Genome-wide identification and characterization of WUSCHEL-related homeobox(WOX) genes in Salix suchowensis

Members of the WUSCHEL-related homeobox(WOX)transcription factor family are essential for determining cell fate and regulating diverse developmental processes in plants.Many WOX genes have been systematically investigated in woody plants such as Populus trichocarpa,but not in Salix suchowensis.Whole-genome sequence data for S.suchowensis is now available for comprehensive study of WOX genes in S.suchowensis.We thus surveyed the genome of S.suchowensis and demonstrated active expression of 15 WOX genes.In a phylogenetic analysis of WOX genes,the 15 SsWOX genes clustered among the modern/WUS,intermediate and ancient clades similar to the WOX genes of Arabidopsis thaliana.Based on the conserved intron/exon structure,SsWOX genes in the same subgroup had similar conserved exon–intron structures and motif domains.Furthermore,among several SsWOX subgroups,WUS(Wuschel)-box and EAR(the ERF-associated amphiphilic repression)-like motifs were conserved.Expression profiles of WOX genes in roots,stems and leaves indicate that SsWOX genes have various conserved roles in the tissues.Comparative analysis of the expression patterns in Salix suchowensis with that of Arabidopsis suggests that different shoot regeneration abilities are controlled by different WOX genes in plants.The analysis provide an overview of differentially expressed SsWOX genes during shoot regeneration,but also contribute to understanding the evolution of WOX genes in Salicaceae and the interrelations of WOX genes and other transcription factors,providing targets for further study.

Organellar genome assembly methods and comparative analysis of horticultural plants

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.

Comparing independent climate-sensitive models of aboveground biomass and diame ter grow th with their compatible simultaneous model system for three larch species in China

Accurate estimate of tree biomass is essential for forest management.In recent years,several climate-sensitive allometric biomass models with diameter at breast height(D)as a predictor have been proposed for various tree species and climate zones to estimate tree aboveground biomass(AGB).But the allometric models only account for the potential effects of climate on tree biomass and do not simultaneously explain the influence of climate on D growth.In this study,based on the AGB data from 256 destructively sampled trees of three larch species randomly distributed across the five secondary climate zones in northeastern and northern China,we first developed a climate-sensitive AGB base model and a climate-sensitive D growth base model using a nonlinear least square regression separately.A compatible simultaneous model system was then developed with the climate-sensitive AGB and D growth models using a nonlinear seemingly unrelated regression.The potential effects of several temperature and precipitation variables on AGB and D growth were evaluated.The fitting results of climatic sensitive base models were compared against those of their compatible simultaneous model system.It was found that a decreased isothermality([mean of monthly(maximum temperatureminimum temperature)]/(Maximum temperature of the warmest month-Minimum temperature of the coldest month))and total growing season precipitation,and increased annual precipitation significantly increased the values of AGB;an increase of temperature seasonality(a standard deviation of the mean monthly temperature)and precipitation seasonality(a standard deviation of the mean monthly precipitation)could lead to the increase of D.The differences of the model fitting results between the compatible simultaneous system with the consideration of climate effects on both AGB and D growth and its corresponding climate-sensitive AGB and D growth base models were very small and insignificant(p>0.05).Compared to the base models,the inhere nt correlation of AGB with D was taken into account effectively by the proposed compatible model system developed with the climate-sensitive AGB and D grow th models.In addition,the compatible properties of the estimated AGB and D were also addressed substantially in the proposed model system.