Comparative analysis of Mutator -like transposases in sugarcane.

The maize Mutator ( Mu) system has been described as the most active and mutagenic plant transposon so far discovered. Mu -like elements (MULEs) are widespread among plants, and many and diverse variants can coexist in a particular genome. The autonomous regulatory element MuDR contains two genes: mudrA encodes the transposase, while the function of the mudrB gene product remains unknown. Although mudrA -like sequences are ubiquitous in plants, mudrB seems to be restricted to the genus Zea. In the SUCEST (the Brazilian Sugarcane EST Sequencing Project) database, several mudrA -like cDNAs have been identified, suggesting the presence of a transcriptionally active Mu system in sugarcane. Phylogenetic studies have revealed the presence in plants of four classes of mudrA -like sequences, which arose prior to the monocot/eudicot split. At least three of the four classes are also found in the progenitors of the sugarcane hybrid (Saccharum spp.), Saccharum officinarum and S. spontaneum. The frequency of putatively functional transposase ORFs varies among the classes, as revealed at both cDNA and genomic levels. The predicted products of some sugarcane mudrA -like transcripts contain both a DNA-binding domain and a transposase catalytic-site motif, supporting the idea that an active Mu system exists in this hybrid genome.

Genomic distribution and characterization of EST-derived resistance gene analogs (RGAs) in sugarcane.

A large sugarcane EST (expressed sequence tag) project recently gave us access to 261,609 EST sequences from sugarcane, assembled into 81,223 clusters. Among these, we identified 88 resistance gene analogs (RGAs) based on their homology to typical pathogen resistance genes, using a stringent BLAST search with a threshold e-value of e(-50). They included representatives of the three major groups of resistance genes with NBS/LRR, LRR or S/T KINASE domains. Fifty RGAs showed a total of 148 single-dose polymorphic RFLP markers, which could be located on the sugarcane reference genetic map (constructed in cultivar R570, 2n=approximately 115). Fifty-five SSR loci corresponding to 134 markers in R570 were also mapped to enable the classification of the various haplotypes into homology groups. Several RGA clusters were found. One cluster of two LRR-like loci mapped close to the only disease resistance gene known so far in sugarcane, which confers resistance to common rust. Detailed sequence comparison between two NBS/LRR RGA clusters in relation to their orthologs in rice and maize suggests their polyphyletic origins, and indicates that the degree of divergence between paralogous RGAs in sugarcane can be larger than that from an ortholog in a distant species.

Retrolycl-1, a member of the tntl retrotransposon super-family in the Lycopersicon peruvianum genome.

Retrotransposons are ubiquitous mobile genetic elements that transpose through an RNA intermediate. One of the best known plant retrotransposon, Tnt1, was isolated from tobacco and showed an extensive distribution in the Nicotiana genus. We investigated the presence of related sequences in the Lycopersicon genus, another member of the Solanaceae family. Hybridization experiments performed using Tnt1 probes indicated that homologous sequences were present in all Lycopersicon species, indicating that these Tnt1-related sequences, that we named Retrolyc1, are distributed throughout the Lycopersicon genus. Different distribution patterns were detected between species, demonstrating a potential use of Retrolyc1 elements as molecular markers. An incomplete Retrolyc1 sequence, that we named Retrolyc1-1, was isolated from an L. peruvianum genomic library. Retrolyc1-1 shows extensive homology with Tnt1 sequences except in the LTR U3 region. Since this region is known to be involved in the control of transcription, this strongly suggests the existence of different patterns of regulation for Tnt1 and Retrolyc1 elements. The study of these two elements within the Solanaceae family may provide interesting models for retrotransposon evolution within this group and transmission in host genomes.

Retrolyc1-1, a member of the Tntl retrotransposon super-family in the Lycopersicon peruvianum genome.

Retrotransposons are ubiquitous mobile genetic elements that transpose through an RNA intermediate. One of the best known plant retrotransposon, Tnt1, was isolated from tobacco and showed an extensive distribution in the Nicotiana genus. We investigated the presence of related sequences in the Lycopersicon genus, another member of the Solanaceae family. Hybridization experiments performed using Tnt1 probes indicated that homologous sequences were present in all Lycopersicon species, indicating that these Tnt1-related sequences, that we named Retrolyc1, are distributed throughout the Lycopersicon genus. Different distribution patterns were detected between species, demonstrating a potential use of Retrolyc1 elements as molecular markers. An incomplete Retrolyc1 sequence, that we named Retrolyc1-1, was isolated from an L. peruvianum genomic library. Retrolyc1-1 shows extensive homology with Tnt1 sequences except in the LTR U3 region. Since this region is known to be involved in the control of transcription, this strongly suggests the existence of different patterns of regulation for Tnt1 and Retrolyc1 elements. The study of these two elements within the Solanaceae family may provide interesting models for retrotransposon evolution within this group and transmission in host genomes.

Retrolyc1 subfamilies defined by different U3 LTR regulatory regions in the Lycopersicon genus.

Retrolycl, a Ty1/copia-like element, was originally isolated from the Lycopersicon peruvianum genome and shown to be present also in other Lycopersicon species. It shares extensive similarities with Tntl, except in its U3 regulatory region. In order to evaluate Retrolycl diversity, we analyzed partial sequences including both coding domains and the U3 regulatory region in four different species of the Lycopersicon genus. Two Retrolycl subfamilies defined by different U3 regions were identified. RetrolyclA is most abundant in L. peruvianum and L. hirsutum, while Retrolyc1B is distributed in all four species studied here. The RetrolyclA U3 region contains tandemly repeated elements of 53 bp. Transient expression analysis suggests that Retrolyc1A is a transcriptionally active family, and that the repeated motifs found in its U3 region are important transcriptional regulatory elements.