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      De novo transcriptome analysis shows differential expression of genes in salivary glands of edible bird’s nest producing swiftlets

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          Abstract

          Background

          Edible bird’s nest (EBN), produced from solidified saliva secretions of specific swiftlet species during the breeding season, is one of the most valuable animal by-products in the world. The composition and medicinal benefits of EBN have been extensively studied, however, genomic and transcriptomic studies of the salivary glands of these birds have not been conducted.

          Results

          The study described the transcriptomes of salivary glands from three swiftlet species (28 samples) generated by RNASeq. A total of 14,835 annotated genes and 428 unmapped genes were cataloged. The current study investigated the genes and pathways that are associated with the development of salivary gland and EBN composition. Differential expression and pathway enrichment analysis indicated that the expression of CREB3L2 and several signaling pathways involved in salivary gland development, namely, the EGFR, BMP, and MAPK signaling pathways, were up-regulated in swiftlets producing white EBN ( Aerodramus fuciphagus) and black EBN ( Aerodramus maximus) compared with non-EBN-producing swiftlets ( Apus affinis). Furthermore, MGAT, an essential gene for the biosynthesis of N-acetylneuraminic acid (sialic acid), was highly expressed in both white- and black-nest swiftlets compared to non-EBN-producing swiftlets. Interspecies comparison between Aerodramus fuciphagus and Aerodramus maximus indicated that the genes involved in N-acetylneuraminic and fatty acid synthesis were up-regulated in Aerodramus fuciphagus, while alanine and aspartate synthesis pathways were up-regulated in Aerodramus maximus. Furthermore, gender-based analysis revealed that N-glycan trimming pathway was significantly up-regulated in male Aerodramus fuciphagus from its natural habitat (cave) compared to their female counterpart.

          Conclusions

          Transcriptomic analysis of salivary glands of different swiftlet species reveal differential expressions of candidate genes that are involved in salivary gland development and in the biosynthesis of various bioactive compounds found in EBN.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s12864-017-3861-9) contains supplementary material, which is available to authorized users.

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          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx

            Background New methods are needed for genomic-scale analysis of emerging model organisms that exemplify important biological questions but lack fully sequenced genomes. For example, there is an urgent need to understand the potential for corals to adapt to climate change, but few molecular resources are available for studying these processes in reef-building corals. To facilitate genomics studies in corals and other non-model systems, we describe methods for transcriptome sequencing using 454, as well as strategies for assembling a useful catalog of genes from the output. We have applied these methods to sequence the transcriptome of planulae larvae from the coral Acropora millepora. Results More than 600,000 reads produced in a single 454 sequencing run were assembled into ~40,000 contigs with five-fold average sequencing coverage. Based on sequence similarity with known proteins, these analyses identified ~11,000 different genes expressed in a range of conditions including thermal stress and settlement induction. Assembled sequences were annotated with gene names, conserved domains, and Gene Ontology terms. Targeted searches using these annotations identified the majority of genes associated with essential metabolic pathways and conserved signaling pathways, as well as novel candidate genes for stress-related processes. Comparisons with the genome of the anemone Nematostella vectensis revealed ~8,500 pairs of orthologs and ~100 candidate coral-specific genes. More than 30,000 SNPs were detected in the coral sequences, and a subset of these validated by re-sequencing. Conclusion The methods described here for deep sequencing of the transcriptome should be widely applicable to generate catalogs of genes and genetic markers in emerging model organisms. Our data provide the most comprehensive sequence resource currently available for reef-building corals, and include an extensive collection of potential genetic markers for association and population connectivity studies. The characterization of the larval transcriptome for this widely-studied coral will enable research into the biological processes underlying stress responses in corals and evolutionary adaptation to global climate change.
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              The epidermal growth factor receptor family: biology driving targeted therapeutics.

              The epidermal growth factor family of receptor tyrosine kinases (ErbBs) plays essential roles in regulating cell proliferation, survival, differentiation and migration. The ErbB receptors carry out both redundant and restricted functions in mammalian development and in the maintenance of tissues in the adult mammal. Loss of regulation of the ErbB receptors underlies many human diseases, most notably cancer. Our understanding of the function and complex regulation of these receptors has fueled the development of targeted therapeutic agents for human malignancies in the last 15 years. Here we review the biology of ErbB receptors, including their structure, signaling, regulation, and roles in development and disease, then briefly touch on their increasing roles as targets for cancer therapy.
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                Author and article information

                Contributors
                looi_daniel@yahoo.com
                haghani_amin@yahoo.com
                aiini@upm.edu.my
                zuki@upm.edu.my
                aro@upm.edu.my
                Journal
                BMC Genomics
                BMC Genomics
                BMC Genomics
                BioMed Central (London )
                1471-2164
                3 July 2017
                3 July 2017
                2017
                : 18
                : 504
                Affiliations
                [1 ]ISNI 0000 0001 2231 800X, GRID grid.11142.37, Institute of Bioscience, , Universiti Putra Malaysia, ; 43400 UPM Serdang, Selangor, Malaysia
                [2 ]ISNI 0000 0001 2231 800X, GRID grid.11142.37, Faculty of Veterinary Medicine, , Universiti Putra Malaysia, ; 43400 UPM Serdang, Selangor, Malaysia
                Article
                3861
                10.1186/s12864-017-3861-9
                5496224
                c6a8cd86-0744-4b15-81b3-57f60873efe8
                © The Author(s). 2017

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 15 September 2016
                : 13 June 2017
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100003200, Kementerian Sains, Teknologi dan Inovasi;
                Award ID: 5450668
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100004577, Kementerian Pertanian dan Industri Asas Tani Malaysia;
                Award ID: : 6371400
                Award Recipient :
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2017

                Genetics
                aerodramus fuciphagus,aerodramus maximus,apus affinis,transcriptome,salivary gland
                Genetics
                aerodramus fuciphagus, aerodramus maximus, apus affinis, transcriptome, salivary gland

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