Integrative analysis of the RNA interference toolbox in two Salicaceae willow species, and their roles in stress response in poplar (Populus trichocarpa Torr. & Gray)

Genome-Wide Identification and Characterization of Argonaute, Dicer-like and RNA-Dependent RNA Polymerase Gene Families and Their Expression Analyses in Fragaria spp

In the growth and development of plants, some non-coding small RNAs (sRNAs) not only mediate RNA interference at the post-transcriptional level, but also play an important regulatory role in chromatin modification at the transcriptional level. In these processes, the protein factors Argonaute (AGO), Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) play very important roles in the synthesis of sRNAs respectively. Though they have been identified in many plants, the information about these gene families in strawberry was poorly understood. In this study, using a genome-wide analysis and a phylogenetic approach, 13 AGO, six DCL, and nine RDR genes were identified in diploid strawberry Fragaria vesca. We also identified 33 AGO, 18 DCL, and 28 RDR genes in octoploid strawberry Fragaria × ananassa, studied the expression patterns of these genes in various tissues and developmental stages of strawberry, and researched the response of these genes to some hormones, finding that almost all genes respond to the five hormone stresses. This study is the first report of a genome-wide analysis of AGO, DCL, and RDR gene families in Fragaria spp., in which we provide basic genomic information and expression patterns for these genes. Additionally, this study provides a basis for further research on the functions of these genes and some evidence for the evolution between diploid and octoploid strawberries.

Evolution and function of ubiquitin-specific proteases (UBPs): Insight into seed development roles in tung tree (Vernicia fordii)

The tung oil produced by the tung tree (Vernicia fordii) provides resources for the manufacture of biodiesel. Ubiquitin-specific proteases (UBPs) are the largest group of deubiquitinases and play key roles in regulating development and stress responses. Here, 21 UBPs were identified in V. fordii, roughly one-half the number found in Manihot esculenta and Hevea brasiliensis. Most UBP duplications are produced from whole-genome duplication (WGD), and significant differences in gene retention existed among Euphorbiaceae. The great majority of UBP-containing blocks in V. fordii, V. montana, Ricinus communis, and Jatropha curcas exhibited extensive conservation with the duplicated regions of M. esculenta and H. brasiliensis. These blocks formed 14 orthologous groups, indicating they shared WGD with UBPs in M. esculenta and H. brasiliensis, but most of these UBPs copies were lost. The UBP orthologs contained significant functional divergence which explained the susceptibility of V. fordii to Fusarium wilt and the resistance of V. montana to Fusarium wilt. The expression patterns and experiments suggested that Vf03G1417 could affect the seed-related traits and positively regulate the seed oil accumulation. This study provided important insights into the evolution of UBPs in Euphorbiaceae and identified important candidate VfUBPs for marker-assisted breeding in V. fordii.

Integrative Analysis of the DICER-like (DCL) Genes From Peach (Prunus persica): A Critical Role in Response to Drought Stress

DICER-likes (DCLs) proteins are the core component for non-coding RNA (ncRNA) biogenesis, playing essential roles in some biological processes. The DCL family has been characterized in model plants, such as Arabidopsis, rice, and poplar. However, the evolutionary aspect and the expression mechanism under drought stress were scarce and have never been reported and characterized in one of the most important worldwide cultivated fruit trees, peach (Prunus persica). Eight DCLs genes in the Prunus persica genome were detected, in addition to 51 DCLs in the other seven Rosaceae genomes. The phylogenetic analysis with Arabidopsis thaliana and RTL1 gene as outgroups suggested that DCL members are divided into four clades: DCL1, DCL2, DCL3, and DCL4 with several gene gain/loss events of DCL gene copies through the evolutionary tract of the Rosacea family. The number of homologous DCL copies within each clade, along with the chromosomal location indicated gene duplication event of the DCL2 gene occurred once for the subfamily Amygdaloideae and twice for Pyrus communis and Prunus dulics and trice for the P. persica on Chromosome number 7 genes. Another duplication event was found for the DCL3 gene that occurred once for all the eight Rosaceae species with no match in A. thaliana. The DCL genetic similarity and activity was evaluated using BLASTp and previously published RNA-seq data among different tissues and over different time points of peach trees exposed to drought conditions. Finally, the expression pattern of PrupeDCLs in response to drought stress was identified, and two of these members, Prupe.7G047900 and Prupe.6G363600, were found as main candidate genes for response to drought stress. Our data presented here provide useful information for a better understanding of the molecular evolution of DCL genes in Rosaceae genomes, and the function of DCLs in P. persica.

Systematic analysis of the Serine/Arginine-Rich Protein Splicing Factors (SRs) and focus on salt tolerance of PtSC27 in Populus trichocarpa

Serine/Arginine-Rich Protein Splicing Factors (SRs) are indispensable splicing factors, which play significant roles in spliceosome assembly, splicing regulation and regulation of plant stress. However, a comprehensive analysis and function research of SRs in the woody plant is still lacking. In this report, we conducted the identification and comprehensive analysis of the 71 SRs in poplar and three other dicots, including basic characterization, phylogenetic, conserved motifs, gene duplication, promoter and splice isoform of these genes. Based on the publicly available transcriptome data, expression pattern of SRs in poplar under low temperature, high temperature, drought and salt stress were further analyzed. Subsequently, a key candidate gene PtSC27 that responded to salt stress was screened. More importantly, overexpression of PtSC27 increased plant survival rate under salt stress, and enhanced salt tolerance by regulating malondialdehyde (MDA) content, peroxidase (POD) and catalase (CAT) enzyme activities in transgenic plants. Meanwhile, overexpression of PtSC27 made transgenic plants insensitive to exogenous ABA and improved the expression of some ABA signal-related genes under salt stress. Overall, our studies lay a foundation for understanding the structure and function of SRs in the poplar and provide useful gene resources for breeding through genetic engineering.

