References
Ambardar, S., Gupta, R., Trakroo, D., Lal, R., & Vakhlu, J. (2016). High Throughput Sequencing: An Overview of Sequencing Chemistry. Indian Journal of Microbiology, 56 (4), 1-11.
An, X. M., Wang, D. M., Wang, Z. L., Li, B., Bo, W. H., Cao, G. L., & Zhang, Z. Y. (2011). Isolation of a LEAFY homolog from Populus tomentosa : expression of PtLFYin P. tomentos a floral buds and PtLFY -IR-mediated gene silencing in tobacco (Nicotiana tabacum ). Plant Cell Rep, 30 (1), 89-100. doi:10.1007/s00299-010-0947-0
An, X. M., Gao, K., Chen, Z., Li, J., Yang, X., Yang, X. Y., Zhou, J., Guo, T., Zhao, T. Y., Huang, S., Miao D. Y., Khan, W. U., Rao, P., Ye, M. X., Lei, B. Q., Liao, W. H., Wang, J., Ji, L. X., Li. Y., Guo, B., Mustafa, N. S., Li, S. W., Yun, Q. Z., Keller, S. R., Mao, J. F., Zhang R. G., & Strauss, S. H. (2020a). PacBio and Illumina sequencing ofPopulus tomentosa . The NCBI Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra), the BioProject accession number, PRJNA613008.
An, X. M., Gao, K., Chen, Z., Li, J., Yang, X., Yang, X. Y., Zhou, J., Guo, T., Zhao, T. Y., Huang, S., Miao D. Y., Khan, W. U., Rao, P., Ye, M. X., Lei, B. Q., Liao, W. H., Wang, J., Ji, L. X., Li. Y., Guo, B., Mustafa, N. S., Li, S. W., Yun, Q. Z., Keller, S. R., Mao, J. F., Zhang R. G., & Strauss, S. H. (2020b). The genome assembly and annotation ofPopulus tomentosa . DDBJ/ENA/GenBank, accession number, JAAWWB000000000.
An, X. M., Gao, K., Chen, Z., Li, J., Yang, X., Yang, X. Y., Zhou, J., Guo, T., Zhao, T. Y., Huang, S., Miao D. Y., Khan, W. U., Rao, P., Ye, M. X., Lei, B. Q., Liao, W. H., Wang, J., Ji, L. X., Li. Y., Guo, B., Mustafa, N. S., Li, S. W., Yun, Q. Z., Keller, S. R., Mao, J. F., Zhang R. G., & Strauss, S. H.(2020c). The transcriptome assemblies ofPopulus grandidentata , Populus davidiana , Populus adenopoda and Populus alba . DDBJ/EMBL/GenBank, accession number, GIKW00000000, GILB00000000, GIKX00000000 and GILC00000000.
An, X. M., Gao, K., Chen, Z., Li, J., Yang, X., Yang, X. Y., Zhou, J., Guo, T., Zhao, T. Y., Huang, S., Miao D. Y., Khan, W. U., Rao, P., Ye, M. X., Lei, B. Q., Liao, W. H., Wang, J., Ji, L. X., Li. Y., Guo, B., Mustafa, N. S., Li, S. W., Yun, Q. Z., Keller, S. R., Mao, J. F., Zhang R. G., & Strauss, S. H. (2021). The chloroplast genome assemblies ofPopulus alba × Populus glandulosa , Populus glandulosa , Populus tremuloides and Populus tomentosa . GneBank, accession numbers, MW537051, MW537052, MW537053 and MK251149.
Apuli, R. P., Bernhardsson, C., Schiffthaler, B., Robinson, K. M., Jansson, S., Street, N. R., & Ingvarsson, P. K. (2020). Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen (Populus tremula ).G3 (Bethesda), 10 (1), 299-309. doi:10.1534/g3.119.400504
Bai, F. Y. (2015). Evaluation of elite tree resourse and construction of parent population for breeding programme in Populus tomentosa carr. (Master), Beijing Forestry University, Beijing.
