Genomes and Genes
Summary: The genetic complement of an insect (INSECTS) as represented in its DNA.
- Wilson A, Ashton P, Calevro F, Charles H, Colella S, Febvay G, et al. Genomic insight into the amino acid relations of the pea aphid, Acyrthosiphon pisum, with its symbiotic bacterium Buchnera aphidicola. Insect Mol Biol. 2010;19 Suppl 2:249-58 pubmed publisher..Overall the genome data suggest that the biosynthesis of certain essential amino acids is shared between the pea aphid and Buchnera APS, providing the opportunity for precise aphid control over Buchnera metabolism...
- Xia Q, Guo Y, Zhang Z, Li D, Xuan Z, Li Z, et al. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science. 2009;326:433-6 pubmed publisher..These data add to our understanding of the domestication processes and may have applications in devising pest control strategies and advancing the use of silkworms as efficient bioreactors. ..
- Jiang N, Emberly E, Cuvier O, Hart C. Genome-wide mapping of boundary element-associated factor (BEAF) binding sites in Drosophila melanogaster links BEAF to transcription. Mol Cell Biol. 2009;29:3556-68 pubmed publisher..These results provide an unexpected link between BEAF and transcription, suggesting that BEAF plays a role in maintaining most associated promoter regions in an environment that facilitates high transcription levels. ..
- Huerta Cepas J, Marcet Houben M, Pignatelli M, Moya A, Gabaldón T. The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes. Insect Mol Biol. 2010;19 Suppl 2:13-21 pubmed publisher..All phylogenies and alignments are accessible through the PhylomeDB database. Here we provide a description of this dataset and provide some examples on how can it be exploited. ..
- Linksvayer T, Rueppell O, Siegel A, Kaftanoglu O, Page R, Amdam G. The genetic basis of transgressive ovary size in honeybee workers. Genetics. 2009;183:693-707, 1SI-13SI pubmed publisher..We discuss how the phenotype of extreme worker ovariole numbers and the underlying genetic factors we identified could be linked to the development of queen traits. ..
- Azad P, Zhang M, Woodruff R. Rapid increase in viability due to new beneficial mutations in Drosophila melanogaster. Genetica. 2010;138:251-63 pubmed publisher..Hence, new advantageous mutations may play an important role in adaptive evolution in higher organisms. ..
- Sengul M, Tu Z. Identification and characterization of odorant-binding protein 1 gene from the Asian malaria mosquito, Anopheles stephensi. Insect Mol Biol. 2010;19:49-60 pubmed publisher..Our results indicate that AsteObp1 is likely to function in the female olfactory response and may also be involved in blood-feeding behaviour. ..
- Bitra K, Tan A, Dowling A, Palli S. Functional characterization of PAS and HES family bHLH transcription factors during the metamorphosis of the red flour beetle, Tribolium castaneum. Gene. 2009;448:74-87 pubmed publisher..These studies demonstrate the power of RNAi for functional characterization of members of the multigene families in this model insect. ..
- Vicoso B, Charlesworth B. Effective population size and the faster-X effect: an extended model. Evolution. 2009;63:2413-26 pubmed publisher..We show that, when the rate of nonsynonymous evolution is normalized by the rate of neutral evolution, a sex difference in mutation rate has no influence on the conditions for faster-X evolution. ..
- Schurko A, Mazur D, Logsdon J. Inventory and phylogenomic distribution of meiotic genes in Nasonia vitripennis and among diverse arthropods. Insect Mol Biol. 2010;19 Suppl 1:165-80 pubmed publisher..The distribution of meiotic genes across arthropods and the impact of gene duplications and reproductive modes on meiotic gene evolution are discussed. ..
- Scott J, Liu N, Kristensen M, Clark A. A case for sequencing the genome of Musca domestica (Diptera: Muscidae). J Med Entomol. 2009;46:175-82 pubmed..The community of researchers investigating Musca domestica are well prepared and highly motivated to apply genomic analyses to their widely varied research programs...
