Genome Assembly of Salicaceae<i>Populus deltoides</i>(Eastern Cottonwood)<i>I-69</i>Based on Nanopore Sequencing and Hi-C Technologies

Bai, Shengjun; Wu, Hualong; Zhang, Jinpeng; Pan, Zhiliang; Zhao, Wei; Li, Zhiting

doi:10.1093/jhered/esab010

Cited by 20 publications

(9 citation statements)

References 62 publications

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“…In order to investigate the advantage of the integrated linkage map over the two parental linkage maps, we first compared their consensuses with the genomic sequences of P. simonii [ 25 ] and P. deltoides [ 31 ]. We found that a total of 68 local regions on the integrated linkage map were discordant with the P. simonii genomic sequence, which contained ~15% (173) of all the RAD tags ( File S1 ; Table 2 ).…”

Section: Resultsmentioning

confidence: 99%

“…Compared with the two parent-specific linkage maps, the integrated linkage map was more consensus with the genomic sequences of P. simonii [ 25 ] and P. deltoides [ 31 ]. Although the available genomic sequences have some shortcomings due to the complexity of genomic assembling, such consensus reflects a certain degree of authenticity in the order of contigs because the genomic assemblies and genetic maps were obtained using independent technologies.…”

Section: Discussionmentioning

confidence: 99%

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A Novel Strategy for Constructing an Integrated Linkage Map in an F1 Hybrid Population of Populus deltoides and Populus simonii

Zhang

Pan

et al. 2022

Genes

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The genetic linkage maps of the traditional F2 population in inbred lines were estimated from the frequency of recombination events in both parents, providing full genetic information for genetic and genomic studies. However, in outbred forest trees, it is almost impossible to generate the F2 population because of their high heterozygosity and long generation times. We proposed a novel strategy to construct an integrated genetic linkage map that contained both parental recombination information, with restriction-site-associated DNA sequencing (RADSeq) data in an F1 hybrid population of Populus deltoides and Populus simonii. We selected a large number of specific RAD tags to construct the linkage map, each of which contained two SNPs, one heterozygous only in the female parent and the other heterozygous only in the male. Consequently, the integrated map contained a total of 1154 RAD tags and 19 linkage groups, with a total length of 5255.49 cM and an average genetic distance of 4.63 cM. Meanwhile, the two parent-specific linkage maps were also constructed with SNPs that were heterozygous in one parent and homozygous in the other. We found that the integrated linkage map was more consensus with the genomic sequences of P. simonii and P. deltoides. Additionally, the likelihood of the marker order in each linkage group of the integrated map was greater than that in both parental maps. The integrated linkage map was more accurate than the parent-specific linkage maps constructed in the same F1 hybrid population, providing a powerful genetic resource for identifying the quantitative trait loci (QTLs) with dominant effects, assembling genomic sequences, and performing comparative genomics in related Populus species. More importantly, this novel strategy can be used in other outbred species to build an integrated linkage map.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

A Novel Strategy for Constructing an Integrated Linkage Map in an F1 Hybrid Population of Populus deltoides and Populus simonii

Zhang

Pan

et al. 2022

Genes

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“…After the release of this landmark genomic resource, other high-quality reference sequences have been recently assembled for eastern cottonwood clone W94 ( (accessed on 22 March 2022)), and for cultivar I-69, which shows 97.4% of anchored sequences and only 0.08% of gaps ( Table 4 ) [ 59 ]. Additional reference sequences have been assembled and annotated for P. pruinose [ 54 ], desert poplar ( P. euphratica ) [ 55 , 56 ], the two aspen species P. tremula and P. tremuloides [ 4 ], white poplar [ 3 , 57 ], P. simonii [ 58 ], and the hybrid P. alba × P. tremula var.…”

Section: Genome Sequences Are Pivotal To Improve Poplar Breeding For ...mentioning

confidence: 99%

“…Overall, more than 45,000 protein-coding genes were annotated on poplar genomes and their functional characterization represents a powerful tool to help dissecting the genetic bases of biotic stress resistance and accelerating poplar breeding [ 4 , 59 ]. For instance, the gene ontology (GO) classification carried out on European aspen and quacking aspen genome sequences allowed the identification of genes putatively involved in disease resistance [ 4 ].…”

Section: Genome Sequences Are Pivotal To Improve Poplar Breeding For ...mentioning

confidence: 99%

Advanced Breeding for Biotic Stress Resistance in Poplar

Biselli

Vietto²,

Rosso³

et al. 2022

Plants

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Poplar is one of the most important forest trees because of its high economic value. Thanks to the fast-growing rate, easy vegetative propagation and transformation, and availability of genomic resources, poplar has been considered the model species for forest genetics, genomics, and breeding. Being a field-growing tree, poplar is exposed to environmental threats, including biotic stresses that are becoming more intense and diffused because of global warming. Current poplar farming is mainly based on monocultures of a few elite clones and the expensive and long-term conventional breeding programmes of perennial tree species cannot face current climate-change challenges. Consequently, new tools and methods are necessary to reduce the limits of traditional breeding related to the long generation time and to discover new sources of resistance. Recent advances in genomics, marker-assisted selection, genomic prediction, and genome editing offer powerful tools to efficiently exploit the Populus genetic diversity and allow enabling molecular breeding to support accurate early selection, increasing the efficiency, and reducing the time and costs of poplar breeding, that, in turn, will improve our capacity to face or prevent the emergence of new diseases or pests.

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“…Several high-quality poplar genomes have become available, including P. trichocarpa (Torr. and Gray) 3 , P. euphratica Oliv 5 , P. alba 6 and P. deltoides 7 , which belong to section Tacamahaca, Turanga, Populus and Aigeiros, respectively. These four species and P. wilsonii grow in different environments and occur across diverse habitats.…”

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confidence: 99%

Chromosome-scale genome assembly provides insights into the molecular mechanisms of tissue development of Populus wilsonii

Xing

et al. 2022

Commun Biol

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Populus wilsonii is an important species of section Leucoides, and the natural populations mainly grow in southwest China. In this study, a single genotype of wild P. wilsonii was sequenced and assembled at genome size of 477.35 Mb in 19 chromosomes with contig N50 of 16.3 Mb. A total of 38,054 genes were annotated, and 49.95% of the genome was annotated as repetitive elements. Phylogenetic analysis identified that the divergence between P. wilsonii and the ancestor of P. deltoides and P. trichocarpa was 12 (3–23) Mya. 4DTv and Ks distributions supported the occurrence of the salicoid WGD event (~65 Mya). The highly conserved collinearity supports the close evolutionary relationship among these species. Some key enzyme-encoding gene families related to the biosynthesis of lignin and flavonoids were expanded and highly expressed in the stems or leaves, which probably resist the damage of the natural environment. In addition, some key gene families related to cellulose biosynthesis were highly expressed in stems, accounting for the high cellulose content of P. wilsonii variety. Our findings provided deep insights into the genetic evolution of P. wilsonii and will contribute to further biological research and breeding as well as for other poplars in Salicaceae.

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Genome Assembly of SalicaceaePopulus deltoides(Eastern Cottonwood)I-69Based on Nanopore Sequencing and Hi-C Technologies

Cited by 20 publications

References 62 publications

A Novel Strategy for Constructing an Integrated Linkage Map in an F1 Hybrid Population of Populus deltoides and Populus simonii

A Novel Strategy for Constructing an Integrated Linkage Map in an F1 Hybrid Population of Populus deltoides and Populus simonii

Advanced Breeding for Biotic Stress Resistance in Poplar

Chromosome-scale genome assembly provides insights into the molecular mechanisms of tissue development of Populus wilsonii

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