
2017: Progress in Molecular Biology and Translational 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
#3
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/28710383/wider-geographic-distribution-and-higher-diversity-of-hexaploids-than-tetraploids-in-carassius-species-complex-reveal-recurrent-polyploidy-effects-on-adaptive-evolution
#4
Xiao-Li Liu, Fang-Fang Jiang, Zhong-Wei Wang, Xi-Yin Li, Zhi Li, Xiao-Juan Zhang, Fan Chen, Jian-Feng Mao, Li Zhou, Jian-Fang Gui
Polyploidy roles on adaptive evolution and ecological novelty have been extensively studied in plants but remained unclear in vertebrates owing to the rare polyploidy incidences. Here, a huge number of 3105 specimens in Carassius species complex including 2211 hexaploids and 894 tetraploids were sampled from 34 locations through mainland China. And hexaploids had wider geographic distribution than tetraploids especially in the areas with high altitude, high latitude and low annual precipitation. Then, an approximate 1050 bp transferrin (tf) fragments were amplified from all the samples, and 526 tf alleles were identified from a total of 37260 sequences at last...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28707250/genomic-prediction-of-starch-content-and-chipping-quality-in-tetraploid-potato-using-genotyping-by-sequencing
#5
Elsa Sverrisdóttir, Stephen Byrne, Ea Høegh Riis Sundmark, Heidi Øllegaard Johnsen, Hanne Grethe Kirk, Torben Asp, Luc Janss, Kåre L Nielsen
Genomic prediction models for starch content and chipping quality show promising results, suggesting that genomic selection is a feasible breeding strategy in tetraploid potato. Genomic selection uses genome-wide molecular markers to predict performance of individuals and allows selections in the absence of direct phenotyping. It is regarded as a useful tool to accelerate genetic gain in breeding programs, and is becoming increasingly viable for crops as genotyping costs continue to fall. In this study, we have generated genomic prediction models for starch content and chipping quality in tetraploid potato to facilitate varietal development...
July 13, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28707113/genetically-engineered-hairy-root-cultures-of-hyoscyamus-senecionis-and-h-muticus-ploidy-as-a-promising-parameter-in-the-metabolic-engineering-of-tropane-alkaloids
#6
Esmaeil Dehghan, Darwin W Reed, Patrick S Covello, Zeinab Hasanpour, Javier Palazon, Kirsi-Marja Oksman-Caldentey, Farajollah Shahriari Ahmadi
Tetraploidy improves overexpression of h6h and scopolamine production of H. muticus, while in H. senecionis, pmt overexpression and elicitation can be used as effective methods for increasing tropane alkaloids. The effects of metabolic engineering in a polyploid context were studied by overexpression of h6h in the tetraploid hairy root cultures of H. muticus. Flow cytometry analysis indicated genetic stability in the majority of the clones, while only a few clones showed genetic instability. Among all the diploid and tetraploid clones, the highest level of h6h transgene expression and scopolamine accumulation was interestingly observed in the tetraploid clones of H...
July 13, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28694102/evolution-of-dmsp-dimethylsulfoniopropionate-biosynthesis-pathway-origin-and-phylogenetic-distribution-in-polyploid-spartina-poaceae-chloridoideae
#7
Hélène Rousseau, Mathieu Rousseau-Gueutin, Xavier Dauvergne, Julien Boutte, Gaëlle Simon, Nathalie Marnet, Alain Bouchereau, Solène Guiheneuf, Jean-Pierre Bazureau, Jérôme Morice, Stéphane Ravanel, Francisco Cabello-Hurtado, Abdelkader Ainouche, Armel Salmon, Jonathan F Wendel, Malika L Ainouche
DMSP (dimethylsulfoniopropionate) is an ecologically important sulfur metabolite commonly produced by marine algae and by some higher plant lineages, including the polyploid salt marsh genus Spartina (Poaceae). The molecular mechanisms and genes involved in the DMSP biosynthesis pathways are still unknown. In this study, we performed comparative analyses of DMSP amounts and molecular phylogenetic analyses to decipher the origin of DMSP in Spartina that represents one of the major source of terrestrial DMSP in coastal marshes...
