Online citations, reference lists, and bibliographies.
← Back to Search

Genome Assembly And Sex-Determining Region Of Male And Female Populus × Sibirica

N. Melnikova, E. Pushkova, Ekaterina M. Dvorianinova, A. Beniaminov, R. Novakovskiy, L. V. Povkhova, N. L. Bolsheva, A. Snezhkina, A. Kudryavtseva, G. Krasnov, A. Dmitriev
Published 2021 · Medicine

Save to my Library
Download PDF
Analyze on Scholarcy Visualize in Litmaps
Share
Reduce the time it takes to create your bibliography by a factor of 10 by using the world’s favourite reference manager
Time to take this seriously.
Get Citationsy
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.
This paper references
Distribution of sex forms in the phanerogamic flora
C. Yampolsky (1922)
Yampolsky (1922)
10.1089/10665270050081478
A Greedy Algorithm for Aligning DNA Sequences
Z. Zhang (2000)
10.3732/ajb.91.9.1398
Phylogeny of Populus (Salicaceae) based on nucleotide sequences of chloroplast TRNT-TRNF region and nuclear rDNA.
Mona Hamzeh (2004)
10.1007/s00122-005-0076-2
Intraspecific and interspecific genetic and phylogenetic relationships in the genus Populus based on AFLP markers
M. Cervera (2005)
10.1126/science.1128691
The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)
G. Tuskan (2006)
10.1007/s11295-007-0085-1
Genetic linkage maps of Populus nigra L. including AFLPs, SSRs, SNPs, and sex trait
M. Gaudet (2007)
Populus trees
A M Rae (2007)
“Populus trees,” in
Rae (2007)
10.1159/000126008
Plant sex chromosomes.
D. Charlesworth (2008)
10.1007/s11295-009-0204-2
Genetic linkage mapping in aspen (Populus tremula L. and Populus tremuloides Michx.)
B. Pakull (2009)
10.1007/s11295-010-0297-7
Genetic linkage maps of Populus alba L. and comparative mapping analysis of sex determination across Populus species
I. Paolucci (2010)
10.1101/gr.113985.110
Adaptive seeds tame genomic sequence comparison.
S. Kiełbasa (2011)
10.1016/j.tig.2011.05.003
Multiple developmental processes underlie sex differentiation in angiosperms.
P. Diggle (2011)
Family salicaceae
S R Mayorov (2012)
“Family salicaceae,” in
Mayorov (2012)
10.1093/bioinformatics/btt086
QUAST: quality assessment tool for genome assemblies
A. Gurevich (2013)
10.1038/nprot.2013.084
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
B. Haas (2013)
10.3732/ajb.1400196
The relative and absolute frequencies of angiosperm sexual systems: dioecy, monoecy, gynodioecy, and an updated online database.
S. Renner (2014)
10.1002/ece3.1028
Fitness dynamics within a poplar hybrid zone: II. Impact of exotic sex on native poplars in an urban jungle
Amanda D. Roe (2014)
10.1111/plb.12048
The sex-linked region in Populus tremuloides Turesson 141 corresponds to a pericentromeric region of about two million base pairs on P. trichocarpa chromosome 19.
B. Kersten (2014)
10.1093/bioinformatics/btu170
Trimmomatic: a flexible trimmer for Illumina sequence data
(2014)
10.1371/journal.pone.0103645
Phylogeny Reconstruction and Hybrid Analysis of Populus (Salicaceae) Based on Nucleotide Sequences of Multiple Single-Copy Nuclear Genes and Plastid Fragments
Z. Wang (2014)
On the systematics of Populus L. II. Importance of fruit characters for identification of cultivated and adventive species in Moscow region.
Kostina (2014)
10.1111/mec.13126
Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus).
A. Geraldes (2015)
10.1111/plb.12217
A simple PCR-based marker to determine sex in aspen.
B. Pakull (2015)
10.1016/j.gpb.2016.05.004
Oxford Nanopore MinION Sequencing and Genome Assembly
Hengyun Lu (2016)
10.1186/s12870-016-0776-6
Genetic origin and composition of a natural hybrid poplar Populus × jrtyschensis from two distantly related species
Dechun Jiang (2016)
10.1146/annurev-arplant-043015-111911
Plant Sex Chromosomes.
D. Charlesworth (2016)
10.1101/gr.215087.116
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
S. Koren (2017)
10.1038/s41598-017-01893-z
Sexual homomorphism in dioecious trees: extensive tests fail to detect sexual dimorphism in Populus
A. McKown (2017)
10.3390/genes9010006
Genome Sequencing and Assembly by Long Reads in Plants
Changsheng Li (2017)
10.1101/gr.214270.116
Fast and accurate de novo genome assembly from long uncorrected reads.
Robert Vaser (2017)
10.1101/gr.213405.116
Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm.
A. Zimin (2017)
“ Family salicaceae , ” in
