Dataset Information

Operons are a conserved feature of nematode genomes.

ABSTRACT: The organization of genes into operons, clusters of genes that are co-transcribed to produce polycistronic pre-mRNAs, is a trait found in a wide range of eukaryotic groups, including multiple animal phyla. Operons are present in the class Chromadorea, one of the two main nematode classes, but their distribution in the other class, the Enoplea, is not known. We have surveyed the genomes of Trichinella spiralis, Trichuris muris, and Romanomermis culicivorax and identified the first putative operons in members of the Enoplea. Consistent with the mechanism of polycistronic RNA resolution in other nematodes, the mRNAs produced by genes downstream of the first gene in the T. spiralis and T. muris operons are trans-spliced to spliced leader RNAs, and we are able to detect polycistronic RNAs derived from these operons. Importantly, a putative intercistronic region from one of these potential enoplean operons confers polycistronic processing activity when expressed as part of a chimeric operon in Caenorhabditis elegans. We find that T. spiralis genes located in operons have an increased likelihood of having operonic C. elegans homologs. However, operon structure in terms of synteny and gene content is not tightly conserved between the two taxa, consistent with models of operon evolution. We have nevertheless identified putative operons conserved between Enoplea and Chromadorea. Our data suggest that operons and "spliced leader" (SL) trans-splicing predate the radiation of the nematode phylum, an inference which is supported by the phylogenetic profile of proteins known to be involved in nematode SL trans-splicing.

SUBMITTER: Pettitt J

PROVIDER: S-EPMC4125394 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Operons are a conserved feature of nematode genomes.

Pettitt Jonathan J Philippe Lucas L Sarkar Debjani D Johnston Christopher C Gothe Henrike Johanna HJ Massie Diane D Connolly Bernadette B Müller Berndt B

Genetics 20140614 4

The organization of genes into operons, clusters of genes that are co-transcribed to produce polycistronic pre-mRNAs, is a trait found in a wide range of eukaryotic groups, including multiple animal phyla. Operons are present in the class Chromadorea, one of the two main nematode classes, but their distribution in the other class, the Enoplea, is not known. We have surveyed the genomes of Trichinella spiralis, Trichuris muris, and Romanomermis culicivorax and identified the first putative operon ...[more]

PMID: 24931407

Similar Datasets

Project description:Root-knot nematodes (RKN; Meloidogyne spp.) are sedentary parasites that affect a high variety of plants with a negative impact in the production of crops such as tomato. The infective RKN induces in the roots 4-7 highly specialized feeding cells (giant cells, GCs) developed into a hypertrophy cellular tissue or visible root swelling called M-bM-^@M-^\gallM-bM-^@M-^]. During GCs differentiation drastic alterations in genes expression occurs. However, information on genome-wide transcriptional profiles specifically in GCs is still lacking. With the aim to identify potential targets specifically regulated in GCs, we performed a temporal and spatial differential transcription profiling of tomato (Solanum lycopersicum), during the course of Meloidogyne javanica infection hybridizing TOM1 microarrays with hand-dissected galls at 1, 3, 7 and 14 days post-infection (dpi) and GCs exclusively isolated by LASER CAPTURE MICRODISSECTION (LCM) at 3 and 7 dpi. A GCs and galls comparison, at the same stage of development, reveals clear differences between their transcriptional patterns. For this purpose, a fast and efficient method to isolate LCM GCs from cryopreserved galls in the earliest differentiation state described to date: 48-72-hour post-infection (3 dpi), allowing good RNA preservation, was developed. In galls transcriptomic anaylsis, about 3000 galls and 4400 control uninfected root fragments were carefully hand-dissected at 1, 3, 7 and 14 dpi. Thus, more than 12 plates with 8 individual infected plants each, and 18 plates with the same number of plants as controls were used for only one independent experiment in each time point. Total RNA from two independent experiments was equimolarly pooled at each time of infection, in order to achieve a biological replicate for galls or control regardless. Therefore, a total of 6 independent experiments were performed to obtain 3 independent biological replicates for each infection point of galls and control analyzed. Following isolation, total RNA pooled from galls and control were subjected to a single round of linear amplification. In GCs transcriptomic analysis, independent biological replicates of aRNA from 300 GCs versus 600 control cells (CCs) from control root LCM at 3 and 7 dpi were obtained. Fifty GCs and 100 CCs were independently captured from sections onto separate CapSure HS LCM caps, and total RNA isolation was performed from each cap. RNA from six separate caps was pooled for a single biological replicate of GCs or CCs, respectively. In total, three independent biological replicates were processed. Thus, near to 7000 individual cells were harvested by LCM. The material was obtained from more that 18 independent infection experiments.

Dataset Information

Operons are a conserved feature of nematode genomes.

Publications

Operons are a conserved feature of nematode genomes.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets