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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 of 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, 231Mb in length with a contig N50 of 18.1 Mb by Hi-C techniques and high-accuracy PacBio HiFi sequencing. The present assembly predicted 32088 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 exhibit many presence/absence variants. Moreover, a large inversion at the 7,588 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 protecting, developing, and utilizing P. tenella germplasm resources.

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.

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.

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.

Populus alba is a foundation species in evolutionary and ecological studies in the northern hemisphere. In this study, the chloroplast genome and gene map of P. alba were constructed. The P. alba chloroplast genome is 156,505 bp in length comprising a large single-copy region, two inverted repeat regions and a small single-copy region. The genome contains 131 genes, including 86 protein-coding genes (77 PCG species), eight ribosomal RNA genes (four rRNA species) and 37 transfer RNA genes (30 tRNA species). Phylogenetic analysis indicates that all Populus chloroplast genome sequences are clustered together and divided into three large branches. Among reported Populus chloroplast genomes, the leuce section formed monophyletic, indicating that all Populus spp. have a common maternal ancestor. P. rotundifolia and P. tremula are closely related and are sisters to P. davidiana. P. alba is closely related to P. adenopoda. Population genetic research in ecology and evolution may be easily developed through chloroplast genomes as they are conserved. This research will benefit future studies related to Populus, one of the world’s most ecologically and economically important genera.

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.

Despite the growing number of recent studies on genome-wide divergence during speciation, the genetic basis and mechanisms of genomic divergence are still incompletely understood. In most species, natural selection plays a key role in heterogeneous genomic divergence. Additionally, intrinsic barriers, such as chromosomal rearrangements or gene incompatibilities, can also cause genomic heterogeneity. Based on whole genome re-sequencing data from 27 Populus alba and 28 P. adenopoda individuals, we explored the reasons for heterogeneous genomic divergence of these two closely related species. The results showed that the two species diverged ~5-10 million years ago (Mya), when the Qinghai-Tibet Plateau reached a certain height and the inland climate of the Asian continent became arid, which is associated with the fact that the two species begin to diverge and eventually led to speciation. In highly differentiated regions, the absolute divergence (dxy) was significantly higher than genomic background, and relative and absolute divergence were highly correlated, which indicates that intrinsic barriers played an important role in maintaining genomic heterogeneous divergence. Additionally, θπ and shared polymorphisms decreased while fixed differences increased in highly differentiated regions, which are characteristics of natural selection. The above description indicates that the combination of intrinsic barriers and natural selection result in heterogeneous genomic divergence and reproductive isolation. We further found some genes that are related to reproduction may be involved in explaining the reproductive isolation of the two species.

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.

Climate and geography oscillations in the Quaternary profoundly influenced the distribution pattern and genetic structure of plant species. Phylogeographic investigations have been numerously conducted in biodiversity hotspot regions. However, other regions have received less attention and these places may serve as potential glacial refugia for plant species. In the study presented here, phylogeographic pattern of Elaeagnus mollis, a plant species exclusively distributed in central China, was investigated using multiple nSSR loci and chloroplast fragments. As an endangered species in China, the genetic diversity of E. mollis was relatively high (Na = 7.82, HO = 0.532, and HE = 0.623). Genetic differentiation (FST) between the two main distribution regions, Shanxi and Shaanxi provinces, was 0.23177. STRUCTURE analysis of nSSR data as well as phylogenetic construction of chloroplast haplotypes clearly distinguished two distantly sublineages, corresponding well with two distribution regions. Multiple factors such as outcrossing were thought to contribute to the high level of genetic diversity. The topographically heterogeneous regions and the low dispersal ability of seed and pollen may lead to high genetic differentiation between these two regions. Two potential glacial refugia for E. mollis located in adjacent regions to the Qinling Mountains and south of the Loess Plateau were revealed, and allopatric divergence in separated glacial refugia may directly lead to the present phylogeographic pattern of this species. This study set a solid foundation for future protection and sustainable utilization of this important germplasm resource.

Two inter-subspecific F1 hybrids have been obtained by crossing olive cultivars (‘Frantoio’ and ‘Coratina’) with pollen donors from olive subspecies (Olea europaea subsp. cuspidata) to enrich the germplasm of cultivated olive in southern China. This study aimed to investigate the characterization of morphological traits and molecular markers in the two hybrids and their parents of crosses. The morphological study showed a significant difference between genotypes according to the main discriminative parameters on qualitative and quantitative traits of leaf, fruit, and endocarp. A set of six co-dominant polymorphic simple sequence repeats (SSRs) were used for molecular identification, and SSR analysis confirmed that two progenies were the offspring of their cited parents based on the presence of parental specific SSR alleles. Three single-copy nuclear loci (SCNL) primer pairs were used for amplification of single-copy genes in the two progenies and their parents and after then PCR products were sequenced. Sequence alignment analysis on the effective data showed a total of 15 different base sites between two progenies, which were confirmed as true inter-specific hybrids between olive cultivars and subsp. cuspidata.