July 7, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28690795/short-term-effect-of-elevated-co2-concentration-0-5-on%C3%A2-mitochondria-in-diploid-and-tetraploid-black-locust-robinia%C3%A2-pseudoacacia-l
#8
Fuling Xu, Mingquan Jiang, Fanjuan Meng
Recent increases in atmospheric CO 2 concentration have affected the growth and physiology of plants. In this study, plants were grown with 0.5% CO 2 for 0, 3, and 6 days. The anatomy, fluorescence intensity of H2O2, respiration rate, and antioxidant activities of the mitochondria were analyzed in diploid (2×) and tetraploid (4×) black locust (Robinia pseudoacacia L.). Exposure to 0.5% CO 2 resulted in clear structural alterations and stomatal closure in the mitochondria. Reduced membrane integrity and increased structural damage were observed in 2× plants at 6 days...
July 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28687778/evolution-of-the-araliaceae-family-inferred-from-complete-chloroplast-genomes-and-45s-nrdnas-of-10-panax-related-species
#9
Kyunghee Kim, Van Binh Nguyen, Jingzhou Dong, Ying Wang, Jee Young Park, Sang-Choon Lee, Tae-Jin Yang
We produced complete sequences and conducted comparative analysis of the maternally inherited chloroplast (cp) genomes and bi-parentally inherited 45S nuclear ribosomal RNA genes (nrDNA) from ten Araliaceae species to elucidate the genetic diversity and evolution in that family. The cp genomes ranged from 155,993 bp to 156,730 bp with 97.1-99.6% similarity. Complete 45S nrDNA units were about 11 kb including a 5.8-kb 45S cistron. Among 79 cp protein-coding genes, 74 showed nucleotide variations among ten species, of which infA, rpl22, rps19 and ndhE genes showed the highest Ks values and atpF, atpE, ycf2 and rps15 genes showed the highest Ka/Ks values...
July 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28685360/deciphering-the-physiological-and-molecular-mechanisms-for-copper-tolerance-in-autotetraploid-arabidopsis
#10
Mingjuan Li, Guoyun Xu, Xinjie Xia, Manling Wang, Xuming Yin, Bin Zhang, Xin Zhang, Yanchun Cui
Autotetraploid Arabidopsis line esd and 4COL exhibit enhanced tolerance to Cu stress by enhancing activation of antioxidative defenses, altering expression of genes related to Cu transport, chelation, and ABA-responsive. Autopolyploidy is ubiquitous among angiosperms and often results in better adaptation to stress conditions. Although copper (Cu) is an essential trace element, excess amounts can inhibit plant growth and even result in death. Here, we report that autotetraploid Arabidopsis thaliana esd and 4COL exhibit higher tolerance to Cu stress...