Boucher, L. D., Manchester, S. R., & Judd, W. S. (2003). An extinct genus of Salicaceae based on twigs with attached flowers, fruits, and foliage from the Eocene Green River Formation of Utah and Colorado, USA. Am J Bot, 90 (9), 1389-1399. doi:10.3732/ajb.90.9.1389
Cantarel, B. L., Korf, I., Robb, S. M. C., Parra, G., Ross, E., Moore, B., . . . Yandell, M. (2008). MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Research, 18 (1), 188-196. doi:10.1101/gr.6743907
Cook, D. E., Lee, T. G., Guo, X., Melito, S., Wang, K., Bayless, A. M., . . . Bent, A. F. (2012). Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science, 338 (6111), 1206-1209. doi:10.1126/science.1228746
Dai, X. G., Hu, Q. J., Cai, Q. L., Feng, K., Ye, N., Tuskan, G. A., . . . Yin, T. M. (2014). The willow genome and divergent evolution from poplar after the common genome duplication. Cell Research, 24 (10), 1274-1277. doi:10.1038/cr.2014.83
Dickmann, D. I., & Isebrands, J. G. (2001). Poplar Culture in North America : NRC Research Press.
Dudchenko, O., Batra, S. S., Omer, A. D., Nyquist, S. K., Hoeger, M., Durand, N. C., . . . Aiden, E. L. (2017). De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 356 (6333), 92-95. doi:10.1126/science.aal3327
Durand, N. C., Shamim, M. S., Machol, I., Rao, S. S., Huntley, M. H., Lander, E. S., & Aiden, E. L. (2016). Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Systems, 3 (1), 95-98. doi:10.1016/j.cels.2016.07.002
Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32 (5), 1792-1797. doi:10.1093/nar/gkh340
El-Metwally, S., Ouda, O. M., & Helmy, M. (2014). Next-Generation Sequencing Platforms. Annual Review of Analytical Chemistry, 6 (4), 287.
Ellegren, H. (2014). Genome sequencing and population genomics in non-model organisms. Trends Ecol Evol, 29 (1), 51-63. doi:10.1016/j.tree.2013.09.008
Gabur, I., Chawla, H. S., Snowdon, R. J., & Parkin, I. A. P. (2019). Connecting genome structural variation with complex traits in crop plants. Theor Appl Genet, 132 (3), 733-750. doi:10.1007/s00122-018-3233-0
Gao, K., Li, J., Khan, W. U., Zhao, T., Yang, X., Yang, X., . . . An, X. (2019). Comparative genomic and phylogenetic analyses of Populus section Leuce using complete chloroplast genome sequences. Tree Genetics & Genomes, 15 (3). doi:10.1007/s11295-019-1342-9
Jiao, Y., Wickett, N. J., Ayyampalayam, S., Chanderbali, A. S., Landherr, L., Ralph, P. E., . . . dePamphilis, C. W. (2011). Ancestral polyploidy in seed plants and angiosperms. Nature, 473 (7345), 97-100. doi:10.1038/nature09916
Kalvari, I., Argasinska, J., Quinones-Olvera, N., Nawrocki, E. P., Rivas, E., Eddy, S. R., . . . Petrov, A. I. (2018). Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Research, 46 (D1), D335-D342. doi:10.1093/nar/gkx1038
Kent, W. J. (2002). BLAT–the BLAST-like alignment tool. Genome Research, 12 (4), 656-664.
Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017). Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research, 27 (5), 722-736. doi:10.1101/gr.215087.116
Li, L., Stoeckert, C. J., Jr., & Roos, D. S. (2003). OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Research, 13 (9), 2178-2189. doi:10.1101/gr.1224503
Li, Y., Li, H., Chen, Z., Ji, L. X., Ye, M. X., Wang, J., . . . An, X. M. (2013). Haploid plants from anther cultures of poplar (Populus x beijingensis ). Plant Cell Tissue and Organ Culture, 114 (1), 39-48. doi:10.1007/s11240-013-0303-5
Lin, Y. C., Wang, J., Delhomme, N., Schiffthaler, B., Sundstrom, G., Zuccolo, A., . . . Street, N. R. (2018). Functional and evolutionary genomic inferences in Populusthrough genome and population sequencing of American and European aspen.Proc Natl Acad Sci U S A, 115 (46), E10970-E10978. doi:10.1073/pnas.1801437115
Lisch, D. (2013). How important are transposons for plant evolution? Nat Rev Genet, 14 (1), 49-61. doi:10.1038/nrg3374
Liu, B., Shi, Y., Yuan, J., Hu, X., Zhang, H., Li, N., . . . Fan, W. (2013). Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects.arXiv .
Liu, Y. J., Wang, X. R., & Zeng, Q. Y. (2019). De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China. Sci China Life Sci, 62 (5), 609-618. doi:10.1007/s11427-018-9455-2
Ma, J., Wan, D., Duan, B., Bai, X., Bai, Q., Chen, N., & Ma, T. (2019). Genome sequence and genetic transformation of a widely distributed and cultivated poplar.Plant Biotechnology Journal, 17 (2), 451-460. doi:10.1111/pbi.12989
Ma, K., Song, Y., Huang, Z., Lin, L., Zhang, Z., & Zhang, D. (2013). The low fertility of Chinese white poplar: dynamic changes in anatomical structure, endogenous hormone concentrations, and key gene expression in the reproduction of a naturally occurring hybrid. Plant Cell Rep, 32 (3), 401-414. doi:10.1007/s00299-012-1373-2
Ma, T., Wang, J. Y., Zhou, G. K., Yue, Z., Hu, Q. J., Chen, Y., . . . Liu, J. Q. (2013). Genomic insights into salt adaptation in a desert poplar. Nature Communications, 4 . doi:10.1038/Ncomms3797
Ma, W., Ay, F., Lee, C., Gulsoy, G., Deng, X., Cook, S., . . . Duan, Z. (2018). Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution. Methods, 142 , 59-73. doi:10.1016/j.ymeth.2018.01.014
Manchester, S. R., Dilcher, D. L., & Tidwell, W. D. (1986). Interconnected Reproductive and Vegetative Remains of Populus (Salicaceae) from the Middle Eocene Green River Formation, Northeastern Utah. Am J Bot, 73 (1), 156-160. doi:10.1002/j.1537-2197.1986.tb09691.x
McHale, L. K., Haun, W. J., Xu, W. W., Bhaskar, P. B., Anderson, J. E., Hyten, D. L., . . . Stupar, R. M. (2012). Structural variants in the soybean genome localize to clusters of biotic stress-response genes. Plant Physiol, 159 (4), 1295-1308. doi:10.1104/pp.112.194605
Morgante, M., De Paoli, E., & Radovic, S. (2007). Transposable elements and the plant pan-genomes.Curr Opin Plant Biol, 10 (2), 149-155. doi:10.1016/j.pbi.2007.02.001
Myburg, A. A., Grattapaglia, D., Tuskan, G. A., Hellsten, U., Hayes, R. D., Grimwood, J., . . . Schmutz, J. (2014). The genome of Eucalyptus grandis . Nature, 510 (7505), 356-+. doi:10.1038/nature13308
Otto, S. P. (2007). The evolutionary consequences of polyploidy. Cell, 131 (3), 452-462. doi:10.1016/j.cell.2007.10.022
Pinosio, S., Giacomello, S., Faivre-Rampant, P., Taylor, G., Jorge, V., Le Paslier, M. C., . . . Morgante, M. (2016). Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation. Mol Biol Evol, 33 (10), 2706-2719. doi:10.1093/molbev/msw161
