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The low phosphorus (P) availability of acidic soils severely limits leguminous plant growth and productivity. Improving the soil P nutritional status can be achieved by increasing the P-content through P-fertilization or stimulating the mineralization of organic P via arbuscular mycorrhizal fungi (AMF) application; however, their corresponding impacts on plant and soil microbiome still remain to be explored. Here, we examined the effects of AMF-inoculation and P-fertilization on the growth of soybean with different P-efficiencies, as well as the composition of rhizo-microbiome in an acidic soil. The growth of recipient soybean NY-1001, which has a lower P-efficiency, was not significantly enhanced by AMF-inoculation or P-fertilization. However, the plant biomass of higher P-efficiency transgenic soybean PT6 was significantly increased by 46.74%–65.22% through AMF-inoculation. Although there was no discernible difference in plant biomass between PT6 and NY-1001 in the absence of AMF-inoculation and P-fertilization, PT6 had approximately 1.9–2.5 times the plant biomass of NY-1001 after AMF-inoculation. Therefore, the growth advantage of higher P-efficiency soybean was achieved through the assistance of AMF rather than P-fertilization in available P-deficient acidic soil. Most nitrogen (N)-fixing bacteria and some functional genes related to N-fixation were abundant in endospheric layer, as were the P-solubilizing Pseudomonas plecoglossicida, and annotated P-metabolism genes. These N-fixing and P-solubilizing bacteria were positive correlated with each other. Lastly, the two most abundant phytopathogenic fungi species accumulated in endospheric layer, they exhibited positive correlations with N-fixing bacteria, but displayed negative interactions with the majority of the other dominant non-pathogenic genera with potential antagonistic activity.

Gymnosperms are a unique lineage of plants that currently lack a high-quality reference genome due to their large genome size and high repetitive sequence content. Here, we report a nearly complete genome assembly for Ginkgo bilobawith a genome size of 9.87 Gb, an N50 contig size of 1.58 Mb and an N50 scaffold size of 775 Mb. We were able to accurately annotate 27,832 protein-coding genes in total, superseding the inaccurate annotation of 41,840 genes in a previous draft genome assembly. We found that expansion of the G. bilobagenome, accompanied by the notable extension of introns, was mainly caused by the insertion of long terminal repeats rather than the recent occurrence of whole-genome duplication events, in contrast to the findings of a previous report. We also identified candidate genes in the central pair, intraflagellar transport and dynein protein families that are associated with the formation of the spermatophore flagellum, which has been lost in all seed plants except ginkgo and cycads. The newly obtained Ginkgogenome provides new insights into the evolution of the gymnosperm genome.

The development of non-recombining sex chromosomes has radical effects on the evolution of discrete sexes and sexual dimorphism. Although dioecy is rare in plants, sex chromosomes have evolved repeatedly throughout the diversification of angiosperms, and many of these sex chromosomes are relatively young compared to those found in vertebrates. In this study, we designed and used a sequence capture array to identify a novel sex-linked region (SLR) in Salix nigra, a basal species in the willow clade, and demonstrated that this species has XY heterogamety. We did not detect any genetic overlap with the previously characterized ZW SLRs in willows, which map to a different chromosome. The S. nigraSLR is characterized by strong recombination suppression across a 2 MB region and an excess of low-frequency alleles, resulting in a low Tajima’s D compared to the remainder of the genome. We speculate that either a recent bottleneck in population size or factors related to positive or background selection generated this differential pattern of Tajima’s D on the X and autosomes. This discovery provides insights into factors that may influence the evolution of sex chromosomes in plants and contributes to a large number of recent observations that underscore their dynamic nature.

Complete mitochondrial genomes (mitogenomes) of plants are valuable resources for nucleocytoplasmic interactions, plant evolution, and plant cytoplasmic male sterile line breeding. However, the complete assembly of plant mitogenomes is challenging due to frequent recombination events and horizontal gene transfers. Previous studies have adopted Illumina, PacBio, and Nanopore sequencing data to assemble plant mitogenomes, but the poor assembly completeness, low sequencing accuracy, and high cost limit the sampling capacity. Here, we present an efficient assembly toolkit (PMAT) for de novoassembly of plant mitogenomes using low-coverage HiFi sequencing data. PMAT has been applied to the de novoassembly of 13 broadly representative plant mitogenomes, outperforming existing organelle genome assemblers in terms of assembly accuracy and completeness. By evaluating the assembly of plant mitogenomes from different sequencing data, it was confirmed that PMAT only requires 1× HiFi sequencing data to obtain a complete plant mitogenome. The source code for PMAT is available at https://github.com/bichangwei/PMAT. The developed PMAT toolkit will indeed accelerate the understanding of evolutionary variation and breeding application of plant mitogenomes.