M. S. Ignatov (2017)
Representatives of the sections aigeiros duby and tacamahaca spach (genus Populus L., Salicaceae) and their hybrids in cities of central and eastern European Russia.
Kostina (2017)
10.1002/aps3.1030
A guide to sequence your favorite plant genomes
F. Li (2018)
10.1186/s12859-018-2485-7
Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies
M. Roach (2018)
10.1093/bioinformatics/bty191
Minimap2: pairwise alignment for nucleotide sequences
H. Li (2017)
10.1371/journal.pone.0206998
Analyzing the phylogeny of poplars based on molecular data
Anpei Zhou (2018)
10.3389/fpls.2018.01660
Current Strategies of Polyploid Plant Genome Sequence Assembly
M. Kyriakidou (2018)
10.1016/j.tig.2018.05.008
The Third Revolution in Sequencing Technology.
E. van Dijk (2018)
10.1093/molbev/msy096
MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar (2018)
10.1016/j.biochi.2019.03.018
Sex-specific polymorphism of MET1 and ARR17 genes in Populus × sibirica.
N. Melnikova (2019)
10.1038/s42003-019-0474-7
The poplar pangenome provides insights into the evolutionary history of the genus.
Bing-Yu Zhang (2019)
10.1038/s41592-019-0669-3
Fast and accurate long-read assembly with wtdbg2
Jue Ruan (2019)
10.1093/bib/bbx147
Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data
Vasanthan Jayakumar (2017)
10.1007/978-1-4939-9173-0_14
BUSCO: Assessing Genome Assembly and Annotation Completeness.
Mathieu Seppey (2019)
10.1038/s41587-019-0072-8
Assembly of long, error-prone reads using repeat graphs
M. Kolmogorov (2019)
10.1016/j.tplants.2019.05.003
Tools and Strategies for Long-Read Sequencing and De Novo Assembly of Plant Genomes.
Hyungtaek Jung (2019)
10.1111/tpj.14744
Survival in the Tropics despite isolation, inbreeding and asexual reproduction: insights from the genome of the world's southernmost poplar (Populus ilicifolia).
Zeyuan Chen (2020)
10.1101/2020.10.09.333229
Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7
Li He (2020)
10.1093/gigascience/giaa146
Comparison of long-read methods for sequencing and assembly of a plant genome
V. Murigneux (2020)
10.1038/s41477-020-0672-9
A single gene underlies the dynamic evolution of poplar sex determination
Niels A. Müller (2020)
10.1371/journal.pcbi.1007981
The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies
A. Zimin (2020)
10.1101/2020.08.07.242461
Raven: a de novo genome assembler for long reads
Robert Vaser (2020)
10.3390/genes11080843
Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa
R. Zhou (2020)
10.1038/s41467-020-19559-2
Evidences for a role of two Y-specific genes in sex determination in Populus deltoides
Liangjiao Xue (2020)
10.1186/s13059-020-1952-4
A willow sex chromosome reveals convergent evolution of complex palindromic repeats
R. Zhou (2020)
10.1093/molbev/msaa261
A General Model to Explain Repeated Turnovers of Sex Determination in the Salicaceae
Wenlu Yang (2020)
10.3389/fgene.2020.00959
High-Quality Genome Assembly of Fusarium oxysporum f. sp. lini
G. Krasnov (2020)
10.1186/s13059-020-02162-5
A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa
Brigitte T. Hofmeister (2020)
10.3389/fgene.2020.590282
Genome Sequencing of Fiber Flax Cultivar Atlant Using Oxford Nanopore and Illumina Platforms
A. Dmitriev (2021)
10.1038/s41587-020-0503-6
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
Kishwar Shafin (2020)
10.1101/2020.03.16.992933
Comparison of long read methods for sequencing and assembly of a plant genome
V. Murigneux (2020)
Fast and accurate long - read assembly with wtdbg 2
H. Li (2020)
High-quality genome assembly of Fusarium oxysporum f
G S Krasnov (2020)
10.3389/fgene.2021.662928
Nanopore and Illumina Genome Sequencing of Fusarium oxysporum f. sp. lini Strains of Different Virulence
Ekaterina M. Dvorianinova (2021)
10.1093/nar/gkaa977
The InterPro protein families and domains database: 20 years on
Matthias Blum (2020)
10.1111/1755-0998.13362
Chromosome‐scale assembly of the genome of Salix dunnii reveals a male‐heterogametic sex determination system on chromosome 7
Li He (2021)
Representatives of the sections aigeiros duby and tacamahaca spach ( genus Populus L . , Salicaceae ) and their hybrids in cities of central and eastern European Russia
G. S. Krasnov
“ Populus trees , ” in
C. Kole



This paper is referenced by
Semantic Scholar Logo Some data provided by SemanticScholar