Qiu, D., Bai, S., Ma, J., Zhang, L., Shao, F., Zhang, K., . . . Sun, G. (2019). The genome of Populus alba x Populus tremula var. glandulosa clone 84K.DNA Res, 26 (5), 423-431. doi:10.1093/dnares/dsz020
Sanderson, M. J. (2003). r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics, 19 (2), 301-302. doi:DOI 10.1093/bioinformatics/19.2.301
Sherman, R. M., & Salzberg, S. L. (2020). Pan-genomics in the human genome era. Nat Rev Genet . doi:10.1038/s41576-020-0210-7
Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31 (19), 3210-3212. doi:10.1093/bioinformatics/btv351
Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30 (9), 1312-1313. doi:10.1093/bioinformatics/btu033
Sun, H., Wu, S., Zhang, G., Jiao, C., Guo, S., Ren, Y., . . . Xu, Y. (2017). Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes.Molecular Plant, 10 (10), 1293-1306. doi:10.1016/j.molp.2017.09.003
Suyama, M., Torrents, D., & Bork, P. (2006). PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Research, 34 , W609-W612. doi:10.1093/nar/gkl315
Tuskan, G. A., Difazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., . . . Rokhsar, D. (2006). The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, 313 (5793), 1596-1604. doi:10.1126/science.1128691
van Berkum, N. L., Lieberman-Aiden, E., Williams, L., Imakaev, M., Gnirke, A., Mirny, L. A., . . . Lander, E. S. (2010). Hi-C: a method to study the three-dimensional architecture of genomes. J Vis Exp (39). doi:10.3791/1869
Van de Peer, Y., Mizrachi, E., & Marchal, K. (2017). The evolutionary significance of polyploidy.Nat Rev Genet, 18 (7), 411-424. doi:10.1038/nrg.2017.26
Wang, D., Wang, Z., Kang, X., & Zhang, J. (2019). Genetic analysis of admixture and hybrid patterns ofPopulus hopeiensis and P. tomentosa . Sci Rep, 9 (1), 4821. doi:10.1038/s41598-019-41320-z
Wang, Y., Tang, H., Debarry, J. D., Tan, X., Li, J., Wang, X., . . . Paterson, A. H. (2012). MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res, 40 (7), e49. doi:10.1093/nar/gkr1293
Wang, Z., Du, S., Dayanandan, S., Wang, D., Zeng, Y., & Zhang, J. (2014). Phylogeny Reconstruction and Hybrid Analysis of Populus (Salicaceae) Based on Nucleotide Sequences of Multiple Single-Copy Nuclear Genes and Plastid Fragments.Plos One, 9 (8), e103645.
Yang, W., Wang, K., Zhang, J., Ma, J., Liu, J., & Ma, T. (2017). The draft genome sequence of a desert tree Populus pruinosa . Gigascience, 6 (9), 1-7. doi:10.1093/gigascience/gix075
Zhang, H., Bian, Y., Gou, X., Dong, Y., Rustgi, S., Zhang, B., . . . Han, F. (2013). Intrinsic karyotype stability and gene copy number variations may have laid the foundation for tetraploid wheat formation. Proc Natl Acad Sci U S A, 110 (48), 19466-19471.
Zhang, L., Hu, J., Han, X., Li, J., Gao, Y., Richards, C. M., . . . Cong, P. (2019). A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. Nature Communications, 10 (1), 1494. doi:10.1038/s41467-019-09518-x
Zhang, Z., Li, J., Zhao, X. Q., Wang, J., Ka-Shu, W. G., & Yu, J. (2006). KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging.Genomics,Proteomics & Bioinformatics, 4 (4), 259-263.
Zhou, Z., Jiang, Y., Wang, Z., Gou, Z., Lyu, J., Li, W., . . . Tian, Z. (2015). Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol, 33 (4), 408-414. doi:10.1038/nbt.3096
Zhu, Z. (1992). Collection, conservation and utilization of plus tree resource of Populus tomentosa in China. Journal of Beijing Forestry University, 14 (S3), 1-25.