Redwood trees (Sequoioideae), including Metasequoia glyptostroboides(dawn redwood), Sequoiadendron giganteum(giant sequoia), and Sequoia sempervirens(coast redwood), are threatened and widely recognized iconic tree species. Genomic resources for redwood trees could provide clues to their evolutionary relationships. Here, we report the 8-Gb reference genome of M. glyptostroboidesand a comparative analysis with two related species. More than 62% of the M. glyptostroboidesgenome is composed of repetitive sequences. Clade-specific bursts of long terminal repeat retrotransposons may have contributed to genomic differentiation in the three species. The chromosomal synteny between M. glyptostroboidesand S. giganteumis extremely high, whereas there has been significant chromosome reorganization in S. sempervirens. Phylogenetic analysis of marker genes indicates that S. sempervirensis an autopolyploid, and more than 48% of the gene trees are incongruent with the species tree. Results of multiple analyses suggest that incomplete lineage sorting (ILS) rather than hybridization explains the inconsistent phylogeny, indicating that genetic variation among redwoods may be due to random retention of polymorphisms in ancestral populations. Functional analysis of ortholog groups indicates that gene families of ion channels, tannin biosynthesis enzymes, and transcription factors for meristem maintenance have expanded in S. giganteumand S. sempervirens, which is consistent with their extreme height. As a wetland-tolerant species, M. glyptostroboidesshows a transcriptional response to flooding stress that is conserved with that of analyzed angiosperm species. Our study offers insights into redwood evolution and adaptation and provides genomic resources to aid in their conservation and management.

Although organellar genomes (including chloroplast and mitochondrial genomes) are smaller than nuclear genomes in size and gene number, organellar genomes are very important for the investigation of plant evolution and molecular ecology mechanisms. Few studies have focused on the organellar genomes of horticultural plants. Approximately 1193 chloroplast genomes and 199 mitochondrial genomes of land plants are available in the National Center for Biotechnology Information (NCBI), of which only 39 are from horticultural plants. In this paper, we report an innovative and efficient method for high-quality horticultural organellar genome assembly from next-generation sequencing (NGS) data. Sequencing reads were first assembled by Newbler, Amos, and Minimus software with default parameters. The remaining gaps were then filled through BLASTN search and PCR. The complete DNA sequence was corrected based on Illumina sequencing data using BWA (Burrows–Wheeler Alignment tool) software. The advantage of this approach is that there is no need to isolate organellar DNA from total DNA during sample preparation. Using this procedure, the complete mitochondrial and chloroplast genomes of an ornamental plant, Salix suchowensis, and a fruit tree, Ziziphus jujuba, were identified. This study shows that horticultural plants have similar mitochondrial and chloroplast sequence organization to other seed plants. Most horticultural plants demonstrate a slight bias toward A+T rich features in the mitochondrial genome. In addition, a phylogenetic analysis of 39 horticultural plants based on 15 protein-coding genes showed that some mitochondrial genes are horizontally transferred from chloroplast DNA. Our study will provide an important reference for organellar genome assembly in other horticultural plants. Furthermore, phylogenetic analysis of the organellar genomes of horticultural plants could accurately clarify the unanticipated relationships among these plants. A new method makes it easier to assemble the DNA sequences of mitochondrial and chloroplast genomes for horticultural plants. Most strategies for assembling the genomes of chloroplasts (which conduct photosynthesis) and mitochondria (which supply cellular energy) require the isolation of organellar DNA from total DNA. However, using bioinformatics software, a team led by Tongming Yin and Ning Ye from Nanjing Forestry University, China, identified a way to pull out all the DNA sequence reads for these organelles from complete next-generation sequencing data, without the need for specialized sample preparation. As a proof-of-principle, the researchers used the protocol to decode the mitochondrial and chloroplast genomes of the ornamental plant Salix suchowensisand the fruit tree Ziziphus jujube. Comparative analyses of mitochondrial and chloroplast genomes assembled in this way could reveal new insights into plant evolutionary relationships.

Twin support vector clustering (TWSVC) is a recently proposed powerful k-plane clustering method. It, however, is prone to outliers due to the utilization of squared L2-norm distance. Besides, TWSVC is computationally expensive, attributing to the need of solving a series of constrained quadratic programming problems (CQPPs) in learning each clustering plane. To address these problems, this brief first develops a new k-plane clustering method called L1-norm distance minimization-based robust TWSVC by using robust L1-norm distance. To achieve this objective, we propose a novel iterative algorithm. In each iteration of the algorithm, one CQPP is solved. To speed up the computation of TWSVC and simultaneously inherit the merit of robustness, we further propose Fast RTWSVC and design an effective iterative algorithm to optimize it. Only a system of linear equations needs to be computed in each iteration. These characteristics make our methods more powerful and efficient than TWSVC. We also conduct some insightful analysis on the existence of local minimum and the convergence of the proposed algorithms. Theoretical insights and effectiveness of our methods are further supported by promising experimental results.

Twin support vector clustering (TWSVC) is a recently proposed powerful k-plane clustering method. It, however, is prone to outliers due to the utilization of squared L2-norm distance. Besides, TWSVC is computationally expensive, attributing to the need of solving a series of constrained quadratic programming problems (CQPPs) in learning each clustering plane. To address these problems, this brief first develops a new k-plane clustering method called L1-norm distance minimization-based robust TWSVC by using robust L1-norm distance. To achieve this objective, we propose a novel iterative algorithm. In each iteration of the algorithm, one CQPP is solved. To speed up the computation of TWSVC and simultaneously inherit the merit of robustness, we further propose Fast RTWSVC and design an effective iterative algorithm to optimize it. Only a system of linear equations needs to be computed in each iteration. These characteristics make our methods more powerful and efficient than TWSVC. We also conduct some insightful analysis on the existence of local minimum and the convergence of the proposed algorithms. Theoretical insights and effectiveness of our methods are further supported by promising experimental results. [ABSTRACT FROM AUTHOR]

Labile sex expression is frequently observed in dioecious plants, but the underlying genetic mechanism remains largely unknown. Sex plasticity is also observed in many Populusspecies. Here we carried out a systematic study on a maleness-promoting gene, MSL, detected in the Populus deltoidesgenome. Our results showed that both strands of MSLcontained multiple cis-activating elements, which generated long non-coding RNAs (lncRNAs) promoting maleness. Although female P. deltoidesdid not have the male-specific MSLgene, a large number of partial sequences with high sequence similarity to this gene were detected in the female poplar genome. Based on sequence alignment, the MSLsequence could be divided into three partial sequences, and heterologous expression of these partial sequences in Arabidopsisconfirmed that they could promote maleness. Since activation of the MSLsequences can only result in female sex lability, we propose that MSL-lncRNAs might play a role in causing sex lability of female poplars.

Semisupervised dimension reduction via virtual label regression first derives the virtual labels of unlabeled data by employing a newly designed label propagation (LP) approach (called Special random walk (SRW)) and then encodes them in a weighted linear regression model. Nie et al. (2011) highlighted two important characteristics of SRW nonexistent in the previous LP approaches: outlier detection and probability value output, which guarantee the elegant encoding of the resultant virtual labels in the weighted label regression. However, in this brief, we show that the relationship between the SRW and the previous work on LP is very close. Naturally, a problem deserving investigation is whether traditional LP approaches are indeed unable to share the above two characteristics of SRW. We aim to address this problem. [ABSTRACT FROM AUTHOR]

Abstract: Quantitative trait locus (QTL) studies are an integral part of plant research and are used to characterize the genetic basis of phenotypic variation observed in structured populations and inform marker-assisted breeding efforts. These QTL intervals can span large physical regions on a chromosome comprising hundreds of genes, thereby hampering candidate gene identification. Genome history, evolution, and expression evidence can be used to narrow the genes in the interval to a smaller list that is manageable for detailed downstream functional genomics characterization. Our primary motivation for the present study was to address the need for a research methodology that identifies candidate genes within a broad QTL interval. Here we present a bioinformatics-based approach for subdividing candidate genes within QTL intervals into alternate groups of high probability candidates. Application of this approach in the context of studying cell wall traits, specifically lignin content and S/G ratios of stem and root in Populus plants, resulted in manageable sets of genes of both known and putative cell wall biosynthetic function. These results provide a roadmap for future experimental work leading to identification of new genes controlling cell wall recalcitrance and, ultimately, in the utility of plant biomass as an energy feedstock.

