MersV1, Ncbi, Merge, bibRecord, 001655

Exploring developmental gene toolkit and associated pathways in a potential new model crustacean using transcriptomic analysis.

Identifieur interne : 001655 ( Ncbi/Merge ); précédent : 001654; suivant : 001656

Exploring developmental gene toolkit and associated pathways in a potential new model crustacean using transcriptomic analysis.

Auteurs : Michael L. Jaramillo [Brésil] ; Frank Guzman [Brésil] ; Christian L B. Paese [Brésil] ; Rogerio Margis [Brésil] ; Evelise M. Nazari [Brésil] ; Dib Ammar [Brésil] ; Yara Maria Rauh Müller [Brésil]

Source :

Development genes and evolution [ 1432-041X ] ; 2016.

RBID : pubmed:27278761

Descripteurs français

KwdFr :
- Analyse de profil d'expression de gènes, Animaux, Embryon non mammalien (métabolisme), Femelle, Modèles animaux, Mâle, Répétitions microsatellites, Transduction du signal.
MESH :
- métabolisme : Embryon non mammalien.
- Analyse de profil d'expression de gènes, Animaux, Femelle, Modèles animaux, Mâle, Répétitions microsatellites, Transduction du signal.

English descriptors

KwdEn :
- Animals, Decapoda (classification), Decapoda (genetics), Decapoda (growth & development), Decapoda (metabolism), Embryo, Nonmammalian (metabolism), Female, Gene Expression Profiling, Male, Microsatellite Repeats, Models, Animal, Signal Transduction.
MESH :
- classification : Decapoda.
- genetics : Decapoda.
- growth & development : Decapoda.
- metabolism : Decapoda, Embryo, Nonmammalian.
- Animals, Female, Gene Expression Profiling, Male, Microsatellite Repeats, Models, Animal, Signal Transduction.

Abstract

The crustaceans are one of the largest, most diverse, and most successful groups of invertebrates. The diversity among the crustaceans is also reflected in embryonic development models. However, the molecular genetics that regulates embryonic development is not known in those crustaceans that have a short germ-band development with superficial cleavage, such as Macrobrachium olfersi. This species is a freshwater decapod and has great potential to become a model for developmental biology, as well as for evolutionary and environmental studies. To obtain sequence data of M. olfersi from an embryonic developmental perspective, we performed de novo assembly and annotation of the embryonic transcriptome. Using a pooling strategy of total RNA, paired-end Illumina sequencing, and assembly with multiple k-mers, a total of 25,636,097 pair reads were generated. In total, 99,751 unigenes were identified, and 20,893 of these returned a Blastx hit. KEGG pathway analysis mapped a total of 6866 unigenes related to 129 metabolic pathways. In general, 21,845 unigenes were assigned to gene ontology (GO) categories: molecular function (19,604), cellular components (10,254), and biological processes (13,841). Of these, 2142 unigenes were assigned to the developmental process category. More specifically, a total of 35 homologs of embryonic development toolkit genes were identified, which included maternal effect (one gene), gap (six), pair-rule (six), segment polarity (seven), Hox (four), Wnt (eight), and dorsoventral patterning genes (three). In addition, genes of developmental pathways were found, including TGF-β, Wnt, Notch, MAPK, Hedgehog, Jak-STAT, VEGF, and ecdysteroid-inducible nuclear receptors. RT-PCR analysis of eight genes related to embryonic development from gastrulation to late morphogenesis/organogenesis confirmed the applicability of the transcriptome analysis.

DOI: 10.1007/s00427-016-0551-6
PubMed: 27278761

Links toward previous steps (curation, corpus...)

to stream PubMed, to step Corpus: 001089
to stream PubMed, to step Curation: 001089
to stream PubMed, to step Checkpoint: 001110

