Publications

4475

Abstract Background Metagenomic sequence data are proving to be a vast resource for the discovery of biological components. Yet analysis of this data to identify functional RNAs lags behind efforts to characterize protein diversity. The genome of 'Candidatus Pelagibacter ubique' HTCC 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. It is also small, contains little non-coding DNA, and has strikingly low GC content. Results To aid the discovery of RNA motifs within the marine metagenome we exploited the genomic properties of 'Cand. P. ubique' by targeting our search to long intergenic regions (IGRs) with relatively high GC content. Analysis of known RNAs (rRNA, tRNA, riboswitches etc.) shows that structured RNAs are significantly enriched in such IGRs. To identify additional candidate structured RNAs, we examined other IGRs with similar characteristics from 'Cand. P. ubique' using comparative genomics approaches in conjunction with marine metagenomic data. Employing this strategy, we discovered four candidate structured RNAs including a new riboswitch class as well as three additional likely cis-regulatory elements that precede genes encoding ribosomal proteins S2 and S12, and the cytoplasmic protein component of the signal recognition particle. We also describe four additional potential RNA motifs with few or no examples occurring outside the metagenomic data. Conclusion This work begins the process of identifying functional RNA motifs present in the metagenomic data and illustrates how existing completed genomes may be used to aid in this task.

The citrus disease Huanglongbing (HLB) is highly destructive in many citrus-growing regions of the world. The putative causal agent of this disease, ‘Candidatus Liberibacter asiaticus’, is difficult to culture, and Koch's postulates have not yet been fulfilled. As a result, efforts have focused on obtaining the genome sequence of ‘Ca. L. asiaticus’ in order to give insight on the physiology of this organism. In this work, three next-generation high-throughput sequencing platforms, 454, Solexa, and SOLiD, were used to obtain metagenomic DNA sequences from phloem tissue of Florida citrus trees infected with HLB. A culture-independent, polymerase chain reaction (PCR)-independent analysis of 16S ribosomal RNA sequences showed that the only bacterium present within the phloem metagenome was ‘Ca L. asiaticus’. No viral or viroid sequences were identified within the metagenome. By reference assembly, the phloem metagenome contained sequences that provided 26-fold coverage of the ‘Ca. L. asiaticus’ contigs in GenBank. By the same approach, phloem metagenomic data yielded less than 0.2-fold coverage of five other alphaproteobacterial genomes. Thus, phloem metagenomic DNA provided a PCR-independent means of verifying the presence of ‘Ca L. asiaticus’ in infected tissue and strongly suggests that no other disease agent was present in phloem. Analysis of these metagenomic data suggest that this approach has a detection limit of one ‘Ca. Liberibacter’ cell for every 52 phloem cells. The phloem sample sequenced here is estimated to have contained 1.7 ‘Ca. Liberibacter’ cells per phloem cell.

Huanglongbing (HLB) is a devastating disease of citrus and threatens the citrus industry worldwide. The suspected causal agent of the disease is a phloem-limited bacterium of the genus Candidatus Liberibacter transmitted through insect vector or grafting with diseased budwood. Currently, most seed source trees for citrus rootstock propagation are located outdoors and unprotected from disease transmission. In addition, fruit from HLB-affected scion varieties in Florida containing seeds enter the commercial trade and move into other citrus-growing areas. The objective of this study was to determine how Ca. L. asiaticus infection affects seed quality and seedling development and whether the disease appears in seedlings grown from infected fruit. Two experiments were conducted involving thousands of seedlings produced from seeds from infected rootstock seed source trees and ‘Valencia’ sweet orange trees, respectively. Infection of trees and fruit with Ca. L. asiaticus significantly reduced seed weight, seed germination, and seedling height. Seedlings did not develop symptoms typical of HLB throughout the experiment. Polymerase chain reaction (PCR) analysis initially identified two of 686 rootstock seedlings and three of 431 sweet orange seedlings positive for the pathogen when they were very young. Resampling and PCR analysis of these five seedlings at older ages consistently indicated they were negative for the pathogen and none of these plants ever developed symptoms of HLB. It is suggested that Ca. L. asiaticus may have been translocated into some part of the embryo during seed development but that it was not present in cells or tissue, which permitted replication or disease development as the seedling grew.