- Arunachalam M, Jayasurya K, Tomancak P, Ohler U. An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes. Bioinformatics. 2010;26:2109-15 pubmed publisher..The software, data and the results used in this article are available at http://www.genome.duke.edu/labs/ohler/research/transcription/fly_enhancer/. ..
- De Freitas Ortiz M, Lorenzatto K, Corrêa B, Loreto E. hAT transposable elements and their derivatives: an analysis in the 12 Drosophila genomes. Genetica. 2010;138:649-55 pubmed publisher..These results suggest that primarily active copies of hAT elements are maintained in the euchromatic regions of the genome and that degenerated copies are removed from the genome by natural selection. ..
- Wilding C, Weetman D, Steen K, Donnelly M. High, clustered, nucleotide diversity in the genome of Anopheles gambiae revealed through pooled-template sequencing: implications for high-throughput genotyping protocols. BMC Genomics. 2009;10:320 pubmed publisher..We illustrate these issues in the context of the design of Illumina GoldenGate assays. ..
- Wang H, Chattopadhyay A, Li Z, Daines B, Li Y, Gao C, et al. Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. Genome Res. 2010;20:981-8 pubmed publisher..Introduction of this and other sequencing-based methods for mutation cloning will enable broader usage of forward genetics screens and have significant impacts in the field of model organisms such as Drosophila. ..
- Nguyen P, Sahara K, Yoshido A, Marec F. Evolutionary dynamics of rDNA clusters on chromosomes of moths and butterflies (Lepidoptera). Genetica. 2010;138:343-354 pubmed publisher..e., homologous recombination between repetitive sequences of non-homologous chromosomes, as a primary motive force in rDNA repatterning...
- Amenya D, Bonizzoni M, Isaacs A, Jasinskiene N, Chen H, Marinotti O, et al. Comparative fitness assessment of Anopheles stephensi transgenic lines receptive to site-specific integration. Insect Mol Biol. 2010;19:263-9 pubmed publisher..These transgenic lines are suitable for future site-specific integrations of antiparasite transgenes into the attP sites. ..
- Runcie D, Noor M. Sequence signatures of a recent chromosomal rearrangement in Drosophila mojavensis. Genetica. 2009;136:5-11 pubmed publisher..We also found no evidence that staggered single-strand breaks caused the inversion. We suggest these features may have contributed to the chromosomal breakages resulting in this inversion...
- Tagu D, Dugravot S, Outreman Y, Rispe C, Simon J, Colella S. The anatomy of an aphid genome: from sequence to biology. C R Biol. 2010;333:464-73 pubmed publisher..Thus, in the second part of the review, we envisage how this genomic resource will fuel many other disciplines such as ecology, evolutionary biology, population genetics and symbiosis. ..
- Kulathinal R, Stevison L, Noor M. The genomics of speciation in Drosophila: diversity, divergence, and introgression estimated using low-coverage genome sequencing. PLoS Genet. 2009;5:e1000550 pubmed publisher..Our study serves as a proof-of-principle on how whole genome sequencing can be applied to formulate and test hypotheses about species formation in lesser-known non-model systems. ..
- Liu F, Ling E, Wu S. Gene expression profiling during early response to injury and microbial challenges in the silkworm, Bombyx mori. Arch Insect Biochem Physiol. 2009;72:16-33 pubmed publisher..Of particular interest is a member of the juvenile hormone-binding protein family, which was highly induced by both injury and microbial challenges. The possible role of juvenile hormone in innate immunity is discussed. ..
- Dombrovsky A, Arthaud L, Ledger T, Tares S, Robichon A. Profiling the repertoire of phenotypes influenced by environmental cues that occur during asexual reproduction. Genome Res. 2009;19:2052-63 pubmed publisher..This overall mechanism allows the renewal of colonies from a few adapted individuals that survive drastic episodic changes in a fluctuating environment. ..
