Exploring developmental gene toolkit and associated pathways in a potential new model crustacean using transcriptomic analysis.
Identifieur interne : 001655 ( Ncbi/Curation ); précédent : 001654; suivant : 001656Exploring 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.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- 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: Pour aller vers cette notice dans l'étape Curation :001089
- to stream PubMed, to step Curation: Pour aller vers cette notice dans l'étape Curation :001089
- to stream PubMed, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :001110
- to stream Ncbi, to step Merge: Pour aller vers cette notice dans l'étape Curation :001655
Links to Exploration step
pubmed:27278761Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Exploring developmental gene toolkit and associated pathways in a potential new model crustacean using transcriptomic analysis.</title><author><name sortKey="Jaramillo, Michael L" sort="Jaramillo, Michael L" uniqKey="Jaramillo M" first="Michael L" last="Jaramillo">Michael L. Jaramillo</name><affiliation wicri:level="2"><nlm:affiliation>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina</wicri:regionArea><placeName><region type="state">Santa Catarina</region></placeName></affiliation></author><author><name sortKey="Guzman, Frank" sort="Guzman, Frank" uniqKey="Guzman F" first="Frank" last="Guzman">Frank Guzman</name><affiliation wicri:level="4"><nlm:affiliation>PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS</wicri:regionArea><placeName><region type="state">Rio Grande do Sul</region><settlement type="city">Porto Alegre</settlement></placeName><orgName type="university">Université fédérale du Rio Grande do Sul</orgName></affiliation></author><author><name sortKey="Paese, Christian L B" sort="Paese, Christian L B" uniqKey="Paese C" first="Christian L B" last="Paese">Christian L B. Paese</name><affiliation wicri:level="2"><nlm:affiliation>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina</wicri:regionArea><placeName><region type="state">Santa Catarina</region></placeName></affiliation></author><author><name sortKey="Margis, Rogerio" sort="Margis, Rogerio" uniqKey="Margis R" first="Rogerio" last="Margis">Rogerio Margis</name><affiliation wicri:level="4"><nlm:affiliation>Departamento de Biofisica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Biofisica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS</wicri:regionArea><placeName><region type="state">Rio Grande do Sul</region><settlement type="city">Porto Alegre</settlement></placeName><orgName type="university">Université fédérale du Rio Grande do Sul</orgName></affiliation></author><author><name sortKey="Nazari, Evelise M" sort="Nazari, Evelise M" uniqKey="Nazari E" first="Evelise M" last="Nazari">Evelise M. Nazari</name><affiliation wicri:level="2"><nlm:affiliation>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina</wicri:regionArea><placeName><region type="state">Santa Catarina</region></placeName></affiliation></author><author><name sortKey="Ammar, Dib" sort="Ammar, Dib" uniqKey="Ammar D" first="Dib" last="Ammar">Dib Ammar</name><affiliation wicri:level="2"><nlm:affiliation>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina</wicri:regionArea><placeName><region type="state">Santa Catarina</region></placeName></affiliation></author><author><name sortKey="Muller, Yara Maria Rauh" sort="Muller, Yara Maria Rauh" uniqKey="Muller Y" first="Yara Maria Rauh" last="Müller">Yara Maria Rauh Müller</name><affiliation wicri:level="2"><nlm:affiliation>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil. yara.rauh@ufsc.br.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina</wicri:regionArea><placeName><region type="state">Santa Catarina</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2016">2016</date><idno type="RBID">pubmed:27278761</idno><idno type="pmid">27278761</idno><idno type="doi">10.1007/s00427-016-0551-6</idno><idno type="wicri:Area/PubMed/Corpus">001089</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001089</idno><idno type="wicri:Area/PubMed/Curation">001089</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001089</idno><idno type="wicri:Area/PubMed/Checkpoint">001110</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001110</idno><idno type="wicri:Area/Ncbi/Merge">001655</idno><idno type="wicri:Area/Ncbi/Curation">001655</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Exploring developmental gene toolkit and associated pathways in a potential new model crustacean using transcriptomic analysis.