Comparative genomics and concerted evolution of beta-tubulin paralogs in Leishmania spp.

abstract：BACKGROUND:Interactions between fish and pathogens, that may be harmless under natural conditions, often result in serious diseases in aquaculture systems. This is especially important due to the fact that the strains used in aquaculture are derived from wild strains that may not have had enough time to adapt to new di...

journal_title：BMC genomics

authors： Rodríguez-Ramilo ST,Toro MA,Bouza C,Hermida M,Pardo BG,Cabaleiro S,Martínez P,Fernández J

更新日期：2011-11-02 00:00:00

abstract：BACKGROUND:Starch and protein are two major components of polished rice, and the amylose and protein contents affect eating and cooking qualities (ECQs). In the present study, genome-wide association study with high-quality re-sequencing data was performed for 10 ECQs in a panel of 227 non-glutinous rice accessions and...

journal_title：BMC genomics

authors： Xu F,Bao J,He Q,Park YJ

更新日期：2016-08-20 00:00:00

abstract：BACKGROUND:Phanerochaete chrysosporium, the model white rot basidiomycetous fungus, has the extraordinary ability to mineralize (to CO2) lignin and detoxify a variety of chemical pollutants. Its cytochrome P450 monooxygenases have recently been implied in several of these biotransformations. Our initial P450 cloning ef...

journal_title：BMC genomics

authors： Doddapaneni H,Chakraborty R,Yadav JS

更新日期：2005-06-14 00:00:00

abstract：BACKGROUND:Genome-wide disease-gene finding approaches may sometimes provide us with a long list of candidate genes. Since using pure experimental approaches to verify all candidates could be expensive, a number of network-based methods have been developed to prioritize candidates. Such tools usually have a set of para...

journal_title：BMC genomics

authors： Hsu CL,Huang YH,Hsu CT,Yang UC

更新日期：2011-11-30 00:00:00

abstract：BACKGROUND:Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem. RESULTS:Existing algorithms are largely optimized for speed and coverage; in con...

journal_title：BMC genomics

authors： Stark M,Berger SA,Stamatakis A,von Mering C

更新日期：2010-08-05 00:00:00

abstract：BACKGROUND:We developed a novel software package, XCAVATOR, for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments. RESULTS:By using simulated and real datasets we showed that our tool, based on read count approac...

journal_title：BMC genomics

authors： Magi A,Pippucci T,Sidore C

更新日期：2017-09-21 00:00:00

abstract：BACKGROUND:Sequencing of the approximately 1.7 billion bases of the zebrafish genome is currently underway. To date, few high resolution genetic maps exist for the zebrafish genome, based mainly on single nucleotide polymorphisms (SNPs) and short microsatellite repeats. The desire to construct a higher resolution genet...

journal_title：BMC genomics

authors： Rouchka EC

更新日期：2010-06-01 00:00:00

abstract：BACKGROUND:Advances in whole genome profiling have revolutionized the cancer research field, but at the same time have raised new bioinformatics challenges. For next generation sequencing (NGS), these include data storage, computational costs, sequence processing and alignment, delineating appropriate statistical measu...

journal_title：BMC genomics

authors： Rodriguez BA,Frankhouser D,Murphy M,Trimarchi M,Tam HH,Curfman J,Huang R,Chan MW,Lai HC,Parikh D,Ball B,Schwind S,Blum W,Marcucci G,Yan P,Bundschuh R

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Many tools exist to predict structural variants (SVs), utilizing a variety of algorithms. However, they have largely been developed and tested on human germline or somatic (e.g. cancer) variation. It seems appropriate to exploit this wealth of technology available for humans also for other species. Objective...

journal_title：BMC genomics

authors： Leung WY,Marschall T,Paudel Y,Falquet L,Mei H,Schönhuth A,Maoz Moss TY

更新日期：2015-03-25 00:00:00

abstract：BACKGROUND:Several in vitro studies document the function of the transcriptional regulator TrmBL1 of Pyrococcus furiosus. These data indicate that the protein can act as repressor or activator and is mainly involved in transcriptional control of sugar uptake and in the switch between glycolysis and gluconeogenesis. The...

journal_title：BMC genomics

authors： Reichelt R,Gindner A,Thomm M,Hausner W

更新日期：2016-01-08 00:00:00

abstract：BACKGROUND:The gilthead sea bream (Sparus aurata) is the main fish species cultured in the Mediterranean area and constitutes an interesting model of research. Nevertheless, transcriptomic and genomic data are still scarce for this highly valuable species. A transcriptome database was constructed by de novo assembly of...