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pubmed:27278761

Le document en format XML

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<front><div type="abstract" xml:lang="en">The crustaceans are one of the largest, most diverse, and most successful groups of invertebrates. The diversity among the crustaceans is also reflected in embryonic development models. However, the molecular genetics that regulates embryonic development is not known in those crustaceans that have a short germ-band development with superficial cleavage, such as Macrobrachium olfersi. This species is a freshwater decapod and has great potential to become a model for developmental biology, as well as for evolutionary and environmental studies. To obtain sequence data of M. olfersi from an embryonic developmental perspective, we performed de novo assembly and annotation of the embryonic transcriptome. Using a pooling strategy of total RNA, paired-end Illumina sequencing, and assembly with multiple k-mers, a total of 25,636,097 pair reads were generated. In total, 99,751 unigenes were identified, and 20,893 of these returned a Blastx hit. KEGG pathway analysis mapped a total of 6866 unigenes related to 129 metabolic pathways. In general, 21,845 unigenes were assigned to gene ontology (GO) categories: molecular function (19,604), cellular components (10,254), and biological processes (13,841). Of these, 2142 unigenes were assigned to the developmental process category. More specifically, a total of 35 homologs of embryonic development toolkit genes were identified, which included maternal effect (one gene), gap (six), pair-rule (six), segment polarity (seven), Hox (four), Wnt (eight), and dorsoventral patterning genes (three). In addition, genes of developmental pathways were found, including TGF-β, Wnt, Notch, MAPK, Hedgehog, Jak-STAT, VEGF, and ecdysteroid-inducible nuclear receptors. RT-PCR analysis of eight genes related to embryonic development from gastrulation to late morphogenesis/organogenesis confirmed the applicability of the transcriptome analysis.</div>
</front>
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<DateCompleted><Year>2017</Year>
<Month>07</Month>
<Day>14</Day>
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<Month>12</Month>
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<ArticleTitle>Exploring developmental gene toolkit and associated pathways in a potential new model crustacean using transcriptomic analysis.</ArticleTitle>
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<Abstract><AbstractText>The crustaceans are one of the largest, most diverse, and most successful groups of invertebrates. The diversity among the crustaceans is also reflected in embryonic development models. However, the molecular genetics that regulates embryonic development is not known in those crustaceans that have a short germ-band development with superficial cleavage, such as Macrobrachium olfersi. This species is a freshwater decapod and has great potential to become a model for developmental biology, as well as for evolutionary and environmental studies. To obtain sequence data of M. olfersi from an embryonic developmental perspective, we performed de novo assembly and annotation of the embryonic transcriptome. Using a pooling strategy of total RNA, paired-end Illumina sequencing, and assembly with multiple k-mers, a total of 25,636,097 pair reads were generated. In total, 99,751 unigenes were identified, and 20,893 of these returned a Blastx hit. KEGG pathway analysis mapped a total of 6866 unigenes related to 129 metabolic pathways. In general, 21,845 unigenes were assigned to gene ontology (GO) categories: molecular function (19,604), cellular components (10,254), and biological processes (13,841). Of these, 2142 unigenes were assigned to the developmental process category. More specifically, a total of 35 homologs of embryonic development toolkit genes were identified, which included maternal effect (one gene), gap (six), pair-rule (six), segment polarity (seven), Hox (four), Wnt (eight), and dorsoventral patterning genes (three). In addition, genes of developmental pathways were found, including TGF-β, Wnt, Notch, MAPK, Hedgehog, Jak-STAT, VEGF, and ecdysteroid-inducible nuclear receptors. RT-PCR analysis of eight genes related to embryonic development from gastrulation to late morphogenesis/organogenesis confirmed the applicability of the transcriptome analysis.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Jaramillo</LastName>
<ForeName>Michael L</ForeName>
<Initials>ML</Initials>
<AffiliationInfo><Affiliation>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil.</Affiliation>
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<Day>08</Day>
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</MeshHeading>
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<MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName>
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<MeshHeading><DescriptorName UI="D018895" MajorTopicYN="N">Microsatellite Repeats</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D023421" MajorTopicYN="N">Models, Animal</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D015398" MajorTopicYN="N">Signal Transduction</DescriptorName>
</MeshHeading>
</MeshHeadingList>
<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Development-related gene</Keyword>
<Keyword MajorTopicYN="Y">Freshwater prawn</Keyword>
<Keyword MajorTopicYN="Y">Macrobrachium olfersi</Keyword>
<Keyword MajorTopicYN="Y">Organogenesis/morphogenesis</Keyword>
<Keyword MajorTopicYN="Y">RNA-seq</Keyword>
<Keyword MajorTopicYN="Y">RT-PCR</Keyword>
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Exploring developmental gene toolkit and associated pathways in a potential new model crustacean using transcriptomic analysis.

Exploring developmental gene toolkit and associated pathways in a potential new model crustacean using transcriptomic analysis.

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