</title><author><name sortKey="Jaramillo, Michael L" sort="Jaramillo, Michael L" uniqKey="Jaramillo M" first="Michael L" last="Jaramillo">Michael L. Jaramillo</name><affiliation wicri:level="2"><nlm:affiliation>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina</wicri:regionArea><placeName><region type="state">Santa Catarina</region></placeName></affiliation></author><author><name sortKey="Guzman, Frank" sort="Guzman, Frank" uniqKey="Guzman F" first="Frank" last="Guzman">Frank Guzman</name><affiliation wicri:level="4"><nlm:affiliation>PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS</wicri:regionArea><placeName><region type="state">Rio Grande do Sul</region><settlement type="city">Porto Alegre</settlement></placeName><orgName type="university">Université fédérale du Rio Grande do Sul</orgName></affiliation></author><author><name sortKey="Paese, Christian L B" sort="Paese, Christian L B" uniqKey="Paese C" first="Christian L B" last="Paese">Christian L B. Paese</name><affiliation wicri:level="2"><nlm:affiliation>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina</wicri:regionArea><placeName><region type="state">Santa Catarina</region></placeName></affiliation></author><author><name sortKey="Margis, Rogerio" sort="Margis, Rogerio" uniqKey="Margis R" first="Rogerio" last="Margis">Rogerio Margis</name><affiliation wicri:level="4"><nlm:affiliation>Departamento de Biofisica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Biofisica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS</wicri:regionArea><placeName><region type="state">Rio Grande do Sul</region><settlement type="city">Porto Alegre</settlement></placeName><orgName type="university">Université fédérale du Rio Grande do Sul</orgName></affiliation></author><author><name sortKey="Nazari, Evelise M" sort="Nazari, Evelise M" uniqKey="Nazari E" first="Evelise M" last="Nazari">Evelise M. Nazari</name><affiliation wicri:level="2"><nlm:affiliation>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina</wicri:regionArea><placeName><region type="state">Santa Catarina</region></placeName></affiliation></author><author><name sortKey="Ammar, Dib" sort="Ammar, Dib" uniqKey="Ammar D" first="Dib" last="Ammar">Dib Ammar</name><affiliation wicri:level="2"><nlm:affiliation>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina</wicri:regionArea><placeName><region type="state">Santa Catarina</region></placeName></affiliation></author><author><name sortKey="Muller, Yara Maria Rauh" sort="Muller, Yara Maria Rauh" uniqKey="Muller Y" first="Yara Maria Rauh" last="Müller">Yara Maria Rauh Müller</name><affiliation wicri:level="2"><nlm:affiliation>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil. yara.rauh@ufsc.br.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina</wicri:regionArea><placeName><region type="state">Santa Catarina</region></placeName></affiliation></author></analytic><series><title level="j">Development genes and evolution</title><idno type="eISSN">1432-041X</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Decapoda (classification)</term><term>Decapoda (genetics)</term><term>Decapoda (growth & development)</term><term>Decapoda (metabolism)</term><term>Embryo, Nonmammalian (metabolism)</term><term>Female</term><term>Gene Expression Profiling</term><term>Male</term><term>Microsatellite Repeats</term><term>Models, Animal</term><term>Signal Transduction</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Animaux</term><term>Embryon non mammalien (métabolisme)</term><term>Femelle</term><term>Modèles animaux</term><term>Mâle</term><term>Répétitions microsatellites</term><term>Transduction du signal</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Decapoda</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Decapoda</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Decapoda</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Decapoda</term><term>Embryo, Nonmammalian</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Embryon non mammalien</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Female</term><term>Gene Expression Profiling</term><term>Male</term><term>Microsatellite Repeats</term><term>Models, Animal</term><term>Signal Transduction</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Animaux</term><term>Femelle</term><term>Modèles animaux</term><term>Mâle</term><term>Répétitions microsatellites</term><term>Transduction du signal</term></keywords></textClass></profileDesc></teiHeader><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></TEI></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Ncbi/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001655 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd -nk 001655 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Ncbi
|étape= Curation
|type= RBID
|clé= pubmed:27278761
|texte= Exploring developmental gene toolkit and associated pathways in a potential new model crustacean using transcriptomic analysis.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/RBID.i -Sk "pubmed:27278761" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |