1. Identifying homozygous-by-descent (HBD) regions in individual genomes is highly valuable to infer the recent history of populations and to provide insights into trait architecture. 2. Here, we present the RZooRoH R-package that implements an efficient and accurate model-based approach to identify HBD segments. The underlying hidden Markov model partitions the genome-wide individual autozygosity into different age-related HBD classes while accounting for genotyping errors and genetic map information. 3. The RZooRoH package is user-friendly and versatile, accepting either genotyping or sequencing (including low-coverage) data in various formats. Through numerical maximization and parallelization, computational performances were improved compared to our initial Fortran implementation of the model. The package allows to evaluate and compare various models defined by their number of HBD classes and it also provides several graphical functions that help interpretation of the results. 4. RZooRoH is an efficient tool that proves particularly suited for sub-optimal datasets (e.g. low marker density, individual low-coverage sequencing, uneven marker spacing) and for individuals from populations with complex demographic histories.

Background Inbreeding coefficients can be estimated either from pedigree data or from genomic data, and with genomic data, they are either global or local (when the linkage map is used). Recently, we developed a new hidden Markov model (HMM) that estimates probabilities of homozygosity-by-descent (HBD) at each marker position and automatically partitions autozygosity in multiple age-related classes (based on the length of HBD segments). Our objectives were to: (1) characterize inbreeding with our model in an intensively selected population such as the Belgian Blue Beef (BBB) cattle breed; (2) compare the properties of the model at different marker densities; and (3) compare our model with other methods. ResultsWhen using 600 K single nucleotide polymorphisms (SNPs), the inbreeding coefficient (probability of sampling an HBD locus in an individual) was on average 0.303 (ranging from 0.258 to 0.375). HBD-classes associated to historical ancestors (with small segments ≤ 200 kb) accounted for 21.6% of the genome length (71.4% of the total length of the genome in HBD segments), whereas classes associated to more recent ancestors accounted for only 22.6% of the total length of the genome in HBD segments. However, these recent classes presented more individual variation than more ancient classes. Although inbreeding coefficients obtained with low SNP densities (7 and 32 K) were much lower (0.060 and 0.093), they were highly correlated with those obtained at higher density (r = 0.934 and 0.975, respectively), indicating that they captured most of the individual variation. At higher SNP density, smaller HBD segments are identified and, thus, more past generations can be explored. We observed very high correlations between our estimates and those based on homozygosity (r = 0.95) or on runs-of-homozygosity (r = 0.95). As expected, pedigree-based estimates were mainly correlated with recent HBD-classes (r = 0.56).ConclusionsAlthough we observed high levels of autozygosity associated with small HBD segments in BBB cattle, recent inbreeding accounted for most of the individual variation. Recent autozygosity can be captured efficiently with low-density SNP arrays and relatively simple models (e.g., two HBD classes). The HMM framework provides local HBD probabilities that are still useful at lower SNP densities.Electronic supplementary materialThe online version of this article (10.1186/s12711-017-0370-x) contains supplementary material, which is available to authorized users.

After extinction in the wild in the beginning of the 20th century, the European bison has been successfully recovered in 2 distinct genetic lines from only 12 and 7 captive founders. We here aimed at characterizing the levels of realized inbreeding in these 2 restored lines to provide empirical insights into the genomic footprints left by population recovery from a small number of founders. To that end, we genotyped 183 European bison born over the last 40 years with the Illumina BovineHD beadchip that contained 22 602 informative autosomal single-nucleotide polymorphisms after data filtering. We then identified homozygous-by-descent (HBD) segments and classified them into different age-related classes relying on a model-based approach. As expected, we observed that the strong and recent founder effect experienced by the 2 lines resulted in very high levels of recent inbreeding and in the presence of long HBD tracks (up to 120 Mb). These long HBD tracks were associated with ancestors living approximately from 4 to 32 generations in the past, suggesting that inbreeding accumulated over multiple generations after the bottleneck. The contribution to inbreeding of the most recent groups of ancestors was however found to be decreasing in both lines. In addition, comparison of Lowland individuals born at different time periods showed that the levels of inbreeding tended to stabilize, HBD segments being shorter in animals born more recently which indicates efficient control of inbreeding. Monitoring HBD segment lengths over generations may thus be viewed as a valuable genomic diagnostic tool for populations in conservation or recovery programs.

Cyanobacteria form one of the most diversified phyla of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are notably difficult to purify and grow axenically, and most strains in culture collections contain heterotrophic bacteria that were probably associated with Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task. Here, we describe a metagenomic pipeline that enables the easy recovery of genomes from non-axenic cultures. We tested this pipeline on 17 cyanobacterial cultures from the BCCM/ULC public collection and generated novel genome sequences for 12 polar or subpolar strains and three temperate ones, including three early-branching organisms that will be useful for phylogenomics. In parallel, we assembled 31 co-cultivated bacteria (12 nearly complete) from the same cultures and showed that they mostly belong to Bacteroidetes and Proteobacteria, some of them being very closely related in spite of geographically distant sampling sites.

Cyanobacteria form one of the most diversified phylum of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are notably difficult to purify and grow axenically, 1 and most strains in culture collections contain heterotrophic bacteria that were likely associated to Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task.Here, we deploy a metagenomic pipeline that enables the easy recovery of highquality genomes from non-axenic cultures. We tested this pipeline on 17 cyanobacterial cultures from the BCCM/ULC public collection and generated novel genome sequences for 15 arctic or subarctic strains, of which 14 early-branching organisms that will be useful for cyanobacterial phylogenomics. In parallel, we managed to assemble 31 co-cultivated bacteria from the same cultures and showed that they mostly belong to Bacteroidetes and Proteobacteria, some of them being very closely related in spite of geographically distant sampling sites. ImportanceComplete genomes of cold-adapted Cyanobacteria are underrepresented in databases, due to the difficulty to grow them axenically. In this work, we report the genome sequencing of 12 (sub)arctic and 3 temperate Cyanobacteria, along with 21 Proteobacteria and 5 Bacteroidetes recovered from their microbiome. Following the use of a state-of-the-art metagenomic pipeline, 12 of our new cyanobacterial genome assemblies are of high-quality, which indicates that even non-axenic cultures can yield complete genomes suitable for phylogenomics and comparative genomics. From a methodological point of view, we investigate the fate of SSU rRNA (16S) genes during metagenomic binning and observe that multi-copy rRNA operons are lost because of higher sequencing coverage and divergent tetranucleotide frequencies. Moreover, we devised a measure of genomic identity to compare metagenomic bins of different completeness, which allowed us to show that 2 Cyanobacteria-associated bacteria can be highly related in spite of considerable distance between collection points.