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berry genomics

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https://www.readbyqxmd.com/read/29126148/consensus-coding-sequence-ccds-database-a-standardized-set-of-human-and-mouse-protein-coding-regions-supported-by-expert-curation
#1
Shashikant Pujar, Nuala A O'Leary, Catherine M Farrell, Jane E Loveland, Jonathan M Mudge, Craig Wallin, Carlos G Girón, Mark Diekhans, If Barnes, Ruth Bennett, Andrew E Berry, Eric Cox, Claire Davidson, Tamara Goldfarb, Jose M Gonzalez, Toby Hunt, John Jackson, Vinita Joardar, Mike P Kay, Vamsi K Kodali, Fergal J Martin, Monica McAndrews, Kelly M McGarvey, Michael Murphy, Bhanu Rajput, Sanjida H Rangwala, Lillian D Riddick, Ruth L Seal, Marie-Marthe Suner, David Webb, Sophia Zhu, Bronwen L Aken, Elspeth A Bruford, Carol J Bult, Adam Frankish, Terence Murphy, Kim D Pruitt
The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID)...
November 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29104938/vitamin-and-amino-acid-auxotrophy-in-anaerobic-consortia-operating-under-methanogenic-conditions
#2
Valerie Hubalek, Moritz Buck, BoonFei Tan, Julia Foght, Annelie Wendeberg, David Berry, Stefan Bertilsson, Alexander Eiler
Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methanogenic conditions...
September 2017: MSystems
https://www.readbyqxmd.com/read/29104582/vvvhp1-2-is-transcriptionally-activated-by-vvmyba1-and-promotes-anthocyanin-accumulation-of-grape-berry-skins-via-glucose-signal
#3
Tianyu Sun, Lili Xu, Hong Sun, Qianyu Yue, Heng Zhai, Yuxin Yao
In this work, four vacuolar H(+)-PPase (VHP) genes were identified in the grape genome. Among them, VvVHP1; 2 was strongly expressed in berry skin and its expression exhibited high correlations to anthocyanin content of berry skin during berry ripening and under ABA and UVB treatments. VvVHP1; 2 was transcriptionally activated directly by VvMYBA1, and VvVHP1; 2 overexpression promoted anthocyanin accumulation in berry skins and Arabidopsis leaves; therefore, VvVHP1; 2 mediated VvMYBA1-regulated berry pigmentation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29080323/seascape-genomics-reveals-fine-scale-patterns-of-dispersal-for-a-reef-fish-along-the-ecologically-divergent-coast-of-northwestern-australia
#4
Joseph D DiBattista, Michael J Travers, Glenn I Moore, Richard D Evans, Stephen J Newman, Ming Feng, Samuel D Moyle, Rebecca J Gorton, Thor Saunders, Oliver Berry
Understanding the drivers of dispersal among populations is a central topic in marine ecology and fundamental for spatially explicit management of marine resources. The extensive coast of Northwestern Australia provides an emerging frontier for implementing new genomic tools to comparatively identify patterns of dispersal across diverse and extreme environmental conditions. Here, we focused on the stripey snapper (Lutjanus carponotatus), which is important to recreational, charter-based and customary fishers throughout the Indo-West Pacific...
October 28, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29058421/authentication-of-zanthoxylum-species-based-on-integrated-analysis-of-complete-chloroplast-genome-sequences-and-metabolite-profiles
#5
Hyeon Ju Lee, Hyun Jo Koo, Jonghoon Lee, Dong Young Lee, Vo Ngoc Linh Giang, Minjung Kim, Hyeonah Shim, Jee Young Park, Ki-Oug Yoo, Sang Hyun Sung, Tae-Jin Yang
We performed chloroplast genome sequencing and comparative analysis of two Rutaceae species, Zanthoxylum schinifolium (Korean pepper tree) and Z. piperitum (Japanese pepper tree), which are medicinal and culinary crops in Asia. We identified more than 837 single nucleotide polymorphisms and 103 insertions/deletions (InDels) based on a comparison of the two chloroplast genomes and developed seven DNA markers derived from five tandem repeats and two InDel variations that discriminated between Korean Zanthoxylum species...
