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

Abstract

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.

Assembling Quality Genomes of Flax Fungal Pathogens from Oxford Nanopore Technologies Data

“…However, the obtained volume of raw reads depends on many factors, such as the organism species, genome size and structure, and purity and mass of the extracted DNA [ 31 , 32 , 33 ]. Using an appropriate protocol for DNA extraction is a key factor in receiving a sufficient amount of raw data to obtain a high-quality whole-genome assembly [ 34 , 35 , 36 , 37 , 38 ]. Unfortunately, the accuracy of the obtained data is limited by the technology itself.…”

Isolating Linum usitatissimum L. Nuclear DNA Enabled Assembling High-Quality Genome

“…To construct an optimal draft genome, we tested a range of assembly tools ( Table 1 ) as the software performs differently depending on the gathered data amount and quality, as well as genome length and complexity. According to our previous research, Canu—an overlap layout consensus algorithm—is the most advantageous software for a large volume of sequencing data [ 43 , 65 , 73 , 74 ]. Probably, it is the read-correction stage included in the pipeline that positively contributes to assembly contiguity.…”

Sex-determining region complements traditionally used in phylogenetic studies nuclear and chloroplast sequences in investigation of Aigeiros Duby and Tacamahaca Spach poplars (genus Populus L., Salicaceae)

“…The species of sections Aigeiros and Tacamahaca are characterized by an XY sex-determination system ( Gaudet et al., 2008 ; Pakull et al., 2009 ; Pakull et al., 2011 ; Kersten et al., 2014 ; Geraldes et al., 2015 ; Pakull et al., 2015 ; McKown et al., 2017 ), which allows the examination of poplar relationships in the male lineage. A series of studies made it possible to identify sex-associated DNA polymorphisms, determine the location and sequence of the SDR in various species of the genus Populus , and establish that sex is determined by the ARABIDOPSIS RESPONSE REGLATOR 17 ( ARR17 ) gene – when ARR17 is turned on, female flowers develop, and when it is turned off – men ones ( Gaudet et al., 2008 ; Yin et al., 2008 ; Pakull et al., 2009 ; Paolucci et al., 2010 ; Kersten et al., 2014 ; Geraldes et al., 2015 ; Pakull et al., 2015 ; McKown et al., 2017 ; Melnikova et al., 2019 ; Muller et al., 2020 ; Xue et al., 2020 ; Zhou et al., 2020 ; Kim et al., 2021 ; Melnikova et al., 2021 ; Yang et al., 2021 ). In species of sections Aigeiros and Tacamahaca , the SDR is localized on the end of chromosome 19, has a length of about 120 thousand nucleotides, and contains several genes, including T-complex protein 1 subunit gamma ( TCP ), Chloride channel protein CLC-c ( CLC ), and DNA-methyltransferase 1 ( MET1 ).…”