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 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.

Although extensive studies have demonstrated that several genera formerly placed in the family Flacourtiaceae are the closest relatives of Populus-Salix. However, the closest relative or relatives remain uncertain due to the relatively low phylogenetic resolution and insufficient phylogenetic information. In addition, the question as to whether Populus and Salix are truly monophyletic remains open because of the absence of comprehensive studies with large-scale samples of both genera. In the present study, 54 species representing 11 genera of Salicaceae sensu lato (now including the genera of Flacourtiaceae) were studied using a combined rbcL and matK gene sequence dataset with a total length of 2134 bp, to explore the closest genera that are relatives of Populus-Salix and to determine the relationships between Populus and Salix. The resulting phylogenetic trees showed high resolution in each of the main clades. The results confirmed that (1) Idesia and Bennettiodendron are the closest relatives to Populus-Salix, followed by Poliothyrsis, and (2) Populus and Salix are a truly monophyletic lineage in which the most recent ancestor is shared by the two genera. This finding is significant for a wide variety of evolutionary studies and for understanding the classification and biosystematics of Salicaceae.

Section Leuce Duby (Populus, Salicaceae) is an important taxon among the 6 sections in the genus Populus. Although biological and taxonomic studies has greatly improved our understanding of this section, the phylogenetic relationships among the species of section Leuce remain uncertain due in part to the limited number of loci for analysis. In the present study, 34 chloroplast DNA fragments, which included 22 new chloroplast DNA fragments as well as 12 chloroplast DNA fragments used previously, were applied to explore interspecific relationships in this section. The inclusion of additional chloroplast DNA fragments recovered a well-resolved phylogeny of section Leuce. According to our phylogenetic tree, (1) we can confirm the monophyly of section Leuce and two sister clade subdivisions; (2) P. tremula L. shows closer affinity to P. davidiana Dode than other species, which has previously been a source of debate; (3) P. tremuloides Michx. and P. grandidentata Michx. form sister subclades; and (4) we propose that the previously unresolved phylogeny of section Leuce is most likely due to insufficient data. Our phylogenetic analysis successfully resolved the phylogeny of section Leuce using a sufficient dataset. This study provides an important foundation for evolutionary studies and for the effective utilization of the wild germplasm resources of section Leuce.

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 regi...

The complete chloroplast genome sequence of Homalium cochinchinense was characterized from Illumina pair-end sequencing. The chloroplast genome of H .cochinchinense was 157,116 bp in length, contai...

Historical tectonism and climate oscillations can isolate and contract the geographical distributions of many plant species, and they are even known to trigger species divergence and ultimately speciation. Here, we estimated the nucleotide variation and speciation in three closely related Populus species, Populus tremuloides, P. tremula and P. davidiana, distributed in North America and Eurasia. We analysed the sequence variation in six single-copy nuclear loci and three chloroplast (cpDNA) fragments in 497 individuals sampled from 33 populations of these three species across their geographic distributions. These three Populus species harboured relatively high levels of nucleotide diversity and showed high levels of nucleotide differentiation. Phylogenetic analysis revealed that P. tremuloides diverged earlier than the other two species. The cpDNA haplotype network result clearly illustrated the dispersal route from North America to eastern Asia and then into Europe. Molecular dating results confirmed that the divergence of these three species coincided with the sundering of the Bering land bridge in the late Miocene and a rapid uplift of the Qinghai-Tibetan Plateau around the Miocene/Pliocene boundary. Vicariance-driven successful allopatric speciation resulting from historical tectonism and climate oscillations most likely played roles in the formation of the disjunct distributions and divergence of these three Populus species.

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. Populus 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.

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.

The recent advances of millimeter-wave technologies for plasma diagnostics in Institute of Plasma Physics Academia Sinica are introduced, particularly the development of digitized millimeter-wave interferometer, the system for millimeter-wave local scattering experiment and the time sequential spectrometer for electron cyclotron emission measurement.

Populus (Salicaceae) is one of the most economically and ecologically important genera of forest trees. The complex reticulate evolution and lack of highly variable orthologous single-copy DNA markers have posed difficulties in resolving the phylogeny of this genus. Based on a large data set of nuclear and plastid DNA sequences, we reconstructed robust phylogeny of Populus using parsimony, maximum likelihood and Bayesian inference methods. The resulting phylogenetic trees showed better resolution at both inter- and intra-sectional level than previous studies. The results revealed that (1) the plastid-based phylogenetic tree resulted in two main clades, suggesting an early divergence of the maternal progenitors of Populus; (2) three advanced sections (Populus, Aigeiros and Tacamahaca) are of hybrid origin; (3) species of the section Tacamahaca could be divided into two major groups based on plastid and nuclear DNA data, suggesting a polyphyletic nature of the section; and (4) many species proved to be of hybrid origin based on the incongruence between plastid and nuclear DNA trees. Reticulate evolution may have played a significant role in the evolution history of Populus by facilitating rapid adaptive radiations into different environments.