October 23, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29049475/potential-of-aqueous-humor-as-a-surrogate-tumor-biopsy-for-retinoblastoma
#6
Jesse L Berry, Liya Xu, A Linn Murphree, Subramanian Krishnan, Kevin Stachelek, Emily Zolfaghari, Kathleen McGovern, Thomas C Lee, Anders Carlsson, Peter Kuhn, Jonathan W Kim, David Cobrinik, James Hicks
Importance: Retinoblastoma (Rb) is one of the first tumors to have a known genetic etiology. However, because biopsy of this tumor is contraindicated, it has not been possible to define the effects of secondary genetic changes on the disease course. Objective: To investigate whether the aqueous humor (AH) of Rb eyes has sufficient tumor-derived DNA to perform genetic analysis of the tumor, including DNA copy number alterations. Design, Setting, and Participants: This investigation was a case series study at a tertiary care hospital (Children's Hospital Los Angeles) with a large Rb treatment center...
November 1, 2017: JAMA Ophthalmology
https://www.readbyqxmd.com/read/29048594/neptune-a-bioinformatics-tool-for-rapid-discovery-of-genomic-variation-in-bacterial-populations
#7
Eric Marinier, Rahat Zaheer, Chrystal Berry, Kelly A Weedmark, Michael Domaratzki, Philip Mabon, Natalie C Knox, Aleisha R Reimer, Morag R Graham, Linda Chui, Laura Patterson-Fortin, Jian Zhang, Franco Pagotto, Jeff Farber, Jim Mahony, Karine Seyer, Sadjia Bekal, Cécile Tremblay, Judy Isaac-Renton, Natalie Prystajecky, Jessica Chen, Peter Slade, Gary Van Domselaar
The ready availability of vast amounts of genomic sequence data has created the need to rethink comparative genomics algorithms using 'big data' approaches. Neptune is an efficient system for rapidly locating differentially abundant genomic content in bacterial populations using an exact k-mer matching strategy, while accommodating k-mer mismatches. Neptune's loci discovery process identifies sequences that are sufficiently common to a group of target sequences and sufficiently absent from non-targets using probabilistic models...
October 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29039721/a-recurrent-splice-site-mutation-in-epha2-causing-congenital-posterior-nuclear-cataract
#8
Vanita Berry, Nikolas Pontikos, Monica Albarca-Aguilera, Vincent Plagnol, Andreas Massouras, DeQuincy Prescott, Anthony T Moore, Gavin Arno, Michael E Cheetham, Michel Michaelides
Intoduction: Inherited cataract, opacification of the lens, is the most common worldwide cause of blindness in children. We aimed to identify the genetic cause of autosomal dominant (AD) posterior nuclear cataract in a four generation British family. METHODS: Whole genome sequence (WGS) was performed on two affected and one unaffected individual of the family and further validated by direct sequencing. Haplotype analysis was performed via genotying. RESULTS: A splice-site mutation c...
October 17, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/29027367/the-parasporal-crystals-of-bacillus-pumilus-strain-15-1-a-potential-virulence-factor
#9
Diana C Garcia-Ramon, Colin Berry, Carmen Tse, Alberto Fernández-Fernández, Antonio Osuna, Susana Vílchez
Bacillus pumilus strain 15.1 was previously found to cause larval mortality in the Med-fly Ceratitis capitata and was shown to produce crystals in association with the spore. As parasporal crystals are well-known as invertebrate-active toxins in entomopathogenic bacteria such as Bacillus thuringiensis (Cry and Cyt toxins) and Lysinibacillus sphaericus (Bin and Cry toxins), the B. pumilus crystals were characterized. The crystals were composed of a 45 kDa protein that was identified as an oxalate decarboxylase by peptide mass fingerprinting, N-terminal sequencing and by comparison with the genome sequence of strain 15...
October 12, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/29020009/genome-sequences-of-lower-great-lakes-microcystis-sp-reveal-strain-specific-genes-that-are-present-and-expressed-in-western-lake-erie-blooms
#10
Kevin Anthony Meyer, Timothy W Davis, Susan B Watson, Vincent J Denef, Michelle A Berry, Gregory J Dick
Blooms of the potentially toxic cyanobacterium Microcystis are increasing worldwide. In the Laurentian Great Lakes they pose major socioeconomic, ecological, and human health threats, particularly in western Lake Erie. However, the interpretation of "omics" data is constrained by the highly variable genome of Microcystis and the small number of reference genome sequences from strains isolated from the Great Lakes. To address this, we sequenced two Microcystis isolates from Lake Erie (Microcystis aeruginosa LE3 and M...
