Comparative analysis of differentially expressed genes in normal and white spot syndrome virus infected Penaeus monodon.

abstract：BACKGROUND:Biocontrol of bacterial pathogens by bacteriophages (phages) represents a promising strategy. Vibrio alginolyticus, a gram-negative bacterium, is a notorious pathogen responsible for the loss of economically important farmed marine animals. To date, few V. alginolyticus phages have been successfully isolated...

journal_title：BMC genomics

authors： Luo P,Yun L,Li Y,Tian Y,Liu Q,Huang W,Hu C

更新日期：2018-10-11 00:00:00

abstract：BACKGROUND:A-to-I RNA editing is a co-/post-transcriptional modification catalyzed by ADAR enzymes, that deaminates Adenosines (A) into Inosines (I). Most of known editing events are located within inverted ALU repeats, but they also occur in coding sequences and may alter the function of encoded proteins. RNA editing ...

journal_title：BMC genomics

authors： Giacopuzzi E,Gennarelli M,Sacco C,Filippini A,Mingardi J,Magri C,Barbon A

更新日期：2018-12-27 00:00:00

abstract：BACKGROUND:Parasites employ proteases to evade host immune systems, feed and replicate and are often the target of anti-parasite strategies to disrupt these interactions. Myxozoans are obligate cnidarian parasites, alternating between invertebrate and fish hosts. Their genes are highly divergent from other metazoans, a...

journal_title：BMC genomics

authors： Hartigan A,Kosakyan A,Pecková H,Eszterbauer E,Holzer AS

更新日期：2020-06-16 00:00:00

abstract：BACKGROUND:Protein effectors of pathogenicity are instrumental in modulating host immunity and disease resistance. The powdery mildew pathogen of grasses Blumeria graminis causes one of the most important diseases of cereal crops. B. graminis is an obligate biotrophic pathogen and as such has an absolute requirement to...

journal_title：BMC genomics

authors： Pedersen C,Ver Loren van Themaat E,McGuffin LJ,Abbott JC,Burgis TA,Barton G,Bindschedler LV,Lu X,Maekawa T,Wessling R,Cramer R,Thordal-Christensen H,Panstruga R,Spanu PD

更新日期：2012-12-11 00:00:00

abstract：BACKGROUND:To generate specific transcript profiles, one must isolate homogenous cell populations using techniques that often yield small amounts of RNA, requiring researchers to employ RNA amplification methods. The data generated by using these methods must be extensively evaluated to determine any technique dependen...

journal_title：BMC genomics

authors： Gold D,Coombes K,Medhane D,Ramaswamy A,Ju Z,Strong L,Koo JS,Kapoor M

更新日期：2004-01-06 00:00:00

abstract：BACKGROUND:Mammalian genomes contain a large number (approximately 1000) of olfactory receptor (OR) genes, many of which (20 to 50%) are pseudogenes. OR gene transcription is not restricted to the olfactory epithelium, but is found in numerous tissues. Using microarray hybridization and RTqPCR, we analyzed the mRNA pro...

journal_title：BMC genomics

authors： Rimbault M,Robin S,Vaysse A,Galibert F

更新日期：2009-12-02 00:00:00

abstract：BACKGROUND:The question of whether bacterial species objectively exist has long divided microbiologists. A major source of contention stems from the fact that bacteria regularly engage in horizontal gene transfer (HGT), making it difficult to ascertain relatedness and draw boundaries between taxa. A natural way to defi...

journal_title：BMC genomics

authors： Wright ES,Baum DA

更新日期：2018-10-03 00:00:00

abstract：BACKGROUND:The ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are found throughout the teleost phylogeny, in quite diverse and unrelated lineages, indicating stomach ...

journal_title：BMC genomics

authors： Lie KK,Tørresen OK,Solbakken MH,Rønnestad I,Tooming-Klunderud A,Nederbragt AJ,Jentoft S,Sæle Ø

更新日期：2018-03-06 00:00:00

abstract：BACKGROUND:Bananas (Musa spp.) are an important crop worldwide. Most modern cultivars resulted from a complex polyploidization history that comprised three whole genome duplications (WGDs) shaping the haploid Musa genome, followed by inter- and intra-specific crosses between Musa acuminata and M. balbisiana (A and B ge...

journal_title：BMC genomics

authors： Cenci A,Hueber Y,Zorrilla-Fontanesi Y,van Wesemael J,Kissel E,Gislard M,Sardos J,Swennen R,Roux N,Carpentier SC,Rouard M

更新日期：2019-03-27 00:00:00

abstract：BACKGROUND:Antimicrobial resistance is one of our most serious health threats. Antimicrobial peptides (AMPs), effecter molecules of innate immune system, can defend host organisms against microbes and most have shown a lowered likelihood for bacteria to form resistance compared to many conventional drugs. Thus, AMPs ar...

