@article {949,
	title = {Transcriptome profiling of the intoxication response of Tenebrio molitor larvae to Bacillus thuringiensis Cry3Aa protoxin.},
	journal = {PloS one},
	volume = {7},
	year = {2012},
	month = {2012},
	pages = {e34624},
	abstract = {Bacillus thuringiensis (Bt) crystal (Cry) proteins are effective against a select number of insect pests, but improvements are needed to increase efficacy and decrease time to mortality for coleopteran pests. To gain insight into the Bt intoxication process in Coleoptera, we performed RNA-Seq on cDNA generated from the guts of Tenebrio molitor larvae that consumed either a control diet or a diet containing Cry3Aa protoxin. Approximately 134,090 and 124,287 sequence reads from the control and Cry3Aa-treated groups were assembled into 1,318 and 1,140 contigs, respectively. Enrichment analyses indicated that functions associated with mitochondrial respiration, signalling, maintenance of cell structure, membrane integrity, protein recycling/synthesis, and glycosyl hydrolases were significantly increased in Cry3Aa-treated larvae, whereas functions associated with many metabolic processes were reduced, especially glycolysis, tricarboxylic acid cycle, and fatty acid synthesis. Microarray analysis was used to evaluate temporal changes in gene expression after 6, 12 or 24 h of Cry3Aa exposure. Overall, microarray analysis indicated that transcripts related to allergens, chitin-binding proteins, glycosyl hydrolases, and tubulins were induced, and those related to immunity and metabolism were repressed in Cry3Aa-intoxicated larvae. The 24 h microarray data validated most of the RNA-Seq data. Of the three intoxication intervals, larvae demonstrated more differential expression of transcripts after 12 h exposure to Cry3Aa. Gene expression examined by three different methods in control vs. Cry3Aa-treated larvae at the 24 h time point indicated that transcripts encoding proteins with chitin-binding domain 3 were the most differentially expressed in Cry3Aa-intoxicated larvae. Overall, the data suggest that T. molitor larvae mount a complex response to Cry3Aa during the initial 24 h of intoxication. Data from this study represent the largest genetic sequence dataset for T. molitor to date. Furthermore, the methods in this study are useful for comparative analyses in organisms lacking a sequenced genome.},
	keywords = {Administration, Animals, Bacterial Proteins, Base Sequence, Biosynthetic Pathways, Complementary, DNA, Endotoxins, Energy Metabolism, Gene Expression Profiling, Hemolysin Proteins, Larva, Microarray Analysis, Molecular Sequence Data, Oral, Sequence Analysis, Tenebrio, Time Factors, Transcriptome},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0034624},
	author = {Oppert, Brenda and Dowd, Scot E and Bouffard, Pascal and Li, Lewyn and Ana Conesa and Lorenzen, Marc{\'e} D and Toutges, Michelle and Marshall, Jeremy and Huestis, Diana L and Fabrick, Jeff and Oppert, Cris and Jurat-Fuentes, Juan Luis}
}
@article {17567924,
	title = {The human phylome},
	journal = {Genome Biol},
	volume = {8},
	number = {6},
	year = {2007},
	note = {Huerta-Cepas, Jaime Dopazo, Hernan Dopazo, Joaquin Gabaldon, Toni Research Support, Non-U.S. Gov{\textquoteright}t England Genome biology Genome Biol. 2007;8(6):R109.},
	pages = {R109},
	abstract = {BACKGROUND: Phylogenomics analyses serve to establish evolutionary relationships among organisms and their genes. A phylome, the complete collection of all gene phylogenies in a genome, constitutes a valuable source of information, but its use in large genomes still constitutes a technical challenge. The use of phylomes also requires the development of new methods that help us to interpret them. RESULTS: We reconstruct here the human phylome, which includes the evolutionary relationships of all human proteins and their homologs among 39 fully sequenced eukaryotes. Phylogenetic techniques used include alignment trimming, branch length optimization, evolutionary model testing and maximum likelihood and Bayesian methods. Although differences with alternative topologies are minor, most of the trees support the Coelomata and Unikont hypotheses as well as the grouping of primates with laurasatheria to the exclusion of rodents. We assess the extent of gene duplication events and their relationship with the functional roles of the protein families involved. We find support for at least one, and probably two, rounds of whole genome duplications before vertebrate radiation. Using a novel algorithm that is independent from a species phylogeny, we derive orthology and paralogy relationships of human proteins among eukaryotic genomes. CONCLUSION: Topological variations among phylogenies for different genes are to be expected, highlighting the danger of gene-sampling effects in phylogenomic analyses. Several links can be established between the functions of gene families duplicated at certain phylogenetic splits and major evolutionary transitions in those lineages. The pipeline implemented here can be easily adapted for use in other organisms.},
	keywords = {Animals *Evolution Evolution, DNA, Molecular Gene Duplication *Genome Humans *Phylogeny Proteins/genetics Sequence Analysis},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17567924},
	author = {Huerta-Cepas, J. and H. Dopazo and Dopazo, J. and Gabald{\'o}n, T.}
}
@article {15830128,
	title = {Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies},
	journal = {Plant Mol Biol},
	volume = {57},
	number = {3},
	year = {2005},
	note = {Forment, J Gadea, J Huerta, L Abizanda, L Agusti, J Alamar, S Alos, E Andres, F Arribas, R Beltran, J P Berbel, A Blazquez, M A Brumos, J Canas, L A Cercos, M Colmenero-Flores, J M Conesa, A Estables, B Gandia, M Garcia-Martinez, J L Gimeno, J Gisbert, A Gomez, G Gonzalez-Candelas, L Granell, A Guerri, J Lafuente, M T Madueno, F Marcos, J F Marques, M C Martinez, F Martinez-Godoy, M A Miralles, S Moreno, P Navarro, L Pallas, V Perez-Amador, M A Perez-Valle, J Pons, C Rodrigo, I Rodriguez, P L Royo, C Serrano, R Soler, G Tadeo, F Talon, M Terol, J Trenor, M Vaello, L Vicente, O Vidal, Ch Zacarias, L Conejero, V Comparative Study Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. Netherlands Plant molecular biology Plant Mol Biol. 2005 Feb;57(3):375-91.},
	pages = {375-91},
	abstract = {A functional genomics project has been initiated to approach the molecular characterization of the main biological and agronomical traits of citrus. As a key part of this project, a citrus EST collection has been generated from 25 cDNA libraries covering different tissues, developmental stages and stress conditions. The collection includes a total of 22,635 high-quality ESTs, grouped in 11,836 putative unigenes, which represent at least one third of the estimated number of genes in the citrus genome. Functional annotation of unigenes which have Arabidopsis orthologues (68\% of all unigenes) revealed gene representation in every major functional category, suggesting that a genome-wide EST collection was obtained. A Citrus clementina Hort. ex Tan. cv. Clemenules genomic library, that will contribute to further characterization of relevant genes, has also been constructed. To initiate the analysis of citrus transcriptome, we have developed a cDNA microarray containing 12,672 probes corresponding to 6875 putative unigenes of the collection. Technical characterization of the microarray showed high intra- and inter-array reproducibility, as well as a good range of sensitivity. We have also validated gene expression data achieved with this microarray through an independent technique such as RNA gel blot analysis.},
	keywords = {Citrus/*genetics DNA, Complementary/chemistry/genetics *Expressed Sequence Tags Gene Expression Profiling Gene Library *Genome, DNA, Plant Genomics/*methods Molecular Sequence Data Oligonucleotide Array Sequence Analysis/*methods RNA, Plant/genetics/metabolism Reproducibility of Results Sequence Analysis},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=15830128},
	author = {J. Forment and J. Gadea and Huerta, L. and Abizanda, L. and Agusti, J. and Alamar, S. and Alos, E. and Andres, F. and Arribas, R. and Beltran, J. P. and Berbel, A. and Blazquez, M. A. and Brumos, J. and Canas, L. A. and Cercos, M. and Colmenero-Flores, J. M. and A. Conesa and Estables, B. and Gandia, M. and Garcia-Martinez, J. L. and Gimeno, J. and Gisbert, A. and Gomez, G. and Gonzalez-Candelas, L. and Granell, A. and Guerri, J. and Lafuente, M. T. and Madueno, F. and Marcos, J. F. and Marques, M. C. and Martinez, F. and Martinez-Godoy, M. A. and Miralles, S. and Moreno, P. and Navarro, L. and Pallas, V. and Perez-Amador, M. A. and Perez-Valle, J. and Pons, C. and Rodrigo, I. and Rodriguez, P. L. and Royo, C. and Serrano, R. and Soler, G. and Tadeo, F. and Talon, M. and Terol, J. and Trenor, M. and Vaello, L. and Vicente, O. and Vidal, Ch and Zacarias, L. and Conejero, V.}
}
@article {11442348,
	title = {Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate},
	journal = {Microb Drug Resist},
	volume = {7},
	number = {2},
	year = {2001},
	note = {Dopazo, J Mendoza, A Herrero, J Caldara, F Humbert, Y Friedli, L Guerrier, M Grand-Schenk, E Gandin, C de Francesco, M Polissi, A Buell, G Feger, G Garcia, E Peitsch, M Garcia-Bustos, J F United States Microbial drug resistance (Larchmont, N.Y.) Microb Drug Resist. 2001 Summer;7(2):99-125.},
	pages = {99-125},
	abstract = {The public availability of numerous microbial genomes is enabling the analysis of bacterial biology in great detail and with an unprecedented, organism-wide and taxon-wide, broad scope. Streptococcus pneumoniae is one of the most important bacterial pathogens throughout the world. We present here sequences and functional annotations for 2.1-Mbp of pneumococcal DNA, covering more than 90\% of the total estimated size of the genome. The sequenced strain is a clinical isolate resistant to macrolides and tetracycline. It carries a type 19F capsular locus, but multilocus sequence typing for several conserved genetic loci suggests that the strain sequenced belongs to a pneumococcal lineage that most often expresses a serotype 15 capsular polysaccharide. A total of 2,046 putative open reading frames (ORFs) longer than 100 amino acids were identified (average of 1,009 bp per ORF), including all described two-component systems and aminoacyl tRNA synthetases. Comparisons to other complete, or nearly complete, bacterial genomes were made and are presented in a graphical form for all the predicted proteins.},
	keywords = {Bacterial Molecular Sequence Data Pneumococcal Infections/*microbiology Prokaryotic Cells RNA, Bacterial/chemistry/genetics Genes, Bacterial/genetics *Genome, DNA, Transfer/metabolism Streptococcus pneumoniae/*genetics},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=11442348},
	author = {Dopazo, J. and Mendoza, A. and Herrero, J. and Caldara, F. and Humbert, Y. and Friedli, L. and Guerrier, M. and Grand-Schenk, E. and Gandin, C. and de Francesco, M. and Polissi, A. and Buell, G. and Feger, G. and Garcia, E. and Peitsch, M. and Garcia-Bustos, J. F.}
}
