Hybrid origin of Populus tomentosa Carr. identified through genome sequencing and phylogenomic analysis

作者: Xinmin An , Kai Gao , Zhong Chen , Juan Li , Xiong Yang

DOI: 10.1101/2020.04.07.030692

关键词: GeneGenome evolutionDNA sequencingPopulus tomentosaGenomeEvolutionary biologyCentral chinaWhite (mutation)Populus adenopodaBiology

摘要: Abstract Populus tomentosa is widely distributed and cultivated in the Northern Central China, where it of great economic ecological importance. However, origin P. remains controversial. Here, we used a PacBio+Hi-C+Illumina strategy to sequence assemble its 740.2 Mb (2n) genome. The assembly accounts for greater than 92.1% 800-megabase genome, comprises 38 chromosomes, contains 59,124 annotated protein-coding genes. Phylogenomic analyses elucidated dynamic genome evolution events among closely related white poplars, revealed that comprised two subgenomes, which deomonstrate likely have resulted from hybridization between adenopoda as female, alba var. pyramidalis male, around 3.93 Mya. We also detected structural variations allele-indels across Our study presents high quality well assembled unveils planted tomentosa, provides powerful resource comparative plant biology, breeding, biotechnology.

参考文章(98)
Nicholas H. Putnam, Brendan L. O'Connell, Jonathan C. Stites, Brandon J. Rice, Marco Blanchette, Robert Calef, Christopher J. Troll, Andrew Fields, Paul D. Hartley, Charles W. Sugnet, David Haussler, Daniel S. Rokhsar, Richard E. Green, Chromosome-scale shotgun assembly using an in vitro method for long-range linkage Genome Research. ,vol. 26, pp. 342- 350 ,(2016) , 10.1101/GR.193474.115
Jennifer Parla, Melissa Kramer, W. Richard McCombie, High-Throughput Sequencing Microbial Forensics (Second Edition). pp. 461- 478 ,(2011) , 10.1016/B978-0-12-382006-8.00027-X
Reinhard Stettler, Toby Bradshaw, Paul Heilman, Tom Hinckley, None, Biology of Populus and its implications for management and conservation Published in <b>1996</b> in Ottawa by NRC research press. pp. 539- ,(1996)
Elaine R Mardis, Next-Generation Sequencing Platforms Springer, New York, NY. pp. 37- 44 ,(2014) , 10.1007/978-1-4939-0715-1_4
Ying Li, Hao Li, Zhong Chen, Le-Xiang Ji, Mei-Xia Ye, Jia Wang, Lina Wang, Xin-Min An, Haploid plants from anther cultures of poplar ( Populus × beijingensis ) Plant Cell Tissue and Organ Culture. ,vol. 114, pp. 39- 48 ,(2013) , 10.1007/S11240-013-0303-5
Zhaoshan Wang, Shuhui Du, Selvadurai Dayanandan, Dongsheng Wang, Yanfei Zeng, Jianguo Zhang, Phylogeny Reconstruction and Hybrid Analysis of Populus (Salicaceae) Based on Nucleotide Sequences of Multiple Single-Copy Nuclear Genes and Plastid Fragments PLoS ONE. ,vol. 9, pp. e103645- ,(2014) , 10.1371/JOURNAL.PONE.0103645
Bruce J. Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A. Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K. Young, Ashlee M. Earl, Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement PLoS ONE. ,vol. 9, pp. e112963- ,(2014) , 10.1371/JOURNAL.PONE.0112963
Chen-Shan Chin, David H Alexander, Patrick Marks, Aaron A Klammer, James Drake, Cheryl Heiner, Alicia Clum, Alex Copeland, John Huddleston, Evan E Eichler, Stephen W Turner, Jonas Korlach, Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data Nature Methods. ,vol. 10, pp. 563- 569 ,(2013) , 10.1038/NMETH.2474
Marguerite Holloway, A Global View Scientific American. ,vol. 271, pp. 76- 83 ,(1994) , 10.1038/SCIENTIFICAMERICAN0894-76