journal_title：BMC genomics

authors： Fu H,Cao Z,Li M,Wang S

更新日期：2020-08-28 00:00:00

abstract：BACKGROUND:For centuries roses have been selected based on a number of traits. Little information exists on the genetic and molecular basis that contributes to these traits, mainly because information on expressed genes for this economically important ornamental plant is scarce. RESULTS:Here, we used a combination of ...

journal_title：BMC genomics

authors： Dubois A,Carrere S,Raymond O,Pouvreau B,Cottret L,Roccia A,Onesto JP,Sakr S,Atanassova R,Baudino S,Foucher F,Le Bris M,Gouzy J,Bendahmane M

更新日期：2012-11-20 00:00:00

abstract：BACKGROUND:Deep sequencing is a powerful tool for assessing viral genetic diversity. Such experiments harness the high coverage afforded by next generation sequencing protocols by treating sequencing reads as a population sample. Distinguishing true single nucleotide variants (SNVs) from sequencing errors remains chall...

journal_title：BMC genomics

authors： McElroy K,Zagordi O,Bull R,Luciani F,Beerenwinkel N

更新日期：2013-07-24 00:00:00

abstract：BACKGROUND:Root-knot nematodes are sedentary endoparasites that can infect more than 3000 plant species. Root-knot nematodes cause an estimated $100 billion annual loss worldwide. For successful establishment of the root-knot nematode in its host plant, it causes dramatic morphological and physiological changes in plan...

journal_title：BMC genomics

authors： Ibrahim HM,Hosseini P,Alkharouf NW,Hussein EH,Gamal El-Din Ael K,Aly MA,Matthews BF

更新日期：2011-05-10 00:00:00

abstract：BACKGROUND:Pectobacterium spp. are necrotrophic bacterial plant pathogens of the family Pectobacteriaceae, responsible for a wide spectrum of diseases of important crops and ornamental plants including soft rot, blackleg, and stem wilt. P. carotovorum is a genetically heterogeneous species consisting of three valid sub...

journal_title：BMC genomics

authors： Li X,Ma Y,Liang S,Tian Y,Yin S,Xie S,Xie H

更新日期：2018-12-07 00:00:00

abstract：BACKGROUND:Epidermal Growth Factor (EGF) is a key regulatory growth factor activating many processes relevant to normal development and disease, affecting cell proliferation and survival. Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based ...

journal_title：BMC genomics

authors： Llorens F,Hummel M,Pastor X,Ferrer A,Pluvinet R,Vivancos A,Castillo E,Iraola S,Mosquera AM,González E,Lozano J,Ingham M,Dohm JC,Noguera M,Kofler R,del Río JA,Bayés M,Himmelbauer H,Sumoy L

更新日期：2011-06-23 00:00:00

abstract：BACKGROUND:Among viruses, bacteriophages are a group of special interest due to their capacity of infecting bacteria that are important for biotechnology and human health. Composting is a microbial-driven process in which complex organic matter is converted into humus-like substances. In thermophilic composting, the de...

journal_title：BMC genomics

authors： Amgarten D,Martins LF,Lombardi KC,Antunes LP,de Souza APS,Nicastro GG,Kitajima EW,Quaggio RB,Upton C,Setubal JC,da Silva AM

更新日期：2017-05-04 00:00:00

abstract：BACKGROUND:Molecular mechanisms underlying coral larval competence, the ability of larvae to respond to settlement cues, determine their dispersal potential and are potential targets of natural selection. Here, we profiled competence, fluorescence and genome-wide gene expression in embryos and larvae of the reef-buildi...

journal_title：BMC genomics

authors： Strader ME,Aglyamova GV,Matz MV

更新日期：2018-01-04 00:00:00

abstract：BACKGROUND:Genotyping-by-sequencing (GBS) is becoming an attractive alternative to array-based methods for genotyping individuals for a large number of single nucleotide polymorphisms (SNPs). Costs can be lowered by reducing the mean sequencing depth, but this results in genotype calls of lower quality. A common analys...

journal_title：BMC genomics

authors： Dodds KG,McEwan JC,Brauning R,Anderson RM,van Stijn TC,Kristjánsson T,Clarke SM

更新日期：2015-12-09 00:00:00

abstract：BACKGROUND:Belonging to lineage I of Brassicaceae, Camelina sativa is formed by two hybridizations of three species (three sub-genomes). The three sub-genomes were diverged from a common ancestor, likely derived from lineage I (Ancestral Crucifer karyotype, ACK). The karyotype evolutionary trajectories of the C. sativa...

journal_title：BMC genomics

authors： Zhang Z,Meng F,Sun P,Yuan J,Gong K,Liu C,Wang W,Wang X

更新日期：2020-10-12 00:00:00

abstract：BACKGROUND:It is becoming apparent that perhaps as much as half of the genome of the human blood fluke Schistosoma mansoni is constituted of mobile genetic element-related sequences. Non-long terminal repeat (LTR) retrotransposons, related to the LINE elements of mammals, comprise much of this repetitive component of t...

