Genome-wide Identification of ATP Binding Cassette (ABC) Transporter and Heavy Metal Associated (HMA) Gene Families in Flax (Linum usitatissimum L.)
Notice bibliographique
Résumé
Abstract Background Flax ( Linum usitatissimum L.) is a self-pollinated crop and diversified into two morphotypes for its stem fibre and seed oil. The availability of the flax reference genome sequence, previously assembled into 15 pseudomolecules, enables the characterization of important gene families. The ABC transporter and HMA gene families are considered important gene families in the control of cadmium (Cd) accumulation in crops. To date, the genome-wide analysis of these two gene families has been successfully conducted in several plant species but no systematic study is available for the flax genome. Results Here we described both gene families in flax to provide a comprehensive overview of its evolution and some support towards the functional annotation of its members. The 198 ABC transporter and 12 HMA genes identified in the flax genome were classified into eight ABC transporter and four HMA subfamilies based on their phylogenetic analysis and domain compositions. Nine of these genes, i.e., LuABCC9, LuABCC10 , LuABCG58, LuABCG59 , LuABCG71 , LuABCG72 , LuABCG73, LuHMA3 , and LuHMA4 , were orthologous with the Cd associated genes in Arabidopsis , rice and maize. Ten motifs were identified from all ABC transporter and HMA genes and several motifs were conserved for all genes with similar gene length, but different subfamilies had their different motif structures. Both the ABC transporter and HMA families were highly conserved among subfamilies of flax and with Arabidopsis . While four types of gene duplication were observed at different frequencies, whole-genome or segmental duplications were the most frequent with 162 genes, followed by 29 dispersed, 14 tandem and 4 proximal, suggesting that segmental duplications contributed substantially to the expansion of both gene families in flax. The rates of non-synonymous to synonymous ( Ka/Ks ) mutations of paired duplicated genes were mostly less than one, indicative of a predominant purifying selection. Only five pairs of genes clearly exhibited positive selection with a Ka/Ks ratio greater than one. Gene ontology analyses suggested that most flax ABC transporter and HMA genes functioned in ATP binding, transporter, catalytic, ATPase activity, and metal ion binding. The RNA-Seq analysis of eight different organs demonstrated diverse expression profiling patterns of the genes and revealed their functional or subfunctional conservation and neo-functionalization. Conclusion Characterization of the ABC transporter and HMA genes will help in the functional analysis of candidate genes in flax and other crop species.
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 distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,001 | 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 | 0,001 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,000 | 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 tête enseignante, 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 ».