Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis.

Global climate change has increased concerns regarding biodiversity loss. However, many key conservation issues still required further research, including demographic history, deleterious mutation load, adaptive evolution, and putative introgression. Here we generated the first chromosome-level genome of the endangered Chinese hazelnut, Corylus chinensis, and compared the genomic signatures with its sympatric widespread C. kwechowensis-C. yunnanensis complex. We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation. Population genomics revealed that both C. chinensis and the C. kwechowensis-C. yunnanensis complex had diverged into two genetic lineages, forming a consistent pattern of southwestern-northern differentiation. Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene, whereas the widespread northern lineages have remained stable (C. chinensis) or have even recovered from population bottlenecks (C. kwechowensis-C. yunnanensis complex) during the Quaternary. Compared with C. kwechowensis-C. yunnanensis complex, C. chinensis showed significantly lower genomic diversity and higher inbreeding level. However, C. chinensis carried significantly fewer deleterious mutations than C. kwechowensis-C. yunnanensis complex, as more effective purging selection reduced the accumulation of homozygous variants. We also detected signals of positive selection and adaptive introgression in different lineages, which facilitated the accumulation of favorable variants and formation of local adaptation. Hence, both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C. chinensis. Overall, our study provides critical insights into lineage differentiation, local adaptation, and the potential for future recovery of endangered trees.

Exploring the binding mechanisms of thermally and ultrasonically induced molten globule-like ß-lactoglobulin with heptanal as revealed by multi-spectroscopic techniques and molecular simulation.

This work employed the model protein ß-lactoglobulin (BLG) to investigate the contribution of microstructural changes to regulating the interaction patterns between protein and flavor compounds through employing computer simulation and multi-spectroscopic techniques. The formation of molten globule (MG) state-like protein during the conformational evolution of BLG, in response to ultrasonic (UC) and heat (HT) treatments, was revealed through multi-spectroscopic characterization. Differential MG structures were distinguished by variations in surface hydrophobicity and the microenvironment of tryptophan residues. Fluorescence quenching measurements indicated that the formation of MG enhanced the binding affinity of heptanal to protein. LC-MS/MS and NMR revealed the covalent bonding between heptanal and BLG formed by Michael addition and Schiff-base reactions, and MG-like BLG exhibited fewer chemical shift residues. Molecular docking and molecular dynamics simulation confirmed the synergistic involvement of hydrophobic interactions and hydrogen bonds in shaping BLG-heptanal complexes thus promoting the stability of BLG structures. These findings indicated that the production of BLG-heptanal complexes was driven synergistically by non-covalent and covalent bonds, and their interaction processes were influenced by processes-induced formation of MG potentially tuning the release and retention behaviors of flavor compounds.

A chromosome-scale genome of Rhus chinensis Mill. provides new insights into plant-insect interaction and gallotannins biosynthesis.

Rhus chinensis Mill., an economically valuable Anacardiaceae species, is parasitized by the galling aphid Schlechtendalia chinensis, resulting in the formation of the Chinese gallnut (CG). Here, we report a chromosomal-level genome assembly of R. chinensis, with a total size of 389.40 Mb and scaffold N50 of 23.02 Mb. Comparative genomic and transcriptome analysis revealed that the enhanced structure of CG and nutritional metabolism contribute to improving the adaptability of R. chinensis to S. chinensis by supporting CG and galling aphid growth. CG was observed to be abundant in hydrolysable tannins (HT), particularly gallotannin and its isomers. Tandem repeat clusters of dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH) and serine carboxypeptidase-like (SCPL) and their homologs involved in HT production were determined as specific to HT-rich species. The functional differentiation of DQD/SDH tandem duplicate genes and the significant contraction in the phenylalanine ammonia-lyase (PAL) gene family contributed to the accumulation of gallic acid and HT while minimizing the production of shikimic acid, flavonoids, and condensed tannins in CG. Furthermore, we identified one UDP glucosyltransferase (UGT84A), three carboxylesterase (CXE), and six SCPL genes from conserved tandem repeat clusters that are involved in gallotannin biosynthesis and hydrolysis in CG. We then constructed a regulatory network of these genes based on co-expression and transcription factor motif analysis. Our findings provide a genomic resource for the exploration of the underlying mechanisms of plant-galling insect interaction and highlight the importance of the functional divergence of tandem duplicate genes in the accumulation of secondary metabolites.

