Search

BackgroundSpiroplasma citri comprises a bacterial complex that cause diseases in citrus, horseradish, carrot, sesame, and also infects a wide array of ornamental and weed species. S. citri is transmitted in a persistent propagative manner by the beet leafhopper, Neoaliturus tenellus in North America and Circulifer haematoceps in the Mediterranean region. Leafhopper transmission and the pathogen's wide host range serve as drivers of genetic diversity. This diversity was examined in silico by comparing the genome sequences of seven S. citri strains from the United States (BR12, CC-2, C5, C189, LB 319, BLH-13, and BLH-MB) collected from different hosts and times with other publicly available spiroplasmas.ResultsPhylogenetic analysis using 16S rRNA sequences from 39 spiroplasmas obtained from NCBI database showed that S. citri strains, along with S. kunkelii and S. phoeniceum, two other plant pathogenic spiroplasmas, formed a monophyletic group. To refine genetic relationships among S. citri strains, phylogenetic analyses with 863 core orthologous sequences were performed. Strains that clustered together were: CC-2 and C5; C189 and R8-A2; BR12, BLH-MB, BLH-13 and LB 319. Strain GII3-3X remained in a separate branch. Sequence rearrangements were observed among S. citri strains, predominantly in the center of the chromosome. One to nine plasmids were identified in the seven S. citri strains analyzed in this study. Plasmids were most abundant in strains isolated from the beet leafhopper, followed by strains from carrot, Chinese cabbage, horseradish, and citrus, respectively. All these S. citri strains contained one plasmid with high similarity to plasmid pSci6 from S. citri strain GII3-3X which is known to confer insect transmissibility. Additionally, 17 to 25 prophage-like elements were identified in these genomes, which may promote rearrangements and contribute to repetitive regions.ConclusionsThe genome of seven S. citri strains were found to contain a single circulariz

Citrus, one of the most economically important fruit crops in the world, is commercially propagated through grafting. Varying scion-rootstock combinations cause substantial effects on trees that often influence yield and fruit quality traits. Presently, the explanation for these differences has not been extensively studied at the molecular level. One potential reason for rootstock effects on fruit quality is the presence of small RNAs, molecules known to affect gene expression and plant development.It was hypothesized that grafting diverse rootstocks influences small RNA populations in citrus, which can greatly impact fruit quality. By using mRNA-seq and small RNA-seq, an integrative analysis of microRNA and mRNA expression profiles was performed on grafted citrus. In this study, fruit and root samples were collected from sweet orange scions grafted onto four genetically differing rootstocks (trifoliate orange, Carrizo citrange, rough lemon, and sweet orange). Differentially expressed microRNA (DEM) and mRNA profiles were identified according to fold change analysis and the relationships between these molecules were identified.A total of 1,633 unique genes in the fruit tissues and 11,368 in the root tissues were identified as differentially expressed between genotypes in at least one collection date during fruit development. The majority of the differences came from the comparisons between trifoliate and rough lemon rootstocks. GO and KEGG functional annotation analyses revealed that genes differentially expressed between trifoliate and rough lemon rootstocks were related to defense response, cell wall organization and biosynthesis, and carbohydrate metabolism. DEGs in fruit tissues grown on these rootstocks were related to transcription regulation and plant hormone signal transduction.The small RNA sequencing data identified 603 known, conserved miRNAs. Of these, 188 were differentially expressed between trifoliate and rough lemon rootstocks. Reads that were not ho

Citrus, one of the most economically important fruit crops in the world, is commercially propagated through grafting. Varying scion-rootstock combinations cause substantial effects on trees that often influence yield and fruit quality traits. Presently, the explanation for these differences has not been extensively studied at the molecular level. One potential reason for rootstock effects on fruit quality is the presence of small RNAs, molecules known to affect gene expression and plant development.It was hypothesized that grafting diverse rootstocks influences small RNA populations in citrus, which can greatly impact fruit quality. By using mRNA-seq and small RNA-seq, an integrative analysis of microRNA and mRNA expression profiles was performed on grafted citrus. In this study, fruit and root samples were collected from sweet orange scions grafted onto four genetically differing rootstocks (trifoliate orange, Carrizo citrange, rough lemon, and sweet orange). Differentially expressed microRNA (DEM) and mRNA profiles were identified according to fold change analysis and the relationships between these molecules were identified.A total of 1,633 unique genes in the fruit tissues and 11,368 in the root tissues were identified as differentially expressed between genotypes in at least one collection date during fruit development. The majority of the differences came from the comparisons between trifoliate and rough lemon rootstocks. GO and KEGG functional annotation analyses revealed that genes differentially expressed between trifoliate and rough lemon rootstocks were related to defense response, cell wall organization and biosynthesis, and carbohydrate metabolism. DEGs in fruit tissues grown on these rootstocks were related to transcription regulation and plant hormone signal transduction.The small RNA sequencing data identified 603 known, conserved miRNAs. Of these, 188 were differentially expressed between trifoliate and rough lemon rootstocks. Reads that were not ho