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.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Genomewide analysis of the lateral organ boundaries domain gene family in Eucalyptus grandis reveals members that differentially impact secondary growth

Lateral Organ Boundaries Domain (LBD) proteins are plant-specific transcription factors playing crucial roles in growth and development. However, the function of LBD proteins in Eucalyptus grandis remains largely unexplored. In this study, LBD genes in E. grandis were identified and characterized using bioinformatics approaches. Gene expression patterns in various tissues and the transcriptional responses of EgLBDs to exogenous hormones were determined by qRT-PCR. Functions of the selected EgLBDs were studied by ectopically overexpressing in a hybrid poplar (Populus alba 9 Populus glandulosa). Expression levels of genes in the transgenic plants were investigated by RNA-seq. Our results showed that there were forty-six EgLBD members in the E. grandis genome and three EgLBDs displayed xylem- (EgLBD29) or phloem-preferential expression (EgLBD22 and EgLBD37). Confocal microscopy indicated that EgLBD22, EgLBD29 and EgLBD37 were localized to the nucleus. Furthermore, we found that EgLBD22, EgLBD29 and EgLBD37 were responsive to the treatments of indol- 3-acetic acid and gibberellic acid. More importantly, we demonstrated EgLBDs exerted different influences on secondary growth. Namely, 35S::EgLBD37 led to significantly increased secondary xylem, 35S::EgLBD29 led to greatly increased phloem fibre production, and 35S:: EgLBD22 showed no obvious effects. We revealed that key genes related to gibberellin, ethylene and auxin signalling pathway as well as cell expansion were significantly up- or down-regulated in transgenic plants. Our new findings suggest that LBD genes in E. grandis play important roles in secondary growth. This provides new mechanisms to increase wood or fibre production.Figure S1 Conserved domains of EgLBD protein family.Figure S2 The chromosomal localization of the LBD gene family in Eucalyptus grandis.Figure S3 Subcellular localization of EgLBD22, EgLBD29 and EgLBD37 proteins.Figure S4 Gel electrophoresis analysis for the presence of the transgene in EgLBD22-oe, EgLBD29-oe and EgLBD37-oe plants.Figure S5 Validation for the expression of the transgene in EgLBD22-oe, EgLBD29-oe and EgLBD37-oe plants by qRT-PCR.Table S1 All the primers used in this study.Table S2 The coding sequences of LBD genes in Eucalyptus grandis.Table S3 The information of LBD gene family in Eucalyptus grandis.Table S4 Conserved motifs predicted by MEME program in EgLBD proteins.Table S5 Protein-protein interaction prediction for possible functional protein association networks of EgLBD22.Table S6 Protein-protein interaction prediction for possible functional protein association networks of EgLBD29.Table S7 Protein-protein interaction prediction for possible functional protein association networks of EgLBD37.Table S8 The differentially expressed genes between EgLBD22-oe and WT-84k plants.Table S9 The differentially expressed genes between EgLBD29-oe and WT-84k plants.Table S10 The differentially expressed genes between EgLBD37-oe and WT-84k plants.Table S11 The information of eight key differentially expressed genes in EgLBD22-oe, EgLBD29-oe and EgLBD37-oe plants.Basic Research Fund of RIF [RIF2014-01]; Natural Science Foundation of China [31670676]; Mondi and Sappi through the Forest Molecular Genetics Programme; Technology and Human Resources for Industry Programme [UID 80118]; National Research Foundation of South Africa [UID 18312, 71255, 86936]http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1467-7652am2018Forestry and Agricultural Biotechnology Institute (FABI)Genetic

Transcriptomic Analysis of Betula halophila in Response to Salt Stress

Soil salinization is a matter of concern worldwide. It can eventually lead to the desertification of land and severely damage local agricultural production and the ecological environment. Betula halophila is a tree with high salt tolerance, so it is of importance to understand and discover the salt responsive genes of B. halophila for breeding salinity resistant varieties of trees. However, there is no report on the transcriptome in response to salt stress in B. halophila. Using Illumina sequencing platform, approximately 460 M raw reads were generated and assembled into 117,091 unigenes. Among these unigenes, 64,551 unigenes (55.12%) were annotated with gene descriptions, while the other 44.88% were unknown. 168 up-regulated genes and 351 down-regulated genes were identified, respectively. These Differentially Expressed Genes (DEGs) involved in multiple pathways including the Salt Overly Sensitive (SOS) pathway, ion transport and uptake, antioxidant enzyme, ABA signal pathway and so on. The gene ontology (GO) enrichments suggested that the DEGs were mainly involved in a plant-type cell wall organization biological process, cell wall cellular component, and structural constituent of cell wall molecular function. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment showed that the top-four enriched pathways were ‘Fatty acid elongation’, ‘Ribosome’, ‘Sphingolipid metabolism’ and ‘Flavonoid biosynthesis’. The expression patterns of sixteen DEGs were analyzed by qRT-PCR to verify the RNA-seq data. Among them, the transcription factor AT-Hook Motif Nuclear Localized gene and dehydrins might play an important role in response to salt stress in B. halophila. Our results provide an important gene resource to breed salt tolerant plants and useful information for further elucidation of the molecular mechanism of salt tolerance in B. halophila

Identification, Molecular Cloning and Expression Analysis of Five RNA-Dependent RNA Polymerase Genes in Salvia miltiorrhiza

RNA-dependent RNA polymerases (RDRs) act as key components of the small RNA biogenesis pathways and play significant roles in post-transcriptional gene silencing (PTGS) and antiviral defense. However, there is no information about the RDR gene family in Salvia miltiorrhiza, an emerging model medicinal plant with great economic value. Through genome-wide predication and subsequent molecular cloning, five full-length S. miltiorrhiza RDR genes, termed SmRDR1–SmRDR5, were identified. The length of SmRDR cDNAs varies between 3,262 (SmRDR5) and 4,130 bp (SmRDR3). The intron number of SmRDR genes varies from 3 (SmRDR1, SmRDR3 and SmRDR4) to 17 (SmRDR5). All of the deduced SmRDR protein sequences contain the conserved RdRp domain. Moreover, SmRDR2 and SmRDR4 have an additional RRM domain. Based on the phylogenetic tree constructed with sixteen RDRs from Arabidopsis, rice and S. miltiorrhiza, plant RDRs may be divided into four groups (RDR1–RDR4). The RDR1 group contains an AtRDR and an OsRDR, while includes two SmRDRs. On the contrary, the RDR3 group contains three AtRDRs and two OsRDRs, but has only one SmRDR. SmRDRs were differentially expressed in flowers, leaves, stems and roots of S. miltiorrhiza and responsive to methyl jasmonate treatment and cucumber mosaic virus infection. The results suggest the involvement of RDRs in S. miltiorrhiza development and response to abiotic and biotic stresses. It provides a foundation for further studying the regulation and biological functions of SmRDRs and the biogenesi

Conserved motifs of SmRDRs proteins identified with the MEME search tool.

<p>Motifs are represented by boxes. The numbers (1–20) and different colors in boxes represent motif 1–motif 20, respectively. Box size indicates the length of motifs. Broken lines indicate locations of the RdRp domain.</p

Phylogenetic relationships of sixteen RDRs from <i>S. miltiorrhiza</i>, <i>Arabidopsis</i> and rice.

<p>The relationships were analyzed for deduced full-length amino acid sequences using MEGA 4.0 by the neighbor-joining (NJ) method with 1000 bootstrap replicates. Bootstrap values are shown near the nodes. Four groups of RDRs, termed RDR1, RDR2, RDR3 and RDR4, respectively, are indicated. The number of introns in open reading frame (ORF) of the corresponding <i>RDR</i> gene is shown in parentheses.</p

<i>SmRDRs</i> responsive to CMV infection.

<p>The expression patterns were analyzed using the quantitative RT-PCR method. PCR was carried out in triplicates for each biological sample. Three independent biological replicates were performed. <i>SmUBQ10</i> was used as a reference. Fold changes of <i>SmRDRs</i> in leaves of <i>S. miltiorrhiza</i> plantlets infected with CMV for 12, 24, 48 and 72 h are shown. The level of transcripts in leaves inoculated with phosphate buffered saline (CK) was arbitrarily set to 1 and the level in tissues inoculated with CMV was given relative to this. Error bars represent standard deviations of mean value from three biological replicates.</p

<i>SmRDRs</i> responsive to MeJA treatment.

<p>The expression patterns were analyzed using the quantitative RT-PCR method. PCR was carried out in triplicates for each biological sample. Three independent biological replicates were performed. <i>SmUBQ10</i> was used as a reference. Fold changes of <i>SmRDRs</i> in leaves of <i>S. miltiorrhiza</i> plantlets treated with MeJA for 12, 24, 36 and 48 h are shown. The level of transcripts in leaves treated with sterile water (CK) was arbitrarily set to 1 and the level in tissues treated with MeJA was given relative to this. Error bars represent standard deviations of mean value from three biological replicates.</p

Gene structures of <i>S. miltiorrhiza SmRDRs</i>.

<p>Filled boxes represent exons with coding regions in green and 5′- and 3′-UTRs in blue. The connecting lines represent introns.</p

Alignment of partial sequences of RDR proteins in <i>S. miltiorrhiza</i> and <i>Arabidopsis</i> using T-coffee.

<p>The DLDGD/DFDGD signature is boxed. Different colors represent the quality of alignment with red for the highest quality, yellow for average, and green for the worst.</p