Retrieving complete plastid genomes of endangered Guibourtia timber using hybridization capture for forensic identification and phylogenetic analysis.

The high economic value and increased demand for timber have led to illegal logging and overexploitation, threatening wild populations. In this context, there is an urgent need to develop effective and accurate forensic tools for identifying endangered Guibourtia timber species to protect forest ecosystem resources and regulate their trade. In this study, a hybridization capture method was developed and applied to explore the feasibility of retrieving complete plastid genomes from Guibourtia sapwood and heartwood specimens stored in a xylarium (wood collection). We then carried out forensic identification and phylogenetic analyses of Guibourtia within the subfamily Detarioideae. This study is the first to successfully retrieve high-quality plastid genomes from xylarium specimens, with 76.95-99.97% coverage. The enrichment efficiency, sequence depth, and coverage of plastid genomes from sapwood were 16.73 times, 70.47 times and 1.14 times higher, respectively, than those from heartwood. Although the DNA capture efficiency of heartwood was lower than that of sapwood, the hybridization capture method used in this study is still suitable for heartwood DNA analysis. Based on the complete plastid genome, we identified six endangered or commonly traded Guibourtia woods at the species level. This technique also has the potential for geographical traceability, especially for Guibourtia demeusei and Guibourtia ehie. Meanwhile, Bayesian phylogenetic analysis suggested that these six Guibourtia species diverged from closely related species within the subfamily Detarioideae ca. 18 Ma during the Miocene. The DNA reference database established based on the xylarium specimens provides admissible evidence for diversity conservation and evolutionary analyses of endangered Guibourtia species.

Copper-Catalyzed Radical Allene C(sp2 )-H Cyanation.

While the hydrogen atom abstraction (HAA) from C(sp3 )-H bond has been well explored, the radical-mediated chemo- and regio-selective functionalization of allenic C(sp2 )-H bond via direct HAA from C(sp2 )-H bond of allene remains an unsolved challenge in synthetic chemistry. This is primarily due to inherent challenges with addition of radical intermediates to allenes, regioselectivity of HAA process, instability of allenyl radical toward propargyl radical et al. Herein, we report a copper catalyzed allenic C(sp2 )-H cyanation of an array of tri- and di-substituted allenes with exceptional site-selectivity, while mono-substituted allene was successfully cyanated, albeit with a low yield. In the developed strategy, steric N-fluoro-N-alkylsulfonamide, serving as precursor of hydrogen atom abstractor, plays a crucial role in achieving the desired regioselectivity and avoiding addition of N-centered radical to allene.

Chromosome-Level Genome Assembly and Population Genomic Analyses Reveal Geographic Variation and Population Genetic Structure of Prunus tenella.

Prunus tenella is a rare and precious relict plant in China. It is an important genetic resource for almond improvement and an indispensable material in ecological protection and landscaping. However, the research into molecular breeding and genetic evolution has been severely restricted due to the lack of genome information. In this investigation, we created a chromosome-level genomic pattern of P. tenella, 231 Mb in length with a contig N50 of 18.1 Mb by Hi-C techniques and high-accuracy PacBio HiFi sequencing. The present assembly predicted 32,088 protein-coding genes, and an examination of the genome assembly indicated that 94.7% among all assembled transcripts were alignable to the genome assembly; most (97.24%) were functionally annotated. By phylogenomic genome comparison, we found that P. tenella is an ancient group that diverged approximately 13.4 million years ago (mya) from 13 additional closely related species and about 6.5 Mya from the cultivated almond. Collinearity analysis revealed that P. tenella is highly syntenic and has high sequence conservation with almond and peach. However, this species also exhibits many presence/absence variants. Moreover, a large inversion at the 7588 kb position of chromosome 5 was observed, which may have a significant association with phenotypic traits. Lastly, population genetic structure analysis in eight different populations indicated a high genetic differentiation among the natural distribution of P. tenella. This high-quality genome assembly provides critical clues and comprehensive information for the systematic evolution, genetic characteristics, and functional gene research of P. tenella. Moreover, it provides a valuable genomic resource for in-depth study in protection, developing, and utilizing P. tenella germplasm resources.

A Genomic Quantitative Study on the Contribution of the Ancestral-State Bases Relative to Derived Bases in the Divergence and Local Adaptation of Populus davidiana.

Identifying alleles associated with adaptation to new environments will advance our understanding of evolution from the molecular level. Previous studies have found that the Populus davidiana southwest population in East Asia has differentiated from other populations in the range. We aimed to evaluate the contributions of the ancestral-state bases (ASBs) relative to derived bases (DBs) in the local adaptation of P. davidiana in the Yunnan-Guizhou Plateau from a quantitative perspective using whole-genome re-sequencing data from 90 P. davidiana samples from three regions across the species range. Our results showed that the uplift of the Qinghai-Tibet Plateau during the Neogene and associated climate fluctuations during the Middle Pleistocene were likely an important factor in the early divergence of P. davidiana. Highly differentiated genomic regions between populations were inferred to have undergone strong linked natural selection, and ASBs are the chief means by which populations of P. davidiana adapt to novel environmental conditions; however, when adapting to regions with high environmental differences relative to the ancestral range, the proportion of DBs was significantly higher than that of background regions, as ASBs are insufficient to cope with these environments. Finally, a number of genes were identified in the outlier region.

Genetic diversity and population dynamic of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow in Central China.

Phylogeographic research concerning Central China has been rarely conducted. Population genetic and phylogeography of Ziziphus jujuba var. spinosa (also called sour jujube) were investigated to improve our understanding of plant phylogeographic patterns in Central China. Single-copy nuclear gene markers and complete chloroplast genome data were applied to 328 individuals collected from 21 natural populations of sour jujube in China. Nucleotide variation of sour jujube was relatively high (π = 0.00720, θ w = 0.00925), which resulted from the mating system and complex population dynamics. Analysis of molecular variation analysis revealed that most of the total variation was attributed to variation within populations, and a high level of genetic differentiation among populations was detected (F st = 0.197). Relatively low long-distance dispersal capability and vitality of pollen contributed to high genetic differentiation among populations. Differences in the environmental conditions and long distance among populations further restricted gene flow. Structure clustering analysis uncovered intraspecific divergence between central and marginal populations. Migrate analysis found a high level of gene flow between these two intraspecific groups. Bayesian skyline plot detected population expansion of these two intraspecific groups. Network and phylogeny analysis of chloroplast haplotypes also found intraspecific divergence, and the divergence time was estimated to occur at about 55.86 Ma. Haplotype native to the Loess Plateau was more ancient, and multiple glacial refugia of sour jujube were found to locate at the Loess Plateau, areas adjacent to the Qinling Mountains and Tianmu Mountains. Species distribution model analysis found a typical contraction-expansion model corresponding to the Quaternary climatic oscillations. In the future, the distribution of sour jujube may shift to high-latitude areas. This study provides new insights for phylogeographic research of temperate plant species distributed in Central China and sets a solid foundation for the application of the scientific management strategy of Z. jujuba var. spinosa.

High-Quality Genome Assembly of Olea europaea subsp. cuspidata Provides Insights Into Its Resistance to Fungal Diseases in the Summer Rain Belt in East Asia.

The olive tree (Olea europaea L.) is the most iconic fruit crop of the Mediterranean Basin. Since the plant was introduced to China in the 1960s, the summer rain climate makes it susceptible to pathogens, leading to some olive diseases. Olea europaea L. subsp. cuspidata is natively distributed in the Yunnan province of China. It has a smaller fruit size, lower oil content, and higher resistance compared to subsp. europaea, which makes subsp. cuspidata a critical germplasm resource to be investigated. Here, a high-quality genome of subsp. cuspidata with 1.38 Gb in size was assembled and anchored onto 23 pseudochromosomes with a mounting rate of 85.57%. It represents 96.6% completeness [benchmarking universal single-copy orthologs (BUSCO)] with a contig N50 of 14.72 Mb and a scaffold N50 of 52.68 Mb, which shows a significant improvement compared with other olive genomes assembled. The evaluation of the genome assembly showed that 92.31% of resequencing reads and an average of 96.52% of assembled transcripts could be aligned to the assembled genome. We found that a positively selected gene, evm.model.Chr16.1133, was shared with the results of transcriptome analysis. This gene belongs to the susceptible gene and negatively regulates the disease resistance process. Furthermore, we identified the Cercospora genus which causes the leaf spot disease in the infected leaves. The high-quality chromosome-level genomic information presented here may facilitate the conservation and utilization of germplasm resources of this subspecies and provide an essential genetic basis for further research into the differences in oil content and resistance between subsp. cuspidata and europaea.

Origin and evolutionary history of Populus (Salicaceae): Further insights based on time divergence and biogeographic analysis.