2017: PloS One
https://www.readbyqxmd.com/read/29019092/rapid-detection-of-human-norovirus-in-frozen-raspberries
#11
Maija Summa, Leena Maunula
Raspberries have lately caused several human norovirus (HuNoV) outbreaks in Europe. In this study, we developed and evaluated for HuNoV reverse transcription (RT)-PCR detection in frozen raspberries extraction methods that have equal sensitivity but are less time-consuming than widely used methods based on polyethylene glycol (PEG) precipitation and chloroform-butanol purification. One method was applied to stored frozen raspberries linked to previous HuNoV outbreaks and berries on sale. In the virus elution-based Method 1, sparkling water eluted viruses most efficiently from the berries...
October 10, 2017: Food and Environmental Virology
https://www.readbyqxmd.com/read/28910288/genomics-enabled-analysis-of-the-emergent-disease-cotton-bacterial-blight
#12
Anne Z Phillips, Jeffrey C Berry, Mark C Wilson, Anupama Vijayaraghavan, Jillian Burke, J Imani Bunn, Tom W Allen, Terry Wheeler, Rebecca S Bart
Cotton bacterial blight (CBB), an important disease of (Gossypium hirsutum) in the early 20th century, had been controlled by resistant germplasm for over half a century. Recently, CBB re-emerged as an agronomic problem in the United States. Here, we report analysis of cotton variety planting statistics that indicate a steady increase in the percentage of susceptible cotton varieties grown each year since 2009. Phylogenetic analysis revealed that strains from the current outbreak cluster with race 18 Xanthomonas citri pv...
September 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28894154/n-terminomics-identifies-widespread-endoproteolysis-and-novel-methionine-excision-in-a-genome-reduced-bacterial-pathogen
#13
Iain J Berry, Veronica M Jarocki, Jessica L Tacchi, Benjamin B A Raymond, Michael Widjaja, Matthew P Padula, Steven P Djordjevic
Proteolytic processing alters protein function. Here we present the first systems-wide analysis of endoproteolysis in the genome-reduced pathogen Mycoplasma hyopneumoniae. 669 N-terminal peptides from 164 proteins were identified, demonstrating that functionally diverse proteins are processed, more than half of which 75 (53%) were accessible on the cell surface. Multiple cleavage sites were characterised, but cleavage with arginine in P1 predominated. Putative functions for a subset of cleaved fragments were assigned by affinity chromatography using heparin, actin, plasminogen and fibronectin as bait...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28894125/elongation-factor-tu-is-a-multifunctional-and-processed-moonlighting-protein
#14
Michael Widjaja, Kate Louise Harvey, Lisa Hagemann, Iain James Berry, Veronica Maria Jarocki, Benjamin Bernard Armando Raymond, Jessica Leigh Tacchi, Anne Gründel, Joel Ricky Steele, Matthew Paul Padula, Ian George Charles, Roger Dumke, Steven Philip Djordjevic
Many bacterial moonlighting proteins were originally described in medically, agriculturally, and commercially important members of the low G + C Firmicutes. We show Elongation factor Tu (Ef-Tu) moonlights on the surface of the human pathogens Staphylococcus aureus (SaEf-Tu) and Mycoplasma pneumoniae (MpnEf-Tu), and the porcine pathogen Mycoplasma hyopneumoniae (MhpEf-Tu). Ef-Tu is also a target of multiple processing events on the cell surface and these were characterised using an N-terminomics pipeline...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28843071/rna-seq-based-transcriptomic-analysis-of-cppu-treated-grape-berries-and-emission-of-volatile-compounds
#15
Wu Wang, Muhammad Khalil-Ur-Rehman, Jiao Feng, Jianmin Tao
Grapevine (Vitis vinifera L.) is considered to be one of the most popular and widespread fruit crops in the world. Numerous value added products are prepared from grape fruit and investments are being made to establish new viticulture region (Hoff et al., 2017; Imran et al., 2017). CPPU [forchlorfenuron N-(2-chloro-4-pyridyl)-N-phenylurea] is a synthetic cytokine-like plant regulator which promotes grape berry set and development. The influence of CPPU [forchlorfenuron N-(2-chloro-4-pyridyl)-N-phenylurea] on berry development of 'Shine Muscat' (Vitis labruscana Bailey×V vinifera L...
