NBS-LRR gene family in banana (Musa acuminata): genome-wide identification and responses to Fusarium oxysporum f. sp. cubense race 1 and tropical race 4

Zhang

et al. 2021

PeerJ

Leaf spot of Hosta ventricosa is a new disease in China. This disease seriously affects the ornamental value and greening function of H. ventricosa. Identification of the causal agent can prevent and control leaf spot in H. ventricosa and promote the healthy development of the H. ventricosa industry. Known incidents of leaf spot of H. ventricosa occurred in three places, and samples were collected. After the fungus were isolated, its pathogenicity was tested according to Koch’s postulates. Isolates ZE-1b and ZE-2b were identified as Fusarium oxysporum based on morphological features and multigene phylogenetic analyses of calmodulin (CMDA), RNA polymerase II subunit A (RPB1), RNA polymerase II second largest subunit (RPB2) and translation elongation factor 1-alpha (TEF1). These results provide a theoretical basis for the control of this disease of H. ventricosa.

Section: Methodsmentioning

confidence: 99%

Leaf spot of Hosta ventricosa caused by Fusarium oxysporum in China

Zhang

et al. 2021

PeerJ

“…The NBS-LRR protein constitutes the largest family of resistance proteins. Since 2007, the NBS-LRR gene has been studied in wild and cultured bananas (Chang et al 2020;Pei et al 2007;Peraza-Echeverria et al 2008;Sutanto et al 2014). However, due to the lack of banana genome data, in these studies, the identi cation of NBS-LRRs was greatly limited by designing a set of degenerate primers based on the conserved NBS domain sequence (Martin et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Codon Bias of NBS-LRR Gene Family in Banana

Fang

et al. 2023

Preprint

As the largest family of plant resistance (R) proteins, nucleotide binding site-leucine-rich repeat ( NBS-LRR ) proteins play an important role in pathogen defense. In order to identify and get the codon usage bias of NBS-LRR gene family in banana. Using software MEGA11, TBtools and CodonW to analyze the codon preference and its influencing factors on genome-wide data from banana. The 74 NBS-LRR genes were divided into 6 subfamilies, 5 conserved motifs and 14 domains were identified. The more similar domain structures in the same phylogenetic tree subfamily and less consistent structures between different subfamilies. It was also found that when the G/C base appears at the third position of the codon, it had a higher usage rate. We identified 16 codons, including UCC and CCC, as the optimal codons. All of the 16 optimal codons ended with G or C, which indicated that the banana genome NBS-LRR gene prefers to use G or C terminated codons. Most of the gene points in the GC3s-ENC distribution map fell near the expected curve, mutation and natural selection during gene expression affected codon selection. The results of PR2-plot showed that most of the genes fell on the upper right side of the plane, and neutrality plot result showed that there was not significant correlation between C12 and GC3, which indicated the main factor of codon preference was natural selection. The results provide scientific basis for codon optimization of exogenous genes and improvement of their expression efficiency.

“…RGC2) [9,10], has been shown to provide immunity in Cavendish against Foc TR4 in the field [12]. Moreover, the genome sequences for some of these wild bananas are already available [13,14], and genome-wide analysis of the NBS-LRR gene family has been recently reported [15]. The genome-wide analysis of different classes of R genes in bananas should facilitate the identification of novel R genes for Foc or P. fijiensis, which could be used to genetically improve the current susceptible banana cultivars, including the forgotten Gros Michel cultivar.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of the LRR-RLP Gene Family in a Wild Banana (Musa acuminata ssp. malaccensis) Uncovers Multiple Fusarium Wilt Resistance Gene Candidates

Álvarez-López

Herrera-Valencia

Góngora-Castillo

et al. 2022

Genes

Banana is the most popular fruit in the world, with a relevant role in food security for more than 400 million people. However, fungal diseases cause substantial losses every year. A better understanding of the banana immune system should facilitate the development of new disease-resistant cultivars. In this study, we performed a genome-wide analysis of the leucine-rich repeat receptor-like protein (LRR-RLP) disease resistance gene family in a wild banana. We identified 78 LRR-RLP genes in the banana genome. Remarkably, seven MaLRR-RLPs formed a gene cluster in the distal part of chromosome 10, where resistance to Fusarium wilt caused by Foc race 1 has been previously mapped. Hence, we proposed these seven MaLRR-RLPs as resistance gene candidates (RGCs) for Fusarium wilt. We also identified seven other banana RGCs based on their close phylogenetic relationships with known LRR-RLP proteins. Moreover, phylogenetic analysis of the banana, rice, and Arabidopsis LRR-RLP families revealed five major phylogenetic clades shared by these plant species. Finally, transcriptomic analysis of the MaLRR-RLP gene family in plants treated with Foc race 1 or Foc TR4 showed the expression of several members of this family, and some of them were upregulated in response to these Foc races. Our study provides novel insights into the structure, distribution, evolution, and expression of the LRR-RLP gene family in bananas as well as valuable RGCs that will facilitate the identification of disease resistance genes for the genetic improvement of this crop.