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Uncovering the novel characteristics of Asian honey bee, Apis cerana , by whole genome sequencing

Published on Dec 1, 2015in BMC Genomics3.50
· DOI :10.1186/1471-2164-16-1
D. J. Park7
Estimated H-index: 7
(SNU: Seoul National University),
Je Won Jung11
Estimated H-index: 11
(SNU: Seoul National University)
+ 12 AuthorsHyung Wook Kwon14
Estimated H-index: 14
(SNU: Seoul National University)
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Abstract
Background The honey bee is an important model system for increasing understanding of molecular and neural mechanisms underlying social behaviors relevant to the agricultural industry and basic science. The western honey bee, Apis mellifera, has served as a model species, and its genome sequence has been published. In contrast, the genome of the Asian honey bee, Apis cerana, has not yet been sequenced. A. cerana has been raised in Asian countries for thousands of years and has brought considerable economic benefits to the apicultural industry. A cerana has divergent biological traits compared to A. mellifera and it has played a key role in maintaining biodiversity in eastern and southern Asia. Here we report the first whole genome sequence of A. cerana.
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  • References (112)
  • Citations (328)
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References112
Newest
Published on Mar 1, 2014in Peptides2.66
D. J. Park7
Estimated H-index: 7
(SNU: Seoul National University),
Je Won Jung11
Estimated H-index: 11
(SNU: Seoul National University)
+ 10 AuthorsYong Sang Song1
Estimated H-index: 1
(SNU: Seoul National University)
Abstract Insect-derived antimicrobial peptides (AMPs) have diverse effects on antimicrobial properties and pharmacological activities such as anti-inflammation and anticancer properties. Naturally occurring genetic polymorphism have a direct and/or indirect influence on pharmacological effect of AMPs, therefore information on single nucleotide polymorphism (SNP) occurring in natural AMPs provides an important clue to therapeutic applications. Here we identified nucleotide polymorphisms in melitt...
Published on Jan 1, 2014in BMC Genomics3.50
Christine G. Elsik25
Estimated H-index: 25
(MU: University of Missouri),
Kim C. Worley55
Estimated H-index: 55
(BCM: Baylor College of Medicine)
+ 45 AuthorsBart Devreese49
Estimated H-index: 49
(UGent: Ghent University)
Background: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome...
Published on Jan 1, 2014in Nucleic Acids Research11.15
Susan E. St. Pierre3
Estimated H-index: 3
(University of Cambridge),
Laura Ponting8
Estimated H-index: 8
(University of Cambridge)
+ 1 AuthorsPeter McQuilton12
Estimated H-index: 12
(University of Cambridge)
FlyBase (http://flybase.org) is the leading website and database of Drosophila genes and genomes. Whether you are using the fruit fly Drosophila melanogaster as an experimental system or wish to understand Drosophila biological knowledge in relation to human disease or to other model systems, FlyBase can help you successfully find the information you are looking for. Here, we demonstrate some of our more advanced searching systems and highlight some of our new tools for searching the wealth of d...
Published on Jan 1, 2014in Nucleic Acids Research11.15
Kim D. Pruitt31
Estimated H-index: 31
(NIH: National Institutes of Health),
Garth Brown10
Estimated H-index: 10
(NIH: National Institutes of Health)
+ 26 AuthorsKelly M. McGarvey4
Estimated H-index: 4
(NIH: National Institutes of Health)
The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of annotated genomic, transcript and protein sequence records derived from data in public sequence archives and from computation, curation and collaboration (http://www.ncbi.nlm.nih.gov/refseq/). We report here on growth of the mammalian and human subsets, changes to NCBI’s eukaryotic annotation pipeline and modifications affecting transcript and protein records. Recent changes to NCBI’s...
Published on Oct 21, 2013in Insects
Anna H. Koetz1
Estimated H-index: 1
Apis cerana Fabricius is endemic to most of Asia, where it has been used for honey production and pollination services for thousands of years. Since the 1980s, A. cerana has been introduced to areas outside its natural range (namely New Guinea, the Solomon Islands, and Australia), which sparked fears that it may become a pest species that could compete with, and negatively affect, native Australian fauna and flora, as well as commercially kept A. mellifera and commercial crops. This literature r...
Published on Sep 1, 2013in Insect Biochemistry and Molecular Biology3.62
Raphael Rytz6
Estimated H-index: 6
(UNIL: University of Lausanne),
Vincent Croset10
Estimated H-index: 10
(UNIL: University of Lausanne),
Richard Benton14
Estimated H-index: 14
(UNIL: University of Lausanne)
Ionotropic Receptors (IRs) are a recently characterized family of olfactory receptors in the fruit fly, Drosophila melanogaster. IRs are not related to insect Odorant Receptors (ORs), but rather have evolved from ionotropic glutamate receptors (iGluRs), a conserved family of synaptic ligand-gated ion channels. Here, we review the expression and function of IRs in Drosophila, highlighting similarities and differences with iGluRs. We also briefly describe the organization of the neuronal circuits ...
Published on Aug 1, 2013in Genome Research9.94
Daniel F. Simola11
Estimated H-index: 11
(UPenn: University of Pennsylvania),
Lothar Wissler7
Estimated H-index: 7
(WWU: University of Münster)
+ 35 AuthorsLumi Viljakainen11
Estimated H-index: 11
(University of Oulu)
.Genomes of eusocial insects code for dramatic examples of phenotypic plasticity and social organization. We compared the genomes of seven ants, the honeybee, and various solitary insects to examine whether eusocial lineages share distinct features of genomic organization. Each ant lineage contains ~4000 novel genes, but only 64 of these genes are conserved among all seven ants. Many gene families have been expanded in ants, notably those involved in chemical communication (e.g., desaturases and...
Published on Aug 1, 2013in Nature Protocols11.33
Brian J. Haas62
Estimated H-index: 62
,
Alexie Papanicolaou21
Estimated H-index: 21
+ 20 AuthorsMatthias Lieber7
Estimated H-index: 7
De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applicati...
Published on Feb 13, 2013in PLOS ONE2.78
Tetsuya Miyamoto9
Estimated H-index: 9
(Texas A&M Health Science Center),
Yan Chen6
Estimated H-index: 6
(Texas A&M Health Science Center)
+ 1 AuthorsHubert Amrein29
Estimated H-index: 29
(Texas A&M Health Science Center)
Evaluation of food compounds by chemosensory cells is essential for animals to make appropriate feeding decisions. In the fruit fly Drosophila melanogaster, structurally diverse chemicals are detected by multimeric receptors composed of members of a large family of Gustatory receptor (Gr) proteins. Putative sugar and bitter receptors are expressed in distinct subsets of Gustatory Receptor Neurons (GRN) of taste sensilla, thereby assigning distinct taste qualities to sugars and bitter tasting com...
Published on Dec 15, 2012in Annual Review of Genetics9.18
Amro Zayed21
Estimated H-index: 21
(York University),
Gene E. Robinson88
Estimated H-index: 88
Behavior is a complex phenotype that is plastic and evolutionarily labile. The advent of genomics has revolutionized the field of behavioral ge- netics by providing tools to quantify the dynamic nature of brain gene expression in relation to behavioral output. The honey bee Apis mel- lifera provides an excellent platform for investigating the relationship between brain gene expression and behavior given both the remarkable behavioral repertoire expressed by members of its intricate society and t...
Cited By328
Newest
Published on Mar 12, 2019in Scientific Reports4.01
Yan Wang11
Estimated H-index: 11
(JLU: Jilin University),
Sen Yang1
Estimated H-index: 1
(JLU: Jilin University)
+ 6 AuthorsQin Ma13
Estimated H-index: 13
(OSU: Ohio State University)
Measuring conditional relatedness between a pair of genes is a fundamental technique and still a significant challenge in computational biology. Such relatedness can be assessed by gene expression similarities while suffering high false discovery rates. Meanwhile, other types of features, e.g., prior-knowledge based similarities, is only viable for measuring global relatedness. In this paper, we propose a novel machine learning model, named Multi-Features Relatedness (MFR), for accurately measur...
Published on 2019in Scientific Reports4.01
Ihteram Ullah3
Estimated H-index: 3
(CAS: Chinese Academy of Sciences),
Mahmoud Magdy4
Estimated H-index: 4
(Ain Shams University)
+ 2 AuthorsXia Li6
Estimated H-index: 6
(HAU: Huazhong Agricultural University)
The gain of function in genes and gene families is a continuous process and is a key factor in understanding gene and genome evolution in plants. TGACG-Binding (TGA) transcription factors (TFs) have long been known for their essential roles in plant defence in Arabidopsis, but their roles in legume symbiosis are yet to be explored. Here, we identified a total of 25 TGA (named GmTGA1-GmTGA25) genes in soybean. Through phylogenetic analysis, we discovered a clade of GmTGA proteins that appear to b...