journal_title：BMC genomics

authors： Calduch-Giner JA,Bermejo-Nogales A,Benedito-Palos L,Estensoro I,Ballester-Lozano G,Sitjà-Bobadilla A,Pérez-Sánchez J

更新日期：2013-03-15 00:00:00

abstract：BACKGROUND:Research on the aryl hydrocarbon receptor (AHR) has largely focused on variations in toxic outcomes resulting from its activation by halogenated aromatic hydrocarbons. But the AHR also plays key roles in regulating pathways critical for development, and after decades of research the mechanisms underlying phy...

journal_title：BMC genomics

authors： Sun RX,Chong LC,Simmons TT,Houlahan KE,Prokopec SD,Watson JD,Moffat ID,Lensu S,Lindén J,P'ng C,Okey AB,Pohjanvirta R,Boutros PC

更新日期：2014-12-03 00:00:00

abstract：BACKGROUND:Tandem mass spectrometry allows biologists to identify and quantify protein samples in the form of digested peptide sequences. When performing peptide identification, spectral library search is more sensitive than traditional database search but is limited to peptides that have been previously identified. An...

journal_title：BMC genomics

authors： Lin YM,Chen CT,Chang JM

更新日期：2019-12-24 00:00:00

abstract：BACKGROUND:Sugarcane is a major sugar and biofuel crop, but genomic research and molecular breeding have lagged behind other major crops due to the complexity of auto-allopolyploid genomes. Sugarcane cultivars are frequently aneuploid with chromosome number ranging from 100 to 130, consisting of 70-80 % S. officinarum,...

journal_title：BMC genomics

authors： Zhang J,Sharma A,Yu Q,Wang J,Li L,Zhu L,Zhang X,Chen Y,Ming R

更新日期：2016-06-10 00:00:00

abstract：BACKGROUND:Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. RESULTS:We describe a Web-...

journal_title：BMC genomics

authors： Tan TW,Xie C,De Silva M,Lim KS,Patro CP,Lim SJ,Govindarajan KR,Tong JC,Choo KH,Ranganathan S,Khan AM

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Parasitoid wasps are well-known natural enemies of major agricultural pests and arthropod borne diseases. The parasitoid wasp Macrocentrus cingulum (Hymenoptera: Braconidae) has been widely used to control the notorious insect pests Ostrinia furnacalis (Asian Corn Borer) and O. nubilalis (European corn borer...

journal_title：BMC genomics

authors： Yin C,Li M,Hu J,Lang K,Chen Q,Liu J,Guo D,He K,Dong Y,Luo J,Song Z,Walters JR,Zhang W,Li F,Chen X

更新日期：2018-05-30 00:00:00

abstract：BACKGROUND:Common Pekin and Muscovy ducks and their intergeneric hinny and mule hybrids have different abilities for fatty liver production. RNA-Seq analyses from the liver of these different genetic types fed ad libitum or overfed would help to identify genes with different response to overfeeding between them. Howeve...

journal_title：BMC genomics

authors： Liu X,Hérault F,Diot C,Corre E

更新日期：2020-10-02 00:00:00

abstract：BACKGROUND:Miniature inverted repeat transposable element (MITE) is one type of transposable element (TE), which is largely found in eukaryotic genomes and involved in a wide variety of biological events. However, only few MITEs were proved to be currently active and their physiological function remains largely unknown...

journal_title：BMC genomics

authors： Dong HT,Zhang L,Zheng KL,Yao HG,Chen J,Yu FC,Yu XX,Mao BZ,Zhao D,Yao J,Li DB

更新日期：2012-04-13 00:00:00

abstract：BACKGROUND:New gene emergence is so far assumed to be mostly driven by duplication and divergence of existing genes. The possibility that entirely new genes could emerge out of the non-coding genomic background was long thought to be almost negligible. With the increasing availability of fully sequenced genomes across ...

journal_title：BMC genomics

authors： Neme R,Tautz D

更新日期：2013-02-21 00:00:00

abstract：BACKGROUND:The unisexual Amazon molly (Poecilia formosa) originated from a hybridization between two sexual species, the sailfin molly (Poecilia latipinna) and the Atlantic molly (Poecilia mexicana). The Amazon molly reproduces clonally via sperm-dependent parthenogenesis (gynogenesis), in which the sperm of closely re...

journal_title：BMC genomics

authors： Schedina IM,Groth D,Schlupp I,Tiedemann R

更新日期：2018-01-03 00:00:00

abstract：BACKGROUND:Hibernation is a physiological state exploited by many animals exposed to prolonged adverse environmental conditions associated with winter. Large changes in metabolism and cellular function occur, with many stress response pathways modulated to tolerate physiological challenges that might otherwise be letha...