Abstract: The capacity to root from cuttings is a key factor for the mass deployment of superior genotypes in clonal forestry. We studied the genetic basis of rooting capacity by mapping quantitative trait loci (QTLs) that control growth rate and form of root traits in a full-sib family of 93 hybrids derived from an interspecific cross between two Populus species, P. deltoides and P. euramericana. The hybrid family was typed for different marker systems (including SSRs, AFLPs, RAPDs, ISSRs, and SNPs), leading to the construction of two linkage maps based on the female P. deltoides (D map) and male P. euramericana (E map) with a pseudotestcross mapping strategy. The two maps were scanned by functional mapping to detect QTLs that control early growth trajectories of two rooting traits, maximal single-root length and the total number of roots per cutting, measured at five time points in water culture. Of the six QTLs detected for these two growth traits, only one is segregating in P. deltoides with poor rooting capacity, while the other five are segregating in P. euramericana showing good rooting capacity. Tests with functional mapping suggest different developmental patterns of the genetic effects of these root QTLs in time course. Five QTLs were detected to change their effects on root growth trajectories with time, whereas one detected to affect root growth consistently in time course. Knowledge about the genetic and developmental control mechanisms of root QTLs will have important implications for the genetic improvement of vegetative propagation traits in Populus.

Growth trajectories are a biological process important to plant and animal breeding, and to evolutionary genetic studies. In this article, we report the detection of quantitative trait loci (QTLs) responsible for growth trajectories in poplars that are used as a model system for the study of forest biology. These QTLs were localized on a genetic linkage map of polymorphic markers using a statistical mapping method incorporating growth-curve models. The effects of the QTLs on growth are described as a function of age, so that age-specific changes in QTL effects can be readily projected throughout the entire growth process. The QTLs identified display increased effects on growth when trees age, yet the timing of QTL activation is earlier for stem height than diameter, which is consistent with the ecological viewpoint of canopy competition. The implications of the results for breeding and silviculture are discussed.

The logistic or S-shaped curve of growth is one of the few universal laws in biology. It is certain that there exist specific genes affecting growth curves, but, due to a lack of statistical models, it is unclear how these genes cause phenotypic differentiation in growth and developmental trajectories. In this paper we present a statistical model for detecting major genes responsible for growth trajectories. This model is incorporated with pervasive logistic growth curves under the maximum likelihood framework and, thus, is expected to improve over previous models in both parameter estimation and inference. The power of this model is demonstrated by an example using forest tree data, in which evidence of major genes affecting stem growth processes is successfully detected. The implications for this model and its extensions are discussed.

Salix suchowensisis an early-flowering shrub willow that provides a desirable system for studies on the basic biology of woody plants. The current reference genome of S. suchowensiswas assembled with 454 sequencing reads. Here, we report a chromosome-scale assembly of S. suchowensisgenerated by combining PacBio sequencing with Hi-C technologies. The obtained genome assemblies covered a total length of 356 Mb. The contig N50 of these assemblies was 263,908 bp, which was ~65-fold higher than that reported previously. The contiguity and completeness of the genome were significantly improved. By applying Hi-C data, 339.67 Mb (95.29%) of the assembled sequences were allocated to the 19 chromosomes of haploid willow. With the chromosome-scale assembly, we revealed a series of major chromosomal fissions and fusions that explain the genome divergence between the sister genera of Salixand Populus. The more complete and accurate willow reference genome obtained in this study provides a fundamental resource for studying many genetic and genomic characteristics of woody plants.

Populus(poplars) and Salix(willows) are sister genera in the Salicaceae family that arise from a common tetraploid ancestor. The karyotypes of these two lineages are distinguished by two major interchromosomal and some minor intrachromosomal rearrangements, but which one is evolutionarily more primitive remains debatable. In this study, we compare the selection pressure acting on the paralogous genes resulting from salicoid duplication (PGRS) within and between the genomes of the two lineages. Purifying selection was determined to act more strongly on the PGRS in willow than on those in poplar, which would cause a faster loss of paralogous duplicates in willow. Therefore, Salixspecies are supposed to evolve faster than Populusspecies, which is consistent with the observation that the former are taxonomically and morphologically more diverse than the latter. In these two lineages, different autosomes were found to have been evolving into sex chromosomes. Examining the ω ratio and the PGRS in the sex determination regions in willow and poplar revealed higher convergent selection pressure and a faster loss of PGRS in the sex determination regions of both lineages. At the chromosome level, the sex chromosome in poplar is characterized by the lowest gene density among all chromosome members, while this feature is not observed on the sex chromosome in willow, suggesting that Populusspecies may inherit the more incipient sex chromosome from their progenitor. Taken together, Salixis supposed to be the nascent lineage arising from the additional round of genome reorganization that distinguishes the karyotypes of the two sister genera. In this study, assessment of ω ratios also detected a list of paralogous genes under unusual selection pressure, which could have special consequences for the adaptive evolution of Salicaceae species. In conclusion, the results of this study provide unique information for better understanding the genetic mechanism accelerating the divergence of these two closely related lineages.