Published on 2019in Scientific Reports4.01
Luo-Luo Wang4
Estimated H-index: 4
(UGent: Ghent University),
Ivan Meeus18
Estimated H-index: 18
(UGent: Ghent University)
+ 3 AuthorsGuy Smagghe51
Estimated H-index: 51
(UGent: Ghent University)
Bee pollinators are exposed to multiple natural and anthropogenic stressors. Understanding the effects of a single stressor in the complex environmental context of antagonistic/synergistic interactions is critical to pollinator monitoring and may serve as early warning system before a pollination crisis. This study aimed to methodically improve the diagnosis of bee stressors using a simultaneous untargeted and targeted metabolomics-based approach. Analysis of 84 Bombus terrestris hemolymph sampl...
Published on Dec 1, 2019in BMC Plant Biology3.67
Zhu Chen , Xiaoyu Lu (AAU: Anhui Agricultural University)+ 5 AuthorsJie Ren
Background Red maple (Acer rubrum L.) is one of the most common and widespread trees with colorful leaves. We found a mutant with red, yellow, and green leaf phenotypes in different branches, which provided ideal materials with the same genetic relationship, and little interference from the environment, for the study of complex metabolic networks that underly variations in the coloration of leaves. We applied a combination of NGS and SMRT sequencing to various red maple tissues.
Published on Apr 6, 2019in Plant Methods3.17
Fang Tang2
Estimated H-index: 2
(NFU: Nanjing Forestry University),
Liwei Chu + 3 AuthorsMengzhu Lu9
Estimated H-index: 9
(NFU: Nanjing Forestry University)
Background Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) is a rapid and sensitive approach to identify miRNA and protein-coding gene expression in plants. However, because of the specially designated reverse transcription and shorter PCR products, very few reference genes have been identified for the quantitative analysis of miRNA expression in plants, and different internal reference genes are needed to normalize the expression of miRNAs and mRNA genes respectively. The...
Published on Dec 1, 2019in BMC Genomics3.50
Octávio Augusto Costa Almeida (USP: University of São Paulo), Gabriel Costa Monteiro Moreira3
Estimated H-index: 3
(USP: University of São Paulo)
+ 6 AuthorsL. L. Coutinho26
Estimated H-index: 26
(USP: University of São Paulo)
Background Natural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be identified using different methodologies, of which some are based on detecting contiguous sequences of homozygous identical-by-descent haplotypes, called runs of homozygosity (ROH), or estimating fixation index (FST) of genomic windows that indicates genetic differentiation. This stud...
Published on Dec 1, 2019in BMC Genomics3.50
Fernando Carazo1
Estimated H-index: 1
(University of Navarra),
Marian Gimeno (University of Navarra)+ 1 AuthorsAngel Rubio19
Estimated H-index: 19
(University of Navarra)
Background Splicing is a genetic process that has important implications in several diseases including cancer. Deciphering the complex rules of splicing regulation is crucial to understand and treat splicing-related diseases. Splicing factors and other RNA-binding proteins (RBPs) play a key role in the regulation of splicing. The specific binding sites of an RBP can be measured using CLIP experiments. However, to unveil which RBPs regulate a condition, it is necessary to have a priori hypotheses...
Published on Feb 27, 2019in BMC Genomics3.50
Xiaoling Zhang1
Estimated H-index: 1
(Sichuan Agricultural University),
Yanli Wang2
Estimated H-index: 2
(Sichuan Agricultural University)
+ 9 AuthorsHuanwei Peng5
Estimated H-index: 5
(Sichuan Agricultural University)
Background Maize is one of the primary crops of genetic manipulation, which provides an excellent means of promoting stress resistance and increasing yield. However, the differences in induction and regeneration capacity of embryonic callus (EC) among various genotypes result in genotypic dependence in genetic transformation.
Published on Jun 12, 2019in Journal of Economic Entomology1.78
Yali Du2
Estimated H-index: 2
(Shanxi Agricultural University),
Kai Xu1
Estimated H-index: 1
+ 5 AuthorsXianchun Li27
Estimated H-index: 27
(UA: University of Arizona)
View next paperAnalysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.