Genome Assembly and Sex-Determining Region of Male and Female Populus × sibirica

The genus Populus is presented by dioecious species, and it became a promising object to study the genetics of sex in plants. In this work, genomes of male and female Populus × sibirica individuals were sequenced for the first time. To achieve high-quality genome assemblies, we used Oxford Nanopore Technologies and Illumina platforms. A protocol for the isolation of long and pure DNA from young poplar leaves was developed, which enabled us to obtain 31 Gb (N50 = 21 kb) for the male poplar and 23 Gb (N50 = 24 kb) for the female one using the MinION sequencer. Genome assembly was performed with different tools, and Canu provided the most complete and accurate assemblies with a length of 818 Mb (N50 = 1.5 Mb) for the male poplar and 816 Mb (N50 = 0.5 Mb) for the female one. After polishing with Racon and Medaka (Nanopore reads) and then with POLCA (Illumina reads), assembly completeness was 98.45% (87.48% duplicated) for the male and 98.20% (76.77% duplicated) for the female according to BUSCO (benchmarking universal single-copy orthologs). A high proportion of duplicated BUSCO and the increased genome size (about 300 Mb above the expected) pointed at the separation of haplotypes in a large part of male and female genomes of P. × sibirica. Due to this, we were able to identify two haplotypes of the sex-determining region (SDR) in both assemblies; and one of these four SDR haplotypes, in the male genome, contained partial repeats of the ARR17 gene (Y haplotype), while the rest three did not (X haplotypes). The analysis of the male P. × sibirica SDR suggested that the Y haplotype originated from P. nigra, while the X haplotype is close to P. trichocarpa and P. balsamifera species. Moreover, we revealed a Populus-specific repeat that could be involved in translocation of the ARR17 gene or its part to the SDR of P. × sibirica and other Populus species. The obtained results expand our knowledge on SDR features in the genus Populus and poplar phylogeny.

The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers

Cattle imported from the Iberian Peninsula spread throughout America in the early years of discovery and colonization to originate Creole breeds, which adapted to a wide diversity of environments and later received influences from other origins, including zebu cattle in more recent years. We analyzed uniparental genetic markers and autosomal microsatellites in DNA samples from 114 cattle breeds distributed worldwide, including 40 Creole breeds representing the whole American continent, and samples from the Iberian Peninsula, British islands, Continental Europe, Africa and American zebu. We show that Creole breeds differ considerably from each other, and most have their own identity or group with others from neighboring regions. Results with mtDNA indicate that T1c-lineages are rare in Iberia but common in Africa and are well represented in Creoles from Brazil and Colombia, lending support to a direct African influence on Creoles. This is reinforced by the sharing of a unique Y-haplotype between cattle from Mozambique and Creoles from Argentina. Autosomal microsatellites indicate that Creoles occupy an intermediate position between African and European breeds, and some Creoles show a clear Iberian signature. Our results confirm the mixed ancestry of American Creole cattle and the role that African cattle have played in their development.

Could Rapidly Mutating Y-STRs be a Potential Forensic Tool in Discriminating Lebanese Monozygotic Twins?

Despite the high power of discrimination that characterizes the well identified 16 to 24 autosomal short tandem repeat markers, monozygotic twins differentiation is generally limited. Arising from a single fertilized egg, monozygotic twins share the same genotype therefore the same DNA profile. This situation imposes a challenge in forensics especially considering that lineage markers are in general less informative than autosomal ones. Although in some cases Y haplotype is considered a powerful investigative tool, it cannot distinguish males belonging to the same paternal lineage. The use of rapidly mutating Y-STRs with mutation rate above 1x10-2 that were recently included in forensic casework is presumed helpful. Since science is always dynamic and each population has its own characteristics, we aim in this study to distinguish between Lebanese monozygotic male twins using rapidly mutating Y-STRs. For this purpose, fourteen unrelated pairs of male monozygotic twins were recruited. Participants filled in a well-designed questionnaire and signed an informed consent. DNA was extracted using PureLink Genomic DNA Mini kit, genotyped using the Identifiler Plus kit, and separated on 3500 Genetic Analyzer to confirm the monozygosity status. DNA samples underwent a second amplification using the Y Filer Plus kit. According to our results, all the Y Filer Plus DNA profiles showed complete match for each twin pair. By consequence, the use of rapidly mutating Y-STRs in this study did not improve discrimination.

Y-Chromosome short tandem repeat (STR) haplotypes in a Campania population sample

Given the lack of information about Y haplotypes for Campania (southern Italy), we analyzed eight Y short tandem repeats in a sample of males from this region with the aim of establishing a Y-haplotype database that can be used for forensic purposes. The eight Y short tandem repeats were amplified by two PCR multiplex reactions: multiplex A for loci