August 12, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28815698/altered-regulation-of-terminal-flower-1-causes-the-unique-vernalisation-response-in-an-arctic-woodland-strawberry-accession
#16
Elli A Koskela, Takeshi Kurokura, Tuomas Toivainen, Anita Sønsteby, Ola M Heide, Daniel J Sargent, Sachiko Isobe, Laura Jaakola, Hrannar Hilmarsson, Paula Elomaa, Timo Hytönen
Vernalisation requirement is an agriculturally important trait that postpones the development of cold-sensitive floral organs until the spring. The family Rosaceae includes many agriculturally important fruit and berry crops that suffer from crop losses caused by frost injury to overwintering flower buds. Recently, a vernalisation-requiring accession of the Rosaceae model woodland strawberry (Fragaria vesca) has been identified in northern Norway. Understanding the molecular basis of the vernalisation requirement in this accession would advance the development of strawberry cultivars better adapted to temperate climate...
August 16, 2017: New Phytologist
https://www.readbyqxmd.com/read/28811336/catastrophic-unbalanced-genome-rearrangements-cause-somatic-loss-of-berry-color-in-grapevine
#17
Pablo Carbonell-Bejerano, Carolina Royo, Rafael Torres-Pérez, Jérôme Grimplet, Lucie Fernandez, José Manuel Franco-Zorrilla, Diego Lijavetzky, Elisa Baroja, Juana Martínez, Enrique García-Escudero, Javier Ibáñez, José Miguel Martínez-Zapater
Grape (Vitis vinifera) color somatic variants that can be used to develop new grapevine cultivars occasionally appear associated with deletion events of uncertain origin. To understand the mutational mechanisms generating somatic structural variation in grapevine, we compared the Tempranillo Blanco (TB) white berry somatic variant with its black berry ancestor, Tempranillo Tinto. Whole-genome sequencing uncovered a catastrophic genome rearrangement in TB that caused the hemizygous deletion of 313 genes, including the loss of the functional copy for the MYB transcription factors required for anthocyanin pigmentation in the berry skin...
October 2017: Plant Physiology
https://www.readbyqxmd.com/read/28791127/patterns-of-genomic-and-phenomic-diversity-in-wine-and-table-grapes
#18
Zoë Migicovsky, Jason Sawler, Kyle M Gardner, Mallikarjuna K Aradhya, Bernard H Prins, Heidi R Schwaninger, Carlos D Bustamante, Edward S Buckler, Gan-Yuan Zhong, Patrick J Brown, Sean Myles
Grapes are one of the most economically and culturally important crops worldwide, and they have been bred for both winemaking and fresh consumption. Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world's largest grape gene banks, the grape germplasm collection of the United States Department of Agriculture. We find that phenological events throughout the growing season are correlated, and quantify the marked difference in size between table and wine grapes...
2017: Horticulture Research
https://www.readbyqxmd.com/read/28780070/identification-of-cry48aa-cry49aa-toxin-ligands-in-the-midgut-of-culex-quinquefasciatus-larvae
#19
Tatiana Maria Teodoro Rezende, Tatiany Patrícia Romão, Michel Batista, Colin Berry, Michael J Adang, Maria Helena Neves Lobo Silva-Filha
A binary mosquitocidal toxin composed of a three-domain Cry-like toxin (Cry48Aa) and a binary-like toxin (Cry49Aa) was identified in Lysinibacillus sphaericus. Cry48Aa/Cry49Aa has action on Culex quinquefasciatus larvae, in particular, to those that are resistant to the Bin Binary toxin, which is the major insecticidal factor from L. sphaericus-based biolarvicides, indicating that Cry48Aa/Cry49Aa interacts with distinct target sites in the midgut and can overcome Bin toxin resistance. This study aimed to identify Cry48Aa/Cry49Aa ligands in C...
September 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28717173/liquid-phase-sequence-capture-and-targeted-re-sequencing-revealed-novel-polymorphisms-in-tomato-genes-belonging-to-the-mep-carotenoid-pathway
#20
Irma Terracciano, Concita Cantarella, Carlo Fasano, Teodoro Cardi, Giuseppe Mennella, Nunzio D'Agostino
Tomato (Solanum lycopersicum L.) plants are characterized by having a variety of fruit colours that reflect the composition and accumulation of diverse carotenoids in the berries. Carotenoids are extensively studied for their health-promoting effects and this explains the great attention these pigments received by breeders and researchers worldwide. In this work we applied Agilent's SureSelect liquid-phase sequence capture and Illumina targeted re-sequencing of 34 tomato genes belonging to the methylerythritol phosphate (MEP) carotenoid pathway on a panel of 48 genotypes which differ for carotenoid content calculated as the sum of β-carotene, cis- and trans-lycopene...
July 17, 2017: Scientific Reports
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