July 6, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28684525/wild-emmer-genome-architecture-and-diversity-elucidate-wheat-evolution-and-domestication
#11
Raz Avni, Moran Nave, Omer Barad, Kobi Baruch, Sven O Twardziok, Heidrun Gundlach, Iago Hale, Martin Mascher, Manuel Spannagl, Krystalee Wiebe, Katherine W Jordan, Guy Golan, Jasline Deek, Batsheva Ben-Zvi, Gil Ben-Zvi, Axel Himmelbach, Ron P MacLachlan, Andrew G Sharpe, Allan Fritz, Roi Ben-David, Hikmet Budak, Tzion Fahima, Abraham Korol, Justin D Faris, Alvaro Hernandez, Mark A Mikel, Avraham A Levy, Brian Steffenson, Marco Maccaferri, Roberto Tuberosa, Luigi Cattivelli, Primetta Faccioli, Aldo Ceriotti, Khalil Kashkush, Mohammad Pourkheirandish, Takao Komatsuda, Tamar Eilam, Hanan Sela, Amir Sharon, Nir Ohad, Daniel A Chamovitz, Klaus F X Mayer, Nils Stein, Gil Ronen, Zvi Peleg, Curtis J Pozniak, Eduard D Akhunov, Assaf Distelfeld
Wheat (Triticum spp.) is one of the founder crops that likely drove the Neolithic transition to sedentary agrarian societies in the Fertile Crescent more than 10,000 years ago. Identifying genetic modifications underlying wheat's domestication requires knowledge about the genome of its allo-tetraploid progenitor, wild emmer (T. turgidum ssp. dicoccoides). We report a 10.1-gigabase assembly of the 14 chromosomes of wild tetraploid wheat, as well as analyses of gene content, genome architecture, and genetic diversity...
July 7, 2017: Science
https://www.readbyqxmd.com/read/28683794/genome-wide-analysis-of-wox-genes-in-upland-cotton-and-their-expression-pattern-under-different-stresses
#12
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/28683152/development-of-a-new-set-of-molecular-markers-for-examining-glu-a1-variants-in-common-wheat-and-ancestral-species
#13
Zhenying Dong, Yushuang Yang, Kunpu Zhang, Yiwen Li, Junjun Wang, Zhaojun Wang, Xin Liu, Huanju Qin, Daowen Wang
In common wheat (Triticum aestivum L.), allelic variations of Glu-A1 locus have important influences on grain end-use quality. Among the three Glu-A1 alleles, Glu-A1a and -A1b encode the high-molecular-weight glutenin subunits (HMW-GSs) 1Ax1 and 1Ax2*, respectively, whereas Glu-A1c does not specify any subunit. Here, we detected a total of 11 Glu-A1 locus haplotypes (H1 to H11) in three wheat species, by developing and using a new set of DNA markers (Xrj5, Xid3, Xrj6, Xid4 and Xrj7). The main haplotypes found in the diploid wheat T...
2017: PloS One
https://www.readbyqxmd.com/read/28681105/chimeras-linked-to-tandem-repeats-and-transposable-elements-in-tetraploid-hybrid-fish
#14
Lihai Ye, Ni Jiao, Xiaojun Tang, Yiyi Chen, Xiaolan Ye, Li Ren, Fangzhou Hu, Shi Wang, Ming Wen, Chun Zhang, Min Tao, Shaojun Liu
The formation of the allotetraploid hybrid lineage (4nAT) encompasses both distant hybridization and polyploidization processes. The allotetraploid offspring have two sets of sub-genomes inherited from both parental species, and therefore, it is important to explore its genetic structure. Herein, we construct a bacterial artificial chromosome library of allotetraploids, and then sequence and analyze the full-length sequences of 19 bacterial artificial chromosomes. Sixty-eight DNA chimeras are identified, which are divided into four models according to the distribution of the genomic DNA derived from the parents...
July 5, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28674743/whole-genome-duplication-enhances-the-photosynthetic-capacity-of-chrysanthemum-nankingense
#15
Bin Dong, Haibin Wang, Tao Liu, Peilei Cheng, Yun Chen, Sumei Chen, Zhiyong Guan, Weimin Fang, Jiafu Jiang, Fadi Chen
Whole genome duplication has a major effect on the phenotype and physiology of higher plants. A comparison between the diploid and tetraploid forms of Chrysanthemum nankingense showed that the latter's leaf contained a higher content of chlorophyll a/b and harbored a larger number of chloroplasts per cell, leading to an enhancement in its photosynthetic capacity and an improved level of productivity with respect to biomass. A transcriptomic analysis of the two ploidy level forms revealed 21,559 differentially transcribed genes...
