In Silico Survey of the Mitochondrial Protein Uptake and Maturation Systems in the Brown Alga Ectocarpus siliculosus

The acquisition of mitochondria was a key event in eukaryote evolution. The aim of this study was to identify homologues of the components of the mitochondrial protein import machinery in the brown alga Ectocarpus and to use this information to investigate the evolutionary history of this fundamental cellular process. Detailed searches were carried out both for components of the protein import system and for related peptidases. Comparative and phylogenetic analyses were used to investigate the evolution of mitochondrial proteins during eukaryote diversification. Key observations include phylogenetic evidence for very ancient origins for many protein import components (Tim21, Tim50, for example) and indications of differences between the outer membrane receptors that recognize the mitochondrial targeting signals, suggesting replacement, rearrangement and/or emergence of new components across the major eukaryotic lineages. Overall, the mitochondrial protein import components analysed in this study confirmed a high level of conservation during evolution, indicating that most are derived from very ancient, ancestral proteins. Several of the protein import components identified in Ectocarpus, such as Tim21, Tim50 and metaxin, have also been found in other stramenopiles and this study suggests an early origin during the evolution of the eukaryotes

High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies

<p>Abstract</p> <p>Background</p> <p>Massively parallel DNA sequencing instruments are enabling the decoding of whole genomes at significantly lower cost and higher throughput than classical Sanger technology. Each of these technologies have been estimated to yield assemblies with more problematic features than the standard method. These problems are of a different nature depending on the techniques used. So, an appropriate mix of technologies may help resolve most difficulties, and eventually provide assemblies of high quality without requiring any Sanger-based input.</p> <p>Results</p> <p>We compared assemblies obtained using Sanger data with those from different inputs from New Sequencing Technologies. The assemblies were systematically compared with a reference finished sequence. We found that the 454 GSFLX can efficiently produce high continuity when used at high coverage. The potential to enhance continuity by scaffolding was tested using 454 sequences from circularized genomic fragments. Finally, we explore the use of Solexa-Illumina short reads to polish the genome draft by implementing a technique to correct 454 consensus errors.</p> <p>Conclusion</p> <p>High quality drafts can be produced for small genomes without any Sanger data input. We found that 454 GSFLX and Solexa/Illumina show great complementarity in producing large contigs and supercontigs with a low error rate.</p

Improvement of the assembly of heterozygous genomes of non-model organisms, a case study of the genomes of two Spodoptera frugiperda host strains

International audienceThe extraction of biological information from the draft genomes of non-model organisms may result in unattainable, incomplete, or even wrong conclusions. In particular, the combination of a high level of heterozygosity and short reads sequencing may have major impact in the annotation of genes [1,2]. This wrong gene content assessment is usually the consequence of the high fragmentation of the genome sequence but it may also come from an overestimation of the genome size. The latter because the assembly of an heterozygous region for which there is a significant divergence between the two haplotypes leads sometimes to the construction of two different contigs, instead of one consensus sequence. To date, new assemblers such as Platanus [3], have been developed in regard to heterozygous data. But, the complete re-assembly of a genome leading to new automatic and manual annotations process is very cost-effective, and may still produce erroneous scaffolds and annotations. Thus, we set up a « soft » method to detect and correct false duplications due to heterozygosity in draft assemblies. In addition, to the identification and removal of the allelic regions (i.e. unmerged haplotypes), our protocol is able to relocate and merge supernumerary gene annotations.We applied this method as a pre-requisite for the comparison of the genomes of 2 Spodoptera frugiperda (Lepidoptera: Noctuidae) strains, in the frame of the WGS project supported by the Fall armyworm International Public Consortium (FAW-IPC). This moth is a well-known pest of crops throughout the Western hemisphere. This species consists of two strains adapted to different larval host-plants: the first feeds preferentially on corn, cotton and sorghum whereas the second is more associated with rice and several pasture grasses. While, the paired-end reads of the rice-variant have been directly assembled using Platanus [3], we cleaned up and corrected the first release of the corn-variant, leading to a drastic reduction of the genome assembly, with the removal of 88Mbp (17%) and the increase of the N50 from 39,593 to 52,781bp. The suppressed fragments included 3,746 gene predictions; about 80% of them have been either relocated or merged with their complementary allele. Subsequently, in order to identify new candidate genes or genomic regions involved in the host-plant adaptation, we compared the genomes and proteomes of the 2 different strains in order to identify orthologous genes, collinear regions and genome rearrangements, taking into consideration the inflated occurrence of splitted genes due to the high fragmentation of the genome

Annotating genomes with massive-scale RNA sequencing

A method for de novo genome annotation using high-throughput cDNA sequencing data

Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species?

International audienceThe moth Spodoptera frugiperda is a well-known pest of crops throughout the Americas, which consists of two strains adapted to different host-plants: the first feeds preferentially on corn, cotton and sorghum whereas the second is more associated with rice and several pasture grasses. Though morphologically indistinguishable, they exhibit differences in their mating behavior, pheromone compositions, and show development variability according to the host-plant. Though the latter suggest that both strains are different species, this issue is still highly controversial because hybrids naturally occur in the wild, not to mention the discrepancies among published results concerning mating success between the two strains. In order to clarify the status of the two host-plant strains of S. frugiperda, we analyze features that possibly reflect the level of post-zygotic isolation: (1) first generation (F1) hybrid lethality and sterility; (2) patterns of meiotic segregation of hybrids in reciprocal second generation (F2), as compared to the meiosis of the two parental strains. We found a significant reduction of mating success in F1 in one direction of the cross and a high level of microsatellite markers showing transmission ratio distortion in the F2 progeny. Our results support the existence of post-zygotic reproductive isolation between the two laboratory strains and are in accordance with the marked level of genetic differentiation that was recovered between individuals of the two strains collected from the field. Altogether these results provide additional evidence in favor of a sibling species status for the two strains