Search

Chinese fir (Cunninghamia lanceolata) is an important coniferous species that accounts for 20–30% of the total commercial timber production in China. Though traditional breeding of Chinese fir has achieved remarkable success, molecular-assisted breeding has made little progress due to limited availability of genomic information. In this study, a survey of Chinese fir genome was performed using the Illumina HiSeq Xten sequencing platform. K-mer analysis indicated that Chinese fir has a large genome of approximately 11.6 Gb with 74.89% repetitive elements and is highly heterozygous. Meanwhile, its genome size was estimated to be 13.2 Gb using flow cytometry. A total of 778.02 Gb clean reads were assembled into 10,982,272 scaffolds with an N50 of 1.57 kb. In total, 362,193 SSR loci were detected with a frequency of 13.18 kb. Dinucleotide repeats were the most abundant (up to 73.6% of the total SSRs), followed by trinucleotide and tetranucleotide repeats. Forty-six polymorphic pairs were developed, and 298 alleles were successfully amplified from 199 Chinese fir clones. The average PIC value was 0.53, indicating that the identified genomic SSR (gSSR) markers have a high degree of polymorphism. In addition, these breeding resources were divided into three groups, and a limited gene flow existed among these inferred groups.

Inorganic phosphate (Pi) is often lacking in natural and agro-climatic environments, which impedes the growth of economically important woody species. Plants have developed strategies to cope with low Pi (LP) availability. MicroRNAs (miRNAs) play important roles in responses to abiotic stresses, including nutrition stress, by regulating target gene expression. However, the miRNA-mediated regulation of these adaptive responses and their underlying coordinating signals are still poorly understood in forestry trees such as Betula luminifera. Transcriptomic libraries, small RNA (sRNA) libraries, and a mixed degradome cDNA library of B. luminifera roots and shoots treated under LP and normal conditions (CK) were constructed and sequenced using next-generation deep sequencing. A comprehensive B. luminifera transcriptome derived from its roots and shoots was constructed, and a total of 76,899 unigenes were generated. Analysis of the transcriptome identified 8,095 and 5,584 differentially expressed genes in roots and shoots, respectively, under LP conditions. sRNA sequencing analyses indicated that 66 and 60 miRNAs were differentially expressed in roots and shoots, respectively, under LP conditions. A total of 109 and 112 miRNA–target pairs were further validated in the roots and shoots, respectively, using degradome sequencing. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differential miRNA targets indicated that the “ascorbate and aldarate metabolism” pathway responded to LP, suggesting miRNA-target pairs might participating in the removing of reactive oxidative species under LP stress. Moreover, a putative network of miRNA–target interactions involved in responses to LP stress in B. luminifera is proposed. Taken together, these findings provide useful information to decipher miRNA functions and establish a framework for exploring P signaling networks regulated by miRNAs in B. luminifera and other woody plants. It may provide new insights into the genetic engineering of high use efficiency of Pi in forestry trees.

Background MADS-box genes encode a large family of transcription factors that play significant roles in plant growth and development. Bamboo is an important non-timber forest product worldwide, but previous studies on the moso bamboo (Phyllostachys edulis) MADS-box gene family were not accurate nor sufficiently detailed. Results Here, a complete genome-wide identification and characterization of the MADS-box genes in moso bamboo was conducted. There was an unusual lack of type-I MADS-box genes in the bamboo genome database (http://202.127.18.221/bamboo/index.php), and some of the PeMADS sequences are fragmented and/or inaccurate. We performed several bioinformatics techniques to obtain more precise sequences using transcriptome assembly. In total, 42 MADS-box genes, including six new type-I MADS-box genes, were identified in bamboo, and their structures, phylogenetic relationships, predicted conserved motifs and promoter cis-elements were systematically investigated. An expression analysis of the bamboo MADS-box genes in floral organs and leaves revealed that several key members are involved in bamboo inflorescence development, like their orthologous genes in Oryza. The ectopic overexpression of one MADS-box gene, PeMADS5, in Arabidopsis triggered an earlier flowering time and the development of an aberrant flower phenotype, suggesting that PeMADS5 acts as a floral activator and is involved in bamboo flowering. Conclusion We produced the most comprehensive information on MADS-box genes in moso bamboo. Additionally, a critical PeMADS gene (PeMADS5) responsible for the transition from vegetative to reproductive growth was identified and shown to be related to bamboo floral development. Electronic supplementary material The online version of this article (10.1186/s12870-018-1394-2) contains supplementary material, which is available to authorized users.

We identified a set of ecotype-specific cold-responsive genes, providing candidate genes for enhancing cold resistance in Phoebe bournei (Hemsl.) Yang and other woody plants. Phoebe bournei (Hemsl.) Yang is an indigenous, endangered, precious timber and ornamental tree in China. Cold stress greatly affects the survival of Phoebe species. To elucidate the molecular mechanisms of cold response and identify candidate genes for improving cold resistance, we used RNA-Seq and qRT-PCR to compare the transcriptomic profiles of two ecotypes of P. bournei, cold-resistant Wuyuan (WY) and cold-sensitive Wuping (WP), under cold stress. A total of 3970 and 4433 genes were differentially expressed in WY and WP, respectively, with 2030 differentially expressed genes (DEGs) were specific to WY. Specifically, the categories “defense response”, “secondary metabolites”, and “ABC transporters” were enriched among WY-specific DEGs. Several transcription factor genes might involve in cold stress response, including RAP2-3, NAC2, NAC43, WRKY47, and WRKY51, were induced only in WY, and CBF3, ZAT10, MYB308, and WER exhibited greater cold stress-induced expression changes in WY compared with WP, which may partially explain the distinct transcriptomic changes induced by cold stress between the two ecotypes. Greater fold changes in the expression of starch metabolism-related genes such as BAM1/3 and lower fold changes in the expression of DPE2 were detected in WY, which was consistent with its greater abundance of total soluble sugars. The stronger transcriptional differentiation of related genes under cold stress in WY may explain its greater cold resistance compared with the WP ecotype, providing important genetic resources for improving cold-resistant characteristics in P. bournei. In addition, two interaction networks were constructed, resulting in identification of a series of hub genes, which facilitates functional dissection of the molecular mechanisms involved in the response to cold stress of P. bournei and extends our ability to improve cold resistance in this valued species.

This paper proposes a miRNA-mediated regulatory network of heat stress response in a tree, Betula luminifera. Plants are sessile organisms that must gauge stressful conditions to ensure survival and reproductive success. In nature, plants often encounter chronic or recurring abiotic stresses, such as heat stress, although the strategies to cope with high temperature are poorly understood in woody plants. In this study, we investigated the potential roles of microRNAs (miRNAs) in heat stress response in Betula luminifera. Using next-generation deep sequencing, we identified a total of 206 miRNAs, comprising 115 known and 84 novel miRNAs, and seven potential miRNA candidates. Of these miRNAs, 98 (57 known and 41 novel miRNAs) were differentially expressed under heat stress. A total of 101 miRNA-target pairs consisting of 44 miRNAs and 71 target genes were verified by degradome sequencing. Target annotation suggested that these miRNAs might be important in the regulation of specific stress-responsive genes, including many transcription factors and a series of genes encoding important enzymes of functional proteins targeted by miRNAs. Further functional analysis suggested that these target genes were related to protein synthesis, transport and turnover, cell wall organization, protein folding, antioxidation, defense response, and modulation of attenuated plant growth and development under heat stress. The expression patterns of 15 randomly selected miRNAs derived from quantitative reverse transcription PCR had similar trends as those derived from high-throughput sequencing, as well as the expression patterns of six target genes under heat stress. These results improve our understanding of the miRNA-mediated regulatory network of heat stress response in B. luminifera, which will contribute to improving heat stress-resistant breeding in woody plants.

Two efficient somatic embryogenesis systems were developed in Chinese fir, the most important conifer for industrial wood production in China. Three development stages (cleavage polyembryony, dominant embryo, and precotyledon) of immature embryos derived from 25 genotypes of open-pollinated mother trees were used as initial explants. Cleavage polyembryony-stage embryos with a 12.44% induction rate was the most embryogenic response stage. The highest frequency of embryogenic callus (13.86%) induction was obtained from DCR medium supplemented with 1.5 mg L−1 2,4-dichlorophenoxyacetic acid (2,4-D) and 0.3 mg L−1 kinetin (KN). An average of 53.33 early somatic embryos were produced from approximately 0.2 g (fresh weight) embryogenic callus after 2 weeks of incubation on medium supplemented with 50 μmol L−1 abscisic acid (ABA) and 100 g L−1 polyethylene glycol (PEG) 6000. About 53% dominant embryos have an embryogenic response after a 6-week cultivation on medium supplemented with 1.0–2.0 mg L−1 benzyladenine (BA), 0.2 mg L−1 naphthylacetic acid (NAA) or 2,4-D, and 0.004 mg L−1 thidiazuron (TDZ). After three successive transfer cultures on medium supplemented with 1.5 mg L−1 BA, 0.2 mg L−1 NAA, and 0.004 mg L−1 TDZ, 4.49–16.51% of the embryos developed into somatic embryos.

To understand how historical and environmental factors have shaped genetic diversity and spatial genetic patterns of tree species, we characterized the genetic diversity and the genetic structure of a coniferous species, Cryptomeria japonica, which is distributed in Japan (two taxonomic groups) and some parts of southeastern China (C. japonica var. sinensis). We investigated population samples for three groups using high-throughput SNP genotyping, sequencing of multiple genes, and then estimated level of genetic diversity, the genetic differentiation, and the divergence time between the three groups. We also investigated the natural distribution during LGM using species distribution modeling. The genetic variation in the Chinese population, var. sinensis, was lower compared to Japanese populations but it harbored some unique genotypes. The species distribution modeling showed that the Chinese population has decreased since Last Glacial Maximum (LGM) because of lower precipitation than present time, but in Japan the favored environment have remained available for this species even in the LGM. Estimated divergence times of the three groups mostly correspond with the time since the Last Glacial. Our data supports the hypothesis that the glacial period, particularly limitations associated with precipitation, strongly influenced the distribution of C. japonica populations. Our findings suggest that climate change plays an important role in speciation processes of C. japonica.

Glycosyltransferase (GT) plays a pivotal role in cell wall biosynthesis in plants. Galacturonosyltransferase-like (GATL) genes, belonging to the GT8 family, have been proven to be involved in pectin and/or xylan biosynthesis of the cell wall. Here, we identified eight GATL genes from the Eucalyptus grandis genome and characterized the gene structure and chromosomal location. The genes were found to be distributed across five chromosomes, including two pairs in block duplication regions. None of the EgrGATL genes contained introns. And, with the exception of EgrGATL8, the remainder of the EgrGATL proteins possessed the three classic motifs characteristic of all GATL proteins. Expression analysis in the different tissues showed that EgrGATL1, EgrGATL4, and EgrGATL8 were highly expressed in xylem and phloem; EgrGATL6 exhibited the highest expression in leaves, and in phloem and leaves, EgrGATL2 and EgrGATL3 both exhibited very low expression. However, the abiotic stress response of plants can be affected by changes in the components and structure of the cell wall. The expression patterns of EgrGALTs under low-temperature, high-temperature, drought, salinity, and abscisic acid (ABA) treatments were assessed by qRT-PCR. The results showed that most of the EgrGATL genes could be induced under low temperature, and some were even able to increase their expression level under high temperature. Under drought conditions, the expression levels of most of the genes initially increased and then decreased. Similar expression patterns were observed in leaves under treatment with NaCl and ABA. Our results provide fundamental information towards the functional dissection of EgrGATL genes and their potential involvement in improving plant abiotic stress tolerance.

BackgroundBetula luminiferaH. Winkler, which is widely distributed in southern China, is an economically important broadleaf tree species. However, little genomic information ofB.luminiferais available, and little is known about the molecular mechanisms of wood formation in this species. Meanwhile, few efforts have focused on investigating the early transcriptional changes during tension wood formation in woody plants.ResultsA reference transcriptome dataset was first generated containing 45,700 Unigenes, and 35,135 (76.9%) Unigenes were annotated by a BLAST similarity search against four public databases. Then, based on an anatomical investigation, the global gene expression changes during the early stages of tension wood formation were analyzed. Gene expression profiling showed that a total of 13,273 Unigenes were differentially regulated during the early stages of tension wood formation. Most genes involved in cellulose and lignin biosynthesis were highlighted to reveal their biological importance in tension wood formation. In addition, the transcription levels of many genes involved in the auxin response pathway were significantly changed during the early stages of tension wood formation. Furthermore, 18 TFs co-expressed with key enzymes of cellulose synthesis were identified.ConclusionsOur results revealed the transcriptional changes associated with TW formation and identified potential key genes in the regulation of this process. These results will help to dissect the molecular mechanism of wood formation and provide key candidate genes for marker-assisted selection inB. luminifera.

microRNAs (miRNAs) play vital roles in plants regulating a panoply of biological processes, such as development, hormone signaling, and stress response, by inhibiting target genes at the post-transcriptional level. However, the roles of miRNAs in Betula luminifera remain elusive. To mine for B. luminifera miRNAs and targets, we used a deep sequencing approach to analyze the sRNAs and degradome sequencing of mixed samples, including roots, stems, and leaves. A total of 114 known miRNAs or miRNA*s from 44 families, and 24 novel miRNAs and 17 miRNA*s plus 15 plausible miRNA candidates were identified, of which 36 known miRNAs, 29 miRNA*s, and all novel miRNAs had precursor sequences. Additionally, 49 targets for 19 known miRNA families and seven miRNA*s, and seven targets for novel miRNAs were identified using a high-throughput degradome-sequencing approach. The conserved miRNA targets were mainly transcription factors, whereas the miRNA* targets were mainly protein-coding genes, with preferential propensity to functional enzymes. A Gene Ontology analysis showed that the predicted targets were classified into 62 biological processes, 20 cellular components, and 28 molecular functions, respectively. We found two different targets for miR396a* and miR396c*, and the target changed when the miR156d precursor cleavage site was shifted toward the 5′-end by two nucleotides, indicating the diverse regulatory roles of MIRNA genes. Furthermore, three targets identified by degradome sequencing were validated further through 5′ rapid amplification of cDNA ends. The expression patterns of the randomly selected miRNAs varied among different tissues. miR164 expression was induced under nitrogen starvation, with tissue-specific expression patterns, and was negatively correlated with the NAC1 target gene in roots and leaves, but not in stems. This study is a transcriptome-based analysis of miRNAs and the degradome, providing useful information to explore the functions of miRNAs and their target genes in B. luminifera.