July 3, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28674545/identification-of-novel-associations-of-candidate-genes-with-resistance-to-late-blight-in-solanum-tuberosum-group-phureja
#16
María F Álvarez, Myrian Angarita, María C Delgado, Celsa García, José Jiménez-Gomez, Christiane Gebhardt, Teresa Mosquera
The genetic basis of quantitative disease resistance has been studied in crops for several decades as an alternative to R gene mediated resistance. The most important disease in the potato crop is late blight, caused by the oomycete Phytophthora infestans. Quantitative disease resistance (QDR), as any other quantitative trait in plants, can be genetically mapped to understand the genetic architecture. Association mapping using DNA-based markers has been implemented in many crops to dissect quantitative traits...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28666092/characterization-of-genome-in-tetraploid-sty-elymus-triticeae-poaceae-species-using-sequential-fish-and-gish
#17
Ruijuan Liu, Richard R-C Wang, Feng Yu, XIngwang Lu, Quan-Wen Dou
Genomes of ten Elymus species, either presumed or known as tetraploid StY, were characterized using fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH). These tetraploid species could be grouped into 3 categories. Type I included StY genome reported species-Roegneria pendulina, R. nutans, R. glaberrima, R. ciliaris, and Elymus nevskii, and StY genome presumed species-R sinica, R. breviglumis, and R. dura, whose genome could be separated into two sets based on different GISH intensities...
June 30, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28654657/hek293t-cell-lines-defective-for-o-linked-glycosylation
#18
James M Termini, Zachary A Silver, Bryony Connor, Aristotelis Antonopoulos, Stuart M Haslam, Anne Dell, Ronald C Desrosiers
Here we describe derivatives of the HEK293T cell line that are defective in their ability to generate mucin-type O-linked glycosylation. Using CRISPR/Cas9 and a single-cell GFP-sorting procedure, the UDP-galactose-4-epimerase (GALE), galactokinase 1 (GALK1), and galactokinase 2 (GALK2) genes were knocked out individually and in combinations with greater than 90% of recovered clones having the desired mutations. Although HEK293T cells are tetraploid, we found this approach to be an efficient method to target and disrupt all 4 copies of the target gene...
2017: PloS One
https://www.readbyqxmd.com/read/28653150/linkage-map-construction-and-qtl-analysis-for-internal-heat-necrosis-in-autotetraploid-potato
#19
Mitchell J Schumann, Zhao-Bang Zeng, Mark E Clough, G Craig Yencho
A tetraploid potato population was mapped for internal heat necrosis (IHN) using the Infinium (®) 8303 potato SNP array, and QTL for IHN were identified on chromosomes 1, 5, 9 and 12 that explained 28.21% of the variation for incidence and 25.3% of the variation for severity. This research represents a significant step forward in our understanding of IHN, and sets the stage for future research focused on testing the utility of these markers in additional breeding populations. Internal heat necrosis (IHN) is a significant non-pathogenic disorder of potato tubers and previous studies have identified AFLP markers linked to IHN susceptibility in the tetraploid, B2721 potato mapping population...
June 26, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28652136/evolution-of-the-receptors-for-growth-hormone-prolactin-erythropoietin-and-thrombopoietin-in-relation-to-the-vertebrate-tetraploidizations
#20
Daniel Ocampo Daza, Dan Larhammar
The receptors for the pituitary hormones growth hormone (GH), prolactin (PRL) and somatolactin (SL), and the hematopoietic hormones erythropoietin (EPO) and thrombopoietin (TPO), comprise a structurally related family in the superfamily of cytokine class-I receptors. GH, PRL and SL receptors have a wide variety of effects in development, osmoregulation, metabolism and stimulation of growth, while EPO and TPO receptors guide the production and differentiation of erythrocytes and thrombocytes, respectively. The evolution of the receptors for GH, PRL and SL has been partially investigated by previous reports suggesting different time points for the hormone and receptor gene duplications...
June 23, 2017: General and Comparative Endocrinology
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