1,721,033 research outputs found
Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies
Full text linkShotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms and viruses in a single experiment, with the possibility of reconstructing de novo the whole metagenome or a set of genes of interest. One of the main factors limiting the use of shotgun metagenomics on wide scale projects is the high cost associated with the approach. We set out to determine if it is possible to use shallow shotgun metagenomics to characterize complex biological matrices while reducing costs. We used a staggered mock community to estimate the optimal threshold for species detection. We measured the variation of several summary statistics simulating a decrease in sequencing depth by randomly subsampling a number of reads. The main statistics that were compared are diversity estimates, species abundance, and ability of reconstructing de novo the metagenome in terms of length and completeness. Our results show that diversity indices of complex prokaryotic, eukaryotic and viral communities can be accurately estimated with 500,000 reads or less, although particularly complex samples may require 1,000,000 reads. On the contrary, any task involving the reconstruction of the metagenome performed poorly, even with the largest simulated subsample (1,000,000 reads). The length of the reconstructed assembly was smaller than the length obtained with the full dataset, and the proportion of conserved genes that were identified in the meta-genome was drastically reduced compared to the full sample. Shallow shotgun metagenomics can be a useful tool to describe the structure of complex matrices, but it is not adequate to reconstruct-even partially-the metagenome
Application of genomics to grapevine improvement
No full textImagine a breeder browsing a grape chromosome nucleotide-by-nucleotide around a trait locus, scrolling
down the list of catalogued genes along a genetic interval, resequencing for a few thousand dollars a
potential parent or a selected breeding line. In the past couple of years, this vision has become a reality.
The availability of the reference genome sequence has provided significant assistance in the saturation of
loci with targeted genetic markers. Grape breeders are now offered unprecedented possibilities for
selecting plants using deoxyribonucleic acid (DNA) sequences within or near the gene that controls a
desirable trait rather than handling their phenotypes. Genomics-assisted selection offers unique advantages
in the correct choice of elite genotypes, in order to improve traits for which limitations of
phenotyping technologies or low hereditability adversely affect the efficiency of phenotypic selection.
DNA technologies enable the application of marker-assisted selection to thousands of grape seedlings
every year, which was previously feasible only for cereals and annuals, enhancing the possibilities of
finding an ideal recombinant in populations bred from highly heterozygous parents. The expected
outcome is a renewal of the varietal choices available to viticulturists, with novel genotypes that meet the
demand for disease-free vines and flavourful grapes. The depth of exploration and characterisation of the
existing germplasm is crucial for translating natural diversity into new varieties that could perform
beyond the fence of the experimental vineyards and gain substantial market share. We review here how
current achievements in genomics and genome sequencing are expected to increase the efficiency of
grapevine breeding programs
Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies [version 4; peer review: 2 approved with reservations, 2 not approved]
No full textShotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms and viruses in a single experiment, with the possibility of reconstructing de novo the whole metagenome or a set of genes of interest. One of the main factors limiting the use of shotgun metagenomics on wide scale projects is the high cost associated with the approach. We set out to determine if it is possible to use shallow shotgun metagenomics to characterize complex biological matrices while reducing costs. We used a staggered mock community to estimate the optimal threshold for species detection. We measured the variation of several summary statistics simulating a decrease in sequencing depth by randomly subsampling a number of reads. The main statistics that were compared are diversity estimates, species abundance, and ability of reconstructing de novo the metagenome in terms of length and completeness. Our results show that diversity indices of complex prokaryotic, eukaryotic and viral communities can be accurately estimated with 500,000 reads or less, although particularly complex samples may require 1,000,000 reads. On the contrary, any task involving the reconstruction of the metagenome performed poorly, even with the largest simulated subsample (1,000,000 reads). The length of the reconstructed assembly was smaller than the length obtained with the full dataset, and the proportion of conserved genes that were identified in the meta-genome was drastically reduced compared to the full sample. Shallow shotgun metagenomics can be a useful tool to describe the structure of complex matrices, but it is not adequate to reconstruct—even partially—the metagenome
Do you cov me? Effect of coverage reduction on species identification and genome reconstruction in complex biological matrices by metagenome shotgun high-throughput sequencing
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Towards the construction of OLEAREP: a database of repeated sequences of Olea europaea L.
No full textGoing Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Characterization of HaCRE1, a complete Copia retrotransposon of sunflower (Helianthus annuus L.).
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