journal_title：BMC genomics

authors： Capraro A,O'Meally D,Waters SA,Patel HR,Georges A,Waters PD

更新日期：2019-06-06 00:00:00

abstract：BACKGROUND:Serine/threonine kinase 33 (STK33) has been shown to be conserved across all major vertebrate classes including reptiles, mammals, amphibians and fish, suggesting its importance within vertebrates. It has been shown to phosphorylate vimentin and might play a role in spermatogenesis and organ ontogenesis. In ...

journal_title：BMC genomics

authors： Lautwein T,Lerch S,Schäfer D,Schmidt ER

更新日期：2015-07-22 00:00:00

abstract：BACKGROUND:Adult neurogenesis, which is the continual production of new neurons in the mature brain, demonstrates the strikingly plastic nature of the nervous system. Adult neural stem cells and their neural precursors, collectively referred to as neural progenitor cells (NPCs), are present in the subgranular zone (SGZ...

journal_title：BMC genomics

authors： Poon A,Goldowitz D

更新日期：2014-03-19 00:00:00

abstract：BACKGROUND:Polyploidy is an important phenomenon in plants because of its roles in agricultural and forestry production as well as in plant tolerance to environmental stresses. Tetraploid black locust (Robinia pseudoacacia L.) is a polyploid plant and a pioneer tree species due to its wide ranging adaptability to adver...

journal_title：BMC genomics

authors： Luo Q,Peng M,Zhang X,Lei P,Ji X,Chow W,Meng F,Sun G

更新日期：2017-08-22 00:00:00

abstract：BACKGROUND:Gonadotropin releasing hormone (GnRH) is responsible for stimulation of gonadotropic hormone (GtH) in the hypothalamus-pituitary-gonadal axis (HPG). The regulatory mechanisms responsible for brain specificity make the promoter attractive for in silico analysis and reporter gene studies in zebrafish (Danio re...

journal_title：BMC genomics

authors： Torgersen J,Nourizadeh-Lillabadi R,Husebye H,Aleström P

更新日期：2002-08-21 00:00:00

abstract：BACKGROUND:Understanding the genome sequence-specific positioning of nucleosomes is essential to understand various cellular processes, such as transcriptional regulation and replication. As a typical example, the 10-bp periodicity of AA/TT and GC dinucleotides has been reported in several species, but it is still uncl...

journal_title：BMC genomics

authors： Tanaka Y,Yamashita R,Suzuki Y,Nakai K

更新日期：2010-05-17 00:00:00

abstract：BACKGROUND:Tandemly arranged nuclear ribosomal DNA (rDNA), encoding 18S, 5.8S and 26S ribosomal RNA (rRNA), exhibit concerted evolution, a pattern thought to result from the homogenisation of rDNA arrays. However rDNA homogeneity at the single nucleotide polymorphism (SNP) level has not been detailed in organisms with ...

journal_title：BMC genomics

authors： Matyášek R,Renny-Byfield S,Fulneček J,Macas J,Grandbastien MA,Nichols R,Leitch A,Kovařík A

更新日期：2012-12-23 00:00:00

abstract：BACKGROUND:There is growing recognition that horizontal DNA transfer, a process known to be common in prokaryotes, is also a significant source of genomic variation in eukaryotes. Horizontal transfer of transposable elements (HTT) may be especially prevalent in eukaryotes given the inherent mobility, widespread occurre...

journal_title：BMC genomics

authors： Gilbert C,Waters P,Feschotte C,Schaack S

更新日期：2013-02-27 00:00:00

abstract：BACKGROUND:Horizontal gene transfer has shaped the evolution of the ammonium transporter/ammonia permease gene family. Horizontal transfers of ammonium transporter/ammonia permease genes into the fungi include one transfer from archaea to the filamentous ascomycetes associated with the adaptive radiation of the leotiom...

journal_title：BMC genomics

authors： McDonald TR,Mueller O,Dietrich FS,Lutzoni F

更新日期：2013-04-04 00:00:00

abstract：BACKGROUND:In natural environments, bacteria must frequently cope with extremely scarce nutrients. Most studies focus on bacterial growth in nutrient replete conditions, while less is known about the stationary phase. Here, we are interested in global gene expression throughout all growth phases, including the adjustme...

journal_title：BMC genomics

authors： Bathke J,Konzer A,Remes B,McIntosh M,Klug G

更新日期：2019-05-09 00:00:00