Genes encoding novel secreted and transmembrane proteins are temporally and spatially regulated during Drosophila melanogasterembryogenesis

Zúñiga, Alejandro; Hödar, Christian; Hanna, Patricia; Ibáñez, Freddy; Moreno, Pablo; Pulgar, Rodrigo; Pastenes, Luis; González, Maurício; Cambiazo, Verónica

doi:10.1186/1741-7007-7-61

Cited by 13 publications

(13 citation statements)

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“…As genomic information of R. ferrugineus is crucial for molecular‐level studies, basic data for RPW transcriptomics from different developmental stages and specific tissues become the first step for producing a comprehensive atlas of gene expression and its dynamics (Zúñiga et al ., ). The developmental gene networks are of essence in understanding processes of cell proliferation, differentiation, body patterning and morphogenesis, such as organogenesis and neurogenesis (Fowlkes et al ., ; Lott et al ., ; Lynch et al ., ).…”

Section: Introductionmentioning

confidence: 97%

Transcriptomic study of the red palm weevil Rhynchophorus ferrugineus embryogenesis

et al. 2014

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The red palm weevil (RPW), Rhynchophorus ferrugineus (Coleoptera: Curculionidae), is an invasive, concealed and destructive tissue borer, and it becomes a lethal pest of the palm family of plants and has been reported to attack 20 palm species around the globe. Here we report a systematic transcriptomic study on embryogenesis of RPW, where we analyze the transcriptomes across five developmental stages of RPW embryogenesis, involving four embryonic stages (E1, E2, E3 and E4) and one larval stage (L1). Using the RNA-seq and next-generation platforms, we generated 80 to 91 million reads for each library and assemble 22 532 genes that are expressed at different embryonic stages. Among the total transcripts from the five embryonic development stages, we found that 30.45 % are differentially expressed, 10.10 % show stage-specificity and even a larger fraction, 62.88 %, exhibit constitutive expression in all the stages. We also analyzes the expression dynamics of several conserved signaling pathways (such as Hedgehog, JAK-STAT, Notch, TGF-β, Ras/MAPK and Wnt), as well as key developmental genes, including those related to apoptosis, axis formation, Hox complex, neurogenesis and segmentation. The datasets provide an essential resource for gene annotation and RPW functional genomics, including studies by using tools and concepts from multiple disciplines, such as development, physiology, biochemistry, molecular biology and genetics.

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Section: Introductionmentioning

confidence: 97%

Transcriptomic study of the red palm weevil Rhynchophorus ferrugineus embryogenesis

et al. 2014

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“…Finally, embryos were washed thrice in 100% methanol and four times in 100% ethanol and stored at − 20°. In situ hybridizations of D. melanogaster embryos were conducted as described in [ 23 ].…”

Section: Methodsmentioning

confidence: 99%

The dorsoventral patterning of Musca domestica embryos: insights into BMP/Dpp evolution from the base of the lower cyclorraphan flies

Hödar

Cambiazo

2018

EvoDevo

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BackgroundIn the last few years, accumulated information has indicated that the evolution of an extra-embryonic membrane in dipterans was accompanied by changes in the gene regulatory network controlled by the BMP/Dpp pathway, which is responsible for dorsal patterning in these insects. However, only comparative analysis of gene expression levels between distant species with two extra-embryonic membranes, like A. gambiae or C. albipunctata, and D. melanogaster, has been conducted. Analysis of gene expression in ancestral species, which evolved closer to the amnioserosa origin, could provide new insights into the evolution of dorsoventral patterning in dipterans.ResultsHere we describe the spatial expression of several key and downstream elements of the Dpp pathway and show the compared patterns of expression between Musca and Drosophila embryos, both dipterans with amnioserosa. Most of the analyzed gene showed a high degree of expression conservation, however, we found several differences in the gene expression pattern of M. domestica orthologs for sog and tolloid. Bioinformatics analysis of the promoter of both genes indicated that the variations could be related to the gain of several binding sites for the transcriptional factor Dorsal in the Md.tld promoter and Snail in the Md.sog enhancer. These altered expressions could explain the unclear formation of the pMad gradient in the M. domestica embryo, compared to the formation of the gradient in D. melanogaster.ConclusionGene expression changes during the dorsal–ventral patterning in insects contribute to the differentiation of extra-embryonic tissues as a consequence of changes in the gene regulatory network controlled by BMP/Dpp. In this work, in early M. domestica embryos, we identified the expression pattern of several genes members involved in the dorsoventral specification of the embryo. We believe that these data can contribute to understanding the evolution of the BMP/Dpp pathway, the regulation of BMP ligands, and the formation of a Dpp gradient in higher cyclorraphan flies.Electronic supplementary materialThe online version of this article (10.1186/s13227-018-0102-5) contains supplementary material, which is available to authorized users.

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“…Using suppression subtractive hybridization (SSH) and microarray analysis, Zúñiga et al [ 7 ] isolated a set of transcripts that are differentially expressed between gastrulating and blastoderm Drosophila embryos. The SSH technique is able to circumvent the inability of most high-throughput gene-expression profiling techniques to isolate transcripts of low abundance [ 8 ].…”

Section: An Integrative Approach To Identify Genes Required For Morphmentioning

confidence: 99%

“…The study by Zúñiga et al . [ 7 ] highlights the value of integrating information from temporal and spatial expression studies with protein sequence analysis to generate a short list of candidate genes for functional analysis. Moreover, the experimental approach undertaken by Zúñiga et al .…”

Section: Future Directions: the Shape Of Things To Comementioning

confidence: 99%

“…The paper published in BMC Biology by Cambiazo and colleagues (Zúñiga et al . [ 7 ]) describes an integrated genome-wide approach to finding genes that are specifically upregulated during early Drosophila development. The authors use differential gene-expression profiling, bioinformatics, in situ analysis and functional characterization to identify a novel gene that is required for embryonic morphogenesis, as well as a number of interesting candidate genes for future functional analysis.…”

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Deciphering the genetic code of morphogenesis using functional genomics

Vichas

Zallen

2009

Journal of Biology

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Genes encoding novel secreted and transmembrane proteins are temporally and spatially regulated during Drosophila melanogasterembryogenesis

Cited by 13 publications

References 68 publications

Transcriptomic study of the red palm weevil Rhynchophorus ferrugineus embryogenesis

Transcriptomic study of the red palm weevil Rhynchophorus ferrugineus embryogenesis

The dorsoventral patterning of Musca domestica embryos: insights into BMP/Dpp evolution from the base of the lower cyclorraphan flies

Deciphering the genetic code of morphogenesis using functional genomics

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