A comparative transcriptome analysis reveals expression profiles conserved across three Eimeria spp. of domestic fowl and associated with multiple developmental stages

Novaes, Jeniffer; Rangel, Luiz Thibério; Ferro, Milene; Abe, Ricardo Y.; Manha, Alessandra P.S.; Mello, Joana Carvalho Moreira de; Varuzza, Leonardo; Durham, Alan Mitchell; Madeira, Alda Maria Backx Noronha; Gruber, Arthur

doi:10.1016/j.ijpara.2011.10.008

Cited by 32 publications

(37 citation statements)

References 57 publications

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“…To predict the most probable coding sequence regions within the transcripts, an empirical homology-based methodology was designed using Novaes et al [124] as a guide, rather than the use of gene prediction tools. The use of gene prediction tools requires the construction of a high-quality training dataset, an arduous task for understudied animals as those used herein.…”

Section: Methodsmentioning

confidence: 99%

Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks

et al. 2016

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BackgroundMollusks display a striking morphological disparity, including, among others, worm-like animals (the aplacophorans), snails and slugs, bivalves, and cephalopods. This phenotypic diversity renders them ideal for studies into animal evolution. Despite being one of the most species-rich phyla, molecular and in silico studies concerning specific key developmental gene families are still scarce, thus hampering deeper insights into the molecular machinery that governs the development and evolution of the various molluscan class-level taxa.ResultsNext-generation sequencing was used to retrieve transcriptomes of representatives of seven out of the eight recent class-level taxa of mollusks. Similarity searches, phylogenetic inferences, and a detailed manual curation were used to identify and confirm the orthology of numerous molluscan Hox and ParaHox genes, which resulted in a comprehensive catalog that highlights the evolution of these genes in Mollusca and other metazoans. The identification of a specific molluscan motif in the Hox paralog group 5 and a lophotrochozoan ParaHox motif in the Gsx gene is described. Functional analyses using KEGG and GO tools enabled a detailed description of key developmental genes expressed in important pathways such as Hedgehog, Wnt, and Notch during development of the respective species. The KEGG analysis revealed Wnt8, Wnt11, and Wnt16 as Wnt genes hitherto not reported for mollusks, thereby enlarging the known Wnt complement of the phylum. In addition, novel Hedgehog (Hh)-related genes were identified in the gastropod Lottia cf. kogamogai, demonstrating a more complex gene content in this species than in other mollusks.ConclusionsThe use of de novo transcriptome assembly and well-designed in silico protocols proved to be a robust approach for surveying and mining large sequence data in a wide range of non-model mollusks. The data presented herein constitute only a small fraction of the information retrieved from the analysed molluscan transcriptomes, which can be promptly employed in the identification of novel genes and gene families, phylogenetic inferences, and other studies using molecular tools. As such, our study provides an important framework for understanding some of the underlying molecular mechanisms involved in molluscan body plan diversification and hints towards functions of key developmental genes in molluscan morphogenesis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3080-9) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks

et al. 2016

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“…Faecal samples quickly lose form in poultry accommodation under the action of bird movement. Intact samples were taken to represent faeces less than 24 h old, although it is important to note that sporulation could still have made significant progress under favourable conditions (Novaes et al, 2012). Other possible factors include the PCR efficiency of the 5S rDNA and IPC qPCRs.…”

Section: Discussionmentioning

confidence: 99%

Real-time PCR-based quantification ofEimeriagenomes: a method to outweigh underestimation of genome numbers due to PCR inhibition

et al. 2013

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“…For the genome, Sanger sequencing was used initially at the Wellcome Trust Sanger Institute, producing approximately eight-fold genome coverage (Shirley et al, 2004;Reid et al, 2014). Complementary projects sequencing the smallest chromosome within the E. tenella genome and open reading frame expressed sequence tag (ORESTES) cDNA reads derived from five E. acervulina, E. maxima and E. tenella lifecycle stages used the same technology (Ling et al, 2007;Novaes et al, 2012). Subsequently NGS technologies promoted an expansion of genome sequencing for Eimeria, using 454 pyrosequencing to generate more than 12-fold coverage of the E. maxima Houghton strain genome and Illumina to improve the E. tenella genome assembly as well as generate the first assemblies for seven other Eimeria species/strains including one species which infects the mouse (Eimeria falciformis; Fig.…”

Section: Application To Eimerian Genomesmentioning

confidence: 99%

“…Exogenous and extracellular endogenous life cycle forms including the oocysts (unsporulated, sporulating and sporulated), sporozoites and merozoites have been most commonly sampled for transcriptomic analyses as a consequence of their availability, first as ESTs/ORESTES and more recently by Illumina-based RNAseq (Fig. 1) (Abrahamsen et al, 1993;Wan et al, 1999;Miska et al, 2008;Kim et al, 2010;Schwarz et al, 2010;Aarthi et al, 2011;Dong et al, 2011;Tuda et al, 2011;Amiruddin et al, 2012;Novaes et al, 2012;Heitlinger et al, 2014;Reid et al, 2014;Walker et al, 2015). As described for genome sequencing, progress from Sanger to NGS technologies has provided opportunities to expand transcriptome sequencing to additional E. tenella life cycle stages and species such as E. falciformis.…”

Section: Transcriptomic Analysesmentioning

confidence: 99%

Eimeria genomics: Where are we now and where are we going?

Blake

2015

Veterinary Parasitology

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A comparative transcriptome analysis reveals expression profiles conserved across three Eimeria spp. of domestic fowl and associated with multiple developmental stages

Cited by 32 publications

References 57 publications

Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks

Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks

Real-time PCR-based quantification ofEimeriagenomes: a method to outweigh underestimation of genome numbers due to PCR inhibition

Eimeria genomics: Where are we now and where are we going?

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