Introduction: Populus (Salicaceae) species harbour rich biodiversity and are widely distributed throughout the Northern Hemisphere. However, the origin and biogeography of Populus remain poorly understood. Methods: We infer the divergence times and the historical biogeography of the genus Populus through phylogenetic analysis of 34 chloroplast fragments based on a large sample. Results and Discussion: Eurasia is the likely location of the early divergences of Salicaceae after the Cretaceous-Paleogene (K-Pg) mass extinction, followed by recurrent spread to the remainder of the Old World and the New World beginning in the Eocene; the extant Populus species began to diversity during the early Oligocene (approximately 27.24 Ma), climate changes during the Oligocene may have facilitated the diversification of modern poplar species; three separate lineages of Populus from Eurasia colonized North America in the Cenozoic via the Bering Land Bridges (BLB); We hypothesize that the present day disjunction in Populus can be explained by two scenarios: (i) Populus likely originated in Eurasia and subsequently colonized other regions, including North America; and (ii) the fact that the ancestor of the genus Populus that was once widely distributed in the Northern Hemisphere and eventually wiped out due to the higher extinction rates in North America, similar to the African Rand flora. We hypothesize that disparities in extinction across the evolutionary history of Populus in different regions shape the modern biogeography of Populus. Further studies with dense sampling and more evidence are required to test these hypotheses. Our research underscores the significance of combining phylogenetic analyses with biogeographic interpretations to enhance our knowledge of the origin, divergence, and distribution of biodiversity in temperate plant floras.

Catalytic Asymmetric Synthesis of 3,3'-Bisindoles Bearing Single Axial Chirality.

A catalytic asymmetric synthesis of 3,3'-bisindoles bearing single axial chirality has been established via chiral phosphoric acid (CPA)-catalyzed enantioselective addition reaction of 3,3'-bisindoles with ninhydrin-derived 3-indolylmethanols. The selection of ninhydrin-derived 3-indolylmethanols as suitable electrophiles is based on the consideration that the symmetric and bulky moiety of ninhydrin would increase the steric congestion around the axis to generate stable axial chirality and avoid the generation of central chirality. By this approach, a series of 3,3'-bisindoles bearing single axial chirality were synthesized via the dynamic kinetic resolution (DKR) process in generally acceptable yields and considerable enantioselectivities. In addition, an in-depth investigation on the property (stability and rotation barrier) of the synthesized axially chiral 3,3'-bisindoles was carried out, thus providing useful information on this class of axially chiral frameworks. This approach makes use of the strategy of dynamic kinetic resolution of 3,3'-bisindoles, therefore expanding the generality and applicability of this strategy for catalytic asymmetric synthesis of 3,3'-bisindoles bearing single axial chirality.

Whole genome re-sequencing of crested traits and expression analysis of key candidate genes in duck.

The crested duck was a duck breed which features a topknot of feathers on the back of their head. In order to explain the reason of crest, we anatomy the head of some crested ducks. The anatomical structures showed that there was a fat body in the head and a hole in the skull. To determine the reason for the formation of the crest, we used whole genome re-sequencing to detect SNPs and InDels in three crested duck and three normal crested duck (without crest). There were 785,202 unique SNPs and 105,596 unique InDels include in crested duck. There were 14,591 SNPs containing genes and 13,784 InDels continuing genes were mapped on BGI_duck_1.0 by BWA 0.7.16a software. We use KEGG and GO to classification the SNP and InDel containing genes function. The PPI network of SNP containing genes and InDels containing genes was constructed by STRING. The result of PPI and KEGG analysis shown that the formation of crest might include feather development, fatty acid deposition, and skull hypoplasia. To determine the regulated of SNP containing genes and InDels containing genes, which related the different trait, of miRNA we used mirmap to predicted target miRNA of those genes. The miRNA-genes network constructed by Cytoscape. In conclusion, the formation of the crest was a complex process. The fatty acid metabolism block, feather growth and skull hypoplasia might lead crest formation. The tissue expression of four candidate genes showed that they were closely related to the formation of the trait, and could be used as important candidate genes to further elaborate the molecular mechanism of their function.

The genome of Populus alba x Populus tremula var. glandulosa clone 84K.

Poplar 84K (Populus alba x P. tremula var. glandulosa) is a fast-growing poplar hybrid. Originated in South Korea, this hybrid has been extensively cultivated in northern China. Due to the economic and ecological importance of this hybrid and high transformability, we now report the de novo sequencing and assembly of a male individual of poplar 84K using PacBio and Hi-C technologies. The final reference nuclear genome (747.5 Mb) has a contig N50 size of 1.99 Mb and a scaffold N50 size of 19.6 Mb. Complete chloroplast and mitochondrial genomes were also assembled from the sequencing data. Based on similarities to the genomes of P. alba var. pyramidalis and P. tremula, we were able to identify two subgenomes, representing 356 Mb from P. alba (subgenome A) and 354 Mb from P. tremula var. glandulosa (subgenome G). The phased assembly allowed us to detect the transcriptional bias between the two subgenomes, and we found that the subgenome from P. tremula displayed dominant expression in both 84K and another widely used hybrid, P. tremula x P. alba. This high-quality poplar 84K genome will be a valuable resource for poplar breeding and for molecular biology studies.

Marginal diversity analysis of conservation of Chinese domestic duck breeds.

The present study aimed to systematically evaluate the genetic diversity of Chinese domestic duck breeds and ensure the most effective allocation and usage of conservation funds. We first performed an analysis of DNA genetic distance in 21 duck breeds by measuring short tandem repeats. Then, we calculated the extinction probability, contribution rate, and marginal diversity for each breed. The results showed that the extinction rate of the Zhongshan duck, Guangxi duck, and Ji'an duck were the highest at 0.67, 0.59, and 0.59, respectively, and that of the Linwu duck, Jinding duck, and Gaoyou duck were the lowest at 0.15, 0.18, and 0.19, respectively. The current diversity of populations was 7.72 and the expected diversity in five hundred years is 5.14 ± 1.15. The marginal diversity of the Chinese Muscovy duck was the largest (-2.20), accounting for 42.61% of the expected diversity, followed by the Guangxi duck (-0.49, 9.44%), whereas the Jinding duck was the smallest (-0.12; 2.32%). The protection potency of the Chinese Muscovy duck was the largest (0.61), followed by Guangxi duck (0.29), whereas the Jinding duck was the smallest (0.02). This study provides a reference for determining the conservation priority of Chinese domestic duck breeds or genetic resources.

Fabrication and Properties of a Bio-Based Biodegradable Thermoplastic Polyurethane Elastomer.

Using the melt polycondensation of five bio-based aliphatic monomers (succinic acid, sebacic acid, fumaric acid, 1,3-propanediol, and 1,4-butanediol), we first synthesized the more flexible and biodegradable polyester diols (BPD) with an average molecular weight of 3825. Then, the BPD was polymerized with excessive 4,4'-diphenylmethane diisocyanate (MDI). Finally, the molecular chain extender of 1,4-butanediol (BDO) was used to fabricate the biodegradable thermoplastic polyurethane elastomer (BTPU), comprising the soft segment of BPD and the hard segment polymerized by MDI and BDO. Atomic force microscope (AFM) images showed the two-phase structure of the BTPU. The tensile strength of the BTPU containing 60% BPD was about 30 MPa and elongation at break of the BTPU was over 800%. Notably, the BTPU had superior biodegradability in lipase solution and the biodegradation weight loss ratio of the BTPU containing 80% BPD reached 36.7% within 14 days in the lipase solution.

Genetic analysis of admixture and hybrid patterns of Populus hopeiensis and P. tomentosa.

Hybridization and introgression have resulted in reticulate evolution within the genus Populus. Consequently, the origin and evolutionary history of some hybrids has become blurred. P. hopeiensis and P. tomentosa are endemic to China, and there is still controversy about their origin. We employ phylogeny, Bayesian estimation of admixture, and approximate Bayesian computation to investigate their origin with 10 nuclear DNA and 6 cpDNA regions. The combined evidences firmly support the hypothesis that they are hybrids and dominated by F1s. P. hopeiensis was generated via hybridization between the paternal species P. alba and maternal species P. davidiana. Surprisingly, P. tomentosa was divided into two genetic types with different maternal parents. P. adenopoda hybridized with P. alba directly to generate the first genetic type (mb1) and hybridized with P. davidiana followed by P. alba to generate the second (mb2). In both genetic types, P. alba acted as the male parent. The maternal parent was P. adenopoda and P. davidiana for mb1 and mb2, respectively. Hybridization not only generated these hybrids but also resulted in a unidirectional gene flow from P. davidiana to P. adenopoda. The Populus species have maintained a delicate balance between their genetic integrity and gene exchange.

The complete chloroplast genome sequence of Flacourtia jangomas.

In this study, the complete chloroplast genome sequence of Flacourtia jangomas was featured from Illumina pair-end sequencing. In F. jangomas, its length was 156,223 bp, consisting of a large single copy (LSC) region of 84,233 bp, two inverted repeat (IR) copies 27,649 bp and a small single copy (SSC) region of 16,693 bp. The entire GC contents were 37%, and in the LSC, SSC, and IR regions were 35, 31, and 42%, respectively. Flacourtia jangomas has 130 unique genes, including 86 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The chloroplast genomes of 12 species of Salicaceae and 1 species of Euphorbiaceae were used to construct the maximum-likelihood phylogenetic tree. It indicated that F. jangomas belongs to Salicaceae and is clustered with Flacourtia indica as sisters.

The complete chloroplast genome sequence of Xylosma congesta.

We sequenced and analyzed the complete chloroplast genome of Xylosma congesta. The chloroplast genome was 156,520 bp in size, containing a large single-copy (84,404 bp) and a small single-copy region (16,474 bp) separated by two inverted repeat regions of 27,821 bp each. A total of 130 genes were annotated, including 86 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The overall GC content of the chloroplast genome was 36.7%. The phylogenomic analysis strongly supported the close relationship between X. congesta and Flacourtia indica.

Phylogeographic analyses of a widely distributed Populus davidiana: Further evidence for the existence of glacial refugia of cool-temperate deciduous trees in northern East Asia.

Despite several phylogeographic studies had provided evidence to support the existence of glacial refugia of cool-temperate deciduous trees in northeast China, the species used in these studies were limited by the species ranges, which could not exclude the possibility that northern populations were the colonists from southern refugial populations during the last glacial maximum (LGM). Here, we estimated the nucleotide variation in Populus davidiana, a widespread species distributed in Eurasia. Three groups in northeast, central, and southwest China were constructed according to the simulation results from SAMOVA, composition of chloroplast haplotypes and structure results. We revealed that the northeast China had endemic haplotypes, the haplotypes and nucleotide diversity in northern regions were not lower than that in southern China, and this species has not experienced population expansion base on the estimation of Bayesian skyline plots. Ecological niche modeling (ENM) indicated that the northeast China had a high suitability score during the last glacial maximum. The combined evidence clearly demonstrated that northeastern and southwestern refugia were maintained across the current distributional range of P. davidiana during the LGM. The genetic differentiation between these two refugia might be mainly caused by differences of climate among these areas. The phylogeographic analyses of a widely distributed P. davidiana provided robust evidence to clarify the issue of refugia in northeast China, and these results are of great importance for understanding the influence of Quaternary glaciations on the distribution and evolution of species in East Asia.

Phylogenetic and Taxonomic Status Analyses of the Abaso Section from Multiple Nuclear Genes and Plastid Fragments Reveal New Insights into the North America Origin of Populus (Salicaceae).

Although, the Abaso section is widely accepted as an independent section, the taxonomic status of Populus mexicana (section Abaso) has not yet been resolved due to the limited availability markers and/or the lack of P. mexicana specimens in previous studies. Thirty-one poplar species that represent six sections of the Populus genus were sampled, and 23 single-copy nuclear DNA and 34 chloroplast fragments were sequenced. The present study obtained two updated phylogenies of Populus. We found that monophyly of the genus Populus is strongly supported by nuclear and plastid gene, which is consistent with previous studies. P. mexicana, diverged first in the nuclear DNA tree, which occupied the basal position, implying that the section Abaso may be the most ancestral lineage in extant populous species. Given that the short branches and low statistical support for the divergence of sections Abaso and Turanga, this observation probably indicated that a rapid radiation evolution following the early split of the genus Populus. In the plastid tree, P. mexicana clustered with modern-day species of section Tacamahaca in the plastid tree. Based on cytoplasmic and single-copy nuclear marker sequences, we hypothesized that chloroplast capture resulted in the inconsistent position of P. mexicana between the phylogenetic trees. Given the first unequivocal records of poplar fossils from the Eocene with similar leaf morphology to the extant P. mexicana and the phylogenetic positions of P. mexicana in our study, we support the hypothesis that the Populus genus originated in North America, which will provide new insights to the development of the origin of Populus species.