Transcriptome Analysis of Transparent Gill Covers of Pterophyllum scalare
Notice bibliographique
Résumé
【Objective】The transparent traits in Pterophyllum scalare has high economic and scientific value. This article aims to explore the differential expression genes (DEG) between transparent gill cover (TGC) and opaque gill cover (OGC) tissues of P. scalare, and explore the relevant signaling pathways affecting the transparent gill cover traits of P. scalare, so as to provide a theoretical basis for the subsequent screening of key genes regulating the transparent gill cover trait of P. scalare and related mechanism studies.【Method】The gill cover tissue of P. scalare (strain: red-topped tri-color) was selected as the research material, and 6 samples were selected from each group of OGC and TGC. Transcriptomic sequencing was carried out based on the Illumina Novaseq 6000 sequencing platform with using Fastp to perform quality control on raw sequencing data. The transcript and the corresponding single gene (Unigene) were obtained by de novo assembling of quality control data by Trinity software, and the initial assembly sequence was deredundancy analysis and result evaluation by CD-HIT software and BUSCO software, respectively. After redundancy, unigene were functionally annotated based on sequence homology. RSEM software was used to calculate the expression of unigene in each sample. DEGs between OGC and TGC were calculated using DESeq2 software. GO and KEGG pathway enrichment analysis was performed on DEGs using Goatools software and KOBAS software, respectively.【Result】(1) After quality control of sequencing data, the average error rate of each sample sequencing base was less than 0.1%, Q20 was higher than 97.78%, and Q30 was higher than 93.58%, and the sequencing quality was reliable. After de novo assembling, 200 303 transcripts were obtained, corresponding to 123 178 unigenes. After deredundancy analysis, a total of 147 932 transcripts are obtained, corresponding to 108 070 unigenes, with an average length of 991.85 bp and N50 is 2 430 bp. (2) A total of 40 180 unigenes were annotated in the NR, KEGG, eggNOG, GO, Pfam, and Swiss-Prot databases, accounting for 37.98% of the total, of which 10 747 genes were annotated simultaneously in 6 databases, accounting for 26.75% of the total. (3) TGC relative to OGC has a total of 432 DEGs, of which TGC significantly up-regulated 267 genes and down-regulated 165 genes relative to OGC. (4) GO enrichment results showed that 432 DEGs were mainly enriched in 5 biological pathways: IMP biosynthesis, IMP metabolism, "de novo" IMP biosynthesis, amino acid binding, and modified amino acid binding. (5) KEGG enrichment results showed that 432 DEGs were mainly enriched in 7 biological pathways: neuroactive ligand-receptor interaction, tyrosine metabolism, purine metabolism, a carbon pool of folate, phenylalanine metabolism, nucleotide metabolism, ubiquinone and other terpene-quinone biosynthesis.【Conclusion】432 genes related to the transparent gill cover trait of P. scalare were obtained by transcriptomic sequencing, which were mainly involved in 12 signaling pathways. The results will provide reference for the mining and functional study of genes related to transparent gill cover trait in P. scalare.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,001 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,001 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».