- Weber G, Rübel O, Huang M, DePace A, Fowlkes C, Keränen S, et al. Visual exploration of three-dimensional gene expression using physical views and linked abstract views. IEEE/ACM Trans Comput Biol Bioinform. 2009;6:296-309 pubmed publisher..Using linking, these selected cells can be viewed in multiple representations. We describe PCX as a 3D gene expression visualization tool and provide examples of how it has been used by BDTNP biologists to generate new hypotheses. ..
- Srinivasan D, Fenton B, Jaubert Possamai S, Jaouannet M. Analysis of meiosis and cell cycle genes of the facultatively asexual pea aphid, Acyrthosiphon pisum (Hemiptera: Aphididae). Insect Mol Biol. 2010;19 Suppl 2:229-39 pubmed publisher..Together, this suggests that cell cycle plasticity may be important in the evolution and mechanism of aphid reproductive plasticity. ..
- Shi W, Kerdelhué C, Ye H. Population genetic structure of the oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) from Yunnan province (China) and nearby sites across the border. Genetica. 2010;138:377-85 pubmed publisher..e., that it is not invasive there). Finally, we found some evidences that the seasonal populations were colonized from nearby year-round populations...
- Song N, Liang A. Complete mitochondrial genome of the small brown planthopper, Laodelphax striatellus (Delphacidae: Hemiptera), with a novel gene order. Zoolog Sci. 2009;26:851-60 pubmed publisher..The results show that Heteroptera is the sister group to all other Hemiptera, and Cicadomorpha is the sister group to the clade Fulgoromorpha+Sternorrhyncha...
- Vibranovski M, Lopes H, Karr T, Long M. Stage-specific expression profiling of Drosophila spermatogenesis suggests that meiotic sex chromosome inactivation drives genomic relocation of testis-expressed genes. PLoS Genet. 2009;5:e1000731 pubmed publisher..These results suggest MSCI as a general mechanism affecting the evolution of some testis-expressed genes. ..
- Bond D, Foley E. A quantitative RNAi screen for JNK modifiers identifies Pvr as a novel regulator of Drosophila immune signaling. PLoS Pathog. 2009;5:e1000655 pubmed publisher..Furthermore, given the pleiotropic involvement of JNK in eukaryotic cell biology, we believe that many of the novel regulators identified in this screen are of interest beyond immune signaling. ..
- Kondylis V, Rabouille C. The Golgi apparatus: lessons from Drosophila. FEBS Lett. 2009;583:3827-38 pubmed publisher..Last, the Golgi function has been involved in specific developmental processes, thus shedding new light on the functions of a number of Golgi proteins. ..
- Zhou J, Vieira F, He X, Smadja C, Liu R, Rozas J, et al. Genome annotation and comparative analyses of the odorant-binding proteins and chemosensory proteins in the pea aphid Acyrthosiphon pisum. Insect Mol Biol. 2010;19 Suppl 2:113-22 pubmed publisher..Our results support the 'birth-and-death' model as the major mechanism explaining aphid OBP sequence evolution, with the main force acting on the evolution being purifying selection...
- González J, Karasov T, Messer P, Petrov D. Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila. PLoS Genet. 2010;6:e1000905 pubmed publisher..We argue that reverse population genomic analyses, as the one described in this work, are necessary to arrive at a comprehensive picture of adaptation. ..
- Michel A, Sim S, Powell T, Taylor M, Nosil P, Feder J. Widespread genomic divergence during sympatric speciation. Proc Natl Acad Sci U S A. 2010;107:9724-9 pubmed publisher..These results highlight how the individual genes driving speciation can be embedded within an actively diverging genome. ..
- Pfleger C, Reiter L. Recent efforts to model human diseases in vivo in Drosophila. Fly (Austin). 2008;2:129-32 pubmed..Here we can only briefly review some of these developments, and we apologize that we do not have the time or space to review all of the findings presented which use Drosophila to understand human disease etiology. ..
- Deloger M, Cavalli F, Lerat E, Biémont C, Sagot M, Vieira C. Identification of expressed transposable element insertions in the sequenced genome of Drosophila melanogaster. Gene. 2009;439:55-62 pubmed publisher..We show that most TE families are transcribed, and we have specifically identified 69 expressed TE insertions, half of which are located inside genes, mostly within introns and 5'UTRs. ..
- Patil D, Atanur S, Dhotre D, Anantharam D, Mahajan V, Walujkar S, et al. Generation, annotation, and analysis of ESTs from midgut tissue of adult female Anopheles stephensi mosquitoes. BMC Genomics. 2009;10:386 pubmed publisher..Failure of some novel transcripts to map on the A. gambiae genome indicates existence of substantial genomic dissimilarities between these two potent malaria vectors. ..
- White B, Cheng C, Sangaré D, Lobo N, Collins F, Besansky N. The population genomics of trans-specific inversion polymorphisms in Anopheles gambiae. Genetics. 2009;183:275-88 pubmed publisher..gambiae and its sibling species An. arabiensis...
- Stage D, Eickbush T. Origin of nascent lineages and the mechanisms used to prime second-strand DNA synthesis in the R1 and R2 retrotransposons of Drosophila. Genome Biol. 2009;10:R49 pubmed publisher..Independent lineages occur more often with R1, possibly because these elements contain their own promoter. Finally, both R1 and R2 use imprecise, rapidly evolving mechanisms to cleave the second strand and prime second strand synthesis. ..
- De Freitas Ortiz M, Silva Loreto E. The hobo-related elements in the melanogaster species group. Genet Res (Camb). 2008;90:243-52 pubmed publisher..These hRSs and their 'MITE-like' counterparts could provide a good example of the steps proposed in models that describe the MITEs origin. ..
- Witsell A, Kane D, McVey M. Super-sized deletions: improved transposon excision screens using a mus309 mutant background. Fly (Austin). 2010;4:137-40 pubmed..In addition, we discuss how the general principle behind this technique can be applied in other contexts where double-strand breaks are being generated for the purpose of genome modification. ..
- Brower Toland B, Riddle N, Jiang H, Huisinga K, Elgin S. Multiple SET methyltransferases are required to maintain normal heterochromatin domains in the genome of Drosophila melanogaster. Genetics. 2009;181:1303-19 pubmed publisher..In addition, the genetic interactions between dSETDB1 and Su(var)3-9 mutations emphasize the importance of maintaining the activities of these histone methyltransferases in balance for normal genome function. ..
- Minervini C, Viggiano L, Caizzi R, Marsano R. Identification of novel LTR retrotransposons in the genome of Aedes aegypti. Gene. 2009;440:42-9 pubmed publisher..These results integrate the knowledge on the complicate genomic structure of an important disease vector. ..
- Kolaczan C, Heard S, Segraves K, Althoff D, Nason J. Spatial and genetic structure of host-associated differentiation in the parasitoid Copidosoma gelechiae. J Evol Biol. 2009;22:1275-83 pubmed publisher..2006), but only weak evidence via AFLPs for genome-wide differentiation, suggesting that this species is at a very early stage of HAD. ..
- Foret S, Kucharski R, Pittelkow Y, Lockett G, Maleszka R. Epigenetic regulation of the honey bee transcriptome: unravelling the nature of methylated genes. BMC Genomics. 2009;10:472 pubmed publisher..Our findings are particularly important in the context of the emerging evidence that environmental factors can influence the epigenetic settings of some genes and lead to serious metabolic and behavioural disorders. ..
- Metta M, Schlotterer C. Non-random genomic integration - an intrinsic property of retrogenes in Drosophila?. BMC Evol Biol. 2010;10:114 pubmed publisher..Rather, we propose that the movement away from the X-chromosome represents a general property of retroposition in Drosophila. ..
- Kijimoto T, Costello J, Tang Z, Moczek A, Andrews J. EST and microarray analysis of horn development in Onthophagus beetles. BMC Genomics. 2009;10:504 pubmed publisher..Here we explore the genetic and genomic basis of a class of traits that is both novel and highly diverse, in a group of organisms that is ecologically complex and experimentally tractable: horned beetles...