Citrus genomic resources unravel putative genetic determinants of Huanglongbing pathogenicity

Gao, Yuxia; Xu, Jin; Li, Zhilong; Zhang, Yunzeng; Riera, Nadia; Xiong, Zhiwei; Ouyang, Zhigang; Liu, Xinjun; Lu, Zhanjun; Seymour, Danelle K.; Zhong, Balian; Wang, Nian

doi:10.1016/j.isci.2023.106024

Cited by 14 publications

(6 citation statements)

References 120 publications

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“…Quinone oxidoreductase 1 acts as a cytoplasmic antioxidant, whereas LysR is a key circuit component in regulating microbial stress responses and is required for bacterial tolerance to H 2 O 2 in vitro 78 . The protective mechanism of CLas is consistent with the model that HLB is a pathogen-triggered immune disease; CLas triggers systemic and chronic production of reactive oxygen species (ROS), leading to phloem tissue cell death and HLB symptoms [79][80][81] . Thus, those proteins will protect CLas from the high ROS levels in the phloem tissues.…”

Section: Discussionsupporting

confidence: 81%

The protein interactome of the citrus Huanglongbing pathogen Candidatus Liberibacter asiaticus

Carter,

Peraza,

Wang

2023

Nat Commun

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The bacterium Candidatus Liberibacter asiaticus (CLas) causes citrus Huanglongbing disease. Our understanding of the pathogenicity and biology of this microorganism remains limited because CLas has not yet been cultivated in artificial media. Its genome is relatively small and encodes approximately 1136 proteins, of which 415 have unknown functions. Here, we use a high-throughput yeast-two-hybrid (Y2H) screen to identify interactions between CLas proteins, thus providing insights into their potential functions. We identify 4245 interactions between 542 proteins, after screening 916 bait and 936 prey proteins. The false positive rate of the Y2H assay is estimated to be 2.9%. Pull-down assays for nine protein-protein interactions (PPIs) likely involved in flagellar function support the robustness of the Y2H results. The average number of PPIs per node in the CLas interactome is 15.6, which is higher than the numbers previously reported for interactomes of free-living bacteria, suggesting that CLas genome reduction has been accompanied by increased protein multi-functionality. We propose potential functions for 171 uncharacterized proteins, based on the PPI results, guilt-by-association analyses, and comparison with data from other bacterial species. We identify 40 hub-node proteins, including quinone oxidoreductase and LysR, which are known to protect other bacteria against oxidative stress and might be important for CLas survival in the phloem. We expect our PPI database to facilitate research on CLas biology and pathogenicity mechanisms.

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Section: Discussionsupporting

confidence: 81%

The protein interactome of the citrus Huanglongbing pathogen Candidatus Liberibacter asiaticus

Carter,

Peraza,

Wang

2023

Nat Commun

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“…The proportion of dispensable genes observed in this study is relatively higher compared with other fruit plants such as apple (18.7%) (Sun et al, 2020), tomato (26%) (Gao et al, 2019), and watermelon (30.5%) (Wu et al, 2023). However, the proportion is similar to cucumber (43.8%) (Li et al, 2022) and smaller than citrus (64.6%) (Gao et al, 2023). Gene ontology (GO) enrichment analysis shows that genes with essential biological functions, including DNA-templated transcription, transmembrane transport and response to cadmium ion were enriched in core genes ( Table S13 ).…”

Section: Resultsmentioning

confidence: 92%

Pan-genome of pear provides insights into the fruit quality traits differentiation between Asian and European pears

Ding,

Hu,

Liu

et al. 2023

Preprint

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The pear (Pyrus spp.) is a remarkable fruit, well known for its diverse flavors, textures, culinary versatility, and global horticultural importance. However, the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored. Here, wede novoassembled and annotated the genomes of the maternal (PsbM) and paternal (PsbF) lines of the hybrid ‘Yuluxiang’ pear and constructed the first pear pangenome of 1.15Gb by combining these two genomes with five previously published pear genomes. Using the constructed pangenome, we identified 21,224 gene PAVs and 1,158,812 SNPs in the non-reference genome that were absent in the PsbM reference genome. Compared with SNP markers, we found that PAV-based analysis provides additional insights into the pear population structure. In addition, we also revealed that some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations. Moreover, our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the genePsbMGH3.1potentially enhances sepal shedding in ‘Xuehuali’ which is vital for pear quality. This research helps further capture the genetic diversity of pear populations and provides valuable genomic resources for accelerating pear breeding.

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“…Gannanzao genome sequence with that of navel orange cv. Newhall (Gao et al 2023) (table 1). The two genomes have similar characteristics, such as genome size, GC content, and values of N50 for contigs and scaffolds (table 1).…”

Section: Genome Sequencing and Assemblymentioning

confidence: 99%

Chromosome-Level Genome Assembly of Navel orange cv. Gannanzao (Citrus sinensisOsbeck cv. Gannanzao)

Gao

Xiong

Yin

et al. 2023

Preprint

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Navel orange cv. Gannanzao is a variant of the navel orange cv. Newhall (C. sinensisOsbeck cv. Newhall) that exhibits an earlier maturation, making it commercially valuable. However, the underlying mechanism underneath its early maturation remains unknown. To address this question, we conducted genome sequencing and de novo assembly of navel orange cv. Gannanzao. The assembled genome sequence is 334.57 Mb in length with a GC content of 31.48%. It comprises 318 contigs (N50 = 3.23 Mb) and 187 scaffolds (N50 = 31.86 Mb). The BUSCO test demonstrates 94.6% completeness. The annotation revealed 23,037 gene models, 164.95 Mb of repetitive sequences, and 2,554 ncRNA. Comparative analysis identified 323 fruit ripening-related genes in navel orange cv. Gannanzao genome, while navel orange cv. Newhall genome contained 345 such genes. These genes were organized into 320 orthologous gene families, with 30.3% of them exhibiting differences in gene copy numbers between the two genomes. Additionally, we identified 15 fruit ripening-related genes that have undergone adaptive evolution, suggesting their potential role in advancing fruit maturation in navel orange cv. Gannanzao. Whole genome sequencing and annotation of navel orange cv. Gannanzao provides a valuable resource to unravel the early maturation mechanism of citrus and enriches the genomic resources for citrus research.

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Citrus genomic resources unravel putative genetic determinants of Huanglongbing pathogenicity

Cited by 14 publications

References 120 publications

The protein interactome of the citrus Huanglongbing pathogen Candidatus Liberibacter asiaticus

The protein interactome of the citrus Huanglongbing pathogen Candidatus Liberibacter asiaticus

Pan-genome of pear provides insights into the fruit quality traits differentiation between Asian and European pears

Chromosome-Level Genome Assembly of Navel orange cv. Gannanzao (Citrus sinensisOsbeck cv. Gannanzao)

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