journal_title：BMC genomics

authors： Laha T,Kewgrai N,Loukas A,Brindley PJ

更新日期：2005-11-04 00:00:00

abstract：BACKGROUND:Cultivated watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is an important agriculture crop world-wide. The fruit of watermelon undergoes distinct stages of development with dramatic changes in its size, color, sweetness, texture and aroma. In order to better understand the genetic and m...

journal_title：BMC genomics

authors： Guo S,Liu J,Zheng Y,Huang M,Zhang H,Gong G,He H,Ren Y,Zhong S,Fei Z,Xu Y

更新日期：2011-09-21 00:00:00

abstract：BACKGROUND:Cultivated peanut (Arachis hypogaea) is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (several millennia) evolutionary origin of A. hypogaea has imposed a bottleneck for allelic and ph...

journal_title：BMC genomics

authors： Nagy ED,Guo Y,Tang S,Bowers JE,Okashah RA,Taylor CA,Zhang D,Khanal S,Heesacker AF,Khalilian N,Farmer AD,Carrasquilla-Garcia N,Penmetsa RV,Cook D,Stalker HT,Nielsen N,Ozias-Akins P,Knapp SJ

更新日期：2012-09-11 00:00:00

abstract：BACKGROUND:Polypyrimidine-tract binding proteins (PTBs) are ubiquitous RNA-binding proteins in plants and animals that play diverse role in RNA metabolic processes. PTB proteins bind to target RNAs through motifs rich in cytosine/uracil residues to fine-tune transcript metabolism. Among tuber and root crops, potato has...

journal_title：BMC genomics

authors： Kondhare KR,Kumar A,Hannapel DJ,Banerjee AK

更新日期：2018-02-07 00:00:00

abstract：BACKGROUND:Excretory/secretory proteins (ESPs) play a major role in parasitic infection as they are present at the host-parasite interface and regulate host immune system. In case of parasitic helminths, transcriptomics has been used extensively to understand the molecular basis of parasitism and for developing novel t...

journal_title：BMC genomics

authors： Garg G,Ranganathan S

更新日期：2011-11-30 00:00:00

abstract：BACKGROUND:Many computational methods are available for assembly and annotation of newly sequenced microbial genomes. However, when new genomes are reported in the literature, there is frequently very little critical analysis of choices made during the sequence assembly and gene annotation stages. These choices have a ...

journal_title：BMC genomics

authors： Morrison SS,Pyzh R,Jeon MS,Amaro C,Roig FJ,Baker-Austin C,Oliver JD,Gibas CJ

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Plants contain significant quantities of small RNAs (sRNAs) derived from various sRNA biogenesis pathways. Many of these sRNAs play regulatory roles in plants. Previous analysis revealed that numerous sRNAs in corn, rice and soybean seeds have high sequence similarity to animal genes. However, exogenous RNA ...

journal_title：BMC genomics

authors： Zhang Y,Wiggins BE,Lawrence C,Petrick J,Ivashuta S,Heck G

更新日期：2012-08-08 00:00:00

abstract：BACKGROUND:Olfaction is a versatile sensory mechanism for detecting thousands of volatile odorants. Although molecular basis of odorant signaling is relatively well understood considerable gaps remain in the complete charting of all relevant gene products. To address this challenge, we applied RNAseq to four well-chara...

journal_title：BMC genomics

authors： Olender T,Keydar I,Pinto JM,Tatarskyy P,Alkelai A,Chien MS,Fishilevich S,Restrepo D,Matsunami H,Gilad Y,Lancet D

更新日期：2016-08-11 00:00:00

abstract：BACKGROUND:The main limitations in the analysis of viral metagenomes are perhaps the high genetic variability and the lack of information in extant databases. To address these issues, several bioinformatic tools have been specifically designed or adapted for metagenomics by improving read assembly and creating more sen...

journal_title：BMC genomics

authors： Vázquez-Castellanos JF,García-López R,Pérez-Brocal V,Pignatelli M,Moya A

更新日期：2014-01-18 00:00:00

abstract：BACKGROUND:Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community. This task is challenging due to the complexity of microbiome composition...

journal_title：BMC genomics

authors： Hua K,Zhang X

更新日期：2019-04-04 00:00:00

abstract：BACKGROUND:Lipoxygenases (LOXs), a type of non-haem iron-containing dioxygenase, are ubiquitous enzymes in plants and participate in the formation of fruit aroma which is a very important aspect of fruit quality. Amongst the various aroma volatiles, saturated and unsaturated alcohols and aldehydes provide the character...

journal_title：BMC genomics

authors： Li M,Li L,Dunwell JM,Qiao X,Liu X,Zhang S

更新日期：2014-06-07 00:00:00