Genome-Wide Identification and Evolutionary Analysis of Argonaute Genes in Hexaploid Bread Wheat

Argonaute (AGO) proteins play a pivotal role in plant growth and development as the core components of RNA-induced silencing complex (RISC). However, no systematic characterization of AGO genes in wheat has been reported to date. In this study, a total number of 69 TaAGO genes in the hexaploid bread wheat (Triticum aestivum cv. Chinese Spring) genome, divided into 10 subfamilies, were identified. Compared to all wheat genes, TaAGOs showed a significantly lower evolutionary rate, which is consistent with their high conservation in eukaryotes. However, the homoeolog retention was remarkably higher than the average, implying the nonredundant biological importance of TaAGO genes in bread wheat. Further homoeologous gene expression bias analyses revealed that TaAGOs may have undergone neofunctionalization after polyploidization and duplication through the divergent expression of homoeologous gene copies, to provide new opportunities for the generation of adaptive traits. Moreover, quantitative real-time polymerase chain reaction (qRT-PCR) analyses indicated that TaAGO gene expression was involved in response to heat, drought, and salt stresses. Our results would provide a theoretical basis for future studies on the biological functions of TaAGO genes in wheat and other gramineous species.

Deciphering the roles of leucine-rich repeat receptor-like protein kinases (LRR-RLKs) in response to Fusarium wilt in the Vernicia fordii (Tung tree)

Leucine-rich repeat receptor-like protein kinases (LRR-RLKs) are vital for plant growth and development, signal transduction, immunity, and play diverse roles in plant defense responses. However, the LRR-RLK genes have not been systematically studied in Vernicia fordii (tung tree), especially its response to Fusarium wilt. Here, we carried out an integrative analysis of LRR-RLKs among five Euphorbiaceae species: Hevea brasiliensis (rubber tree), Manihot esculenta (cassava), Jatropha curcas (physic nut), Ricinus communis (castor bean), and V. fordii, which contained 223, 311, 186, 138, and 167 LRR-RLKs, respectively. Maximum-likelihood tree was estimated using LRR-RLKs of Arabidopsis thaliana as a template, and they allowed us to divide Euphorbiaceae LRR-RLKs into 22 groups. There are 126 segmental and 30 tandem duplications in these Euphorbiaceae genomes by synteny analysis. The tissue-specific expression patterns revealed that V. fordii LRR-RLKs (VfLRR-RLKs) were differentially expressed in various tissues, and some of them exhibited specific expression in meristems tissues, which suggested their potential functions during organ formation and cell fate specification. Two VfLRR-RLK pairs (Vf01G2125 and Vf03G1740, Vf06G2687 and Vf10G1659), which generated by tandem duplication events, were associated with possible resistance to Fusarium wilt infection. The qRT-PCR confirmed these four VfLRR-RLKs contained opposite expression profiles during pathogen infection in V. fordii and V. montana. Taken together, our data systematically analyzed the LRR-RLK family in Euphorbiaceae genomes for the first time. We highlight the putative roles of VfLRR-RLKs in response to Fusarium wilt infection, and VfLRR-RLKs may be further applied in marker-assisted breeding to control Fusarium wilt in V. fordii.

SWEET Transporters and the Potential Functions of These Sequences in Tea (Camellia sinensis)

Tea (Camellia sinensis) is an important economic beverage crop. Its flowers and leaves could be used as healthcare tea for its medicinal value. SWEET proteins were recently identified in plants as sugar transporters, which participate in diverse physiological processes, including pathogen nutrition, seed filling, nectar secretion, and phloem loading. Although SWEET genes have been characterized and identified in model plants, such as Arabidopsis thaliana and Oryza sativa, there is very little knowledge of these genes in C. sinensis. In this study, 28 CsSWEETs were identified in C. sinensis and further phylogenetically divided into four subfamilies with A. thaliana. These identified CsSWEETs contained seven transmembrane helixes (TMHs) which were generated by an ancestral three-TMH unit with an internal duplication experience. Microsynteny analysis revealed that the large-scale duplication events were the main driving forces for members from CsSWEET family expansion in C. sinensis. The expression profiles of the 28 CsSWEETs revealed that some genes were highly expressed in reproductive tissues. Among them, CsSWEET1a might play crucial roles in the efflux of sucrose, and CsSWEET17b could control fructose content as a hexose transporter in C. sinensis. Remarkably, CsSWEET12 and CsSWEET17c were specifically expressed in flowers, indicating that these two genes might be involved in sugar transport during flower development. The expression patterns of all CsSWEETs were differentially regulated under cold and drought treatments. This work provided a systematic understanding of the members from the CsSWEET gene family, which would be helpful for further functional studies of CsSWEETs in C. sinensis.

Systematic analysis of the OFP genes in six Rosaceae genomes and their roles in stress response in Chinese pear (Pyrus bretschneideri)

OVATE family proteins (OFPs) are the plant-specific transcription factors, and have significant functions in regulating plant growth, development and resistance. The OFP genes have been investigated in several plants, but they still lack a systematic analysis of OFP genes in Chinese pear and some other five Rosaceae genomes. Here, 28 PbrOFPs were identified within Chinese pear and compared them with those of other five Rosaceae genomes. Evolutionary tree revealed that all OFP genes from six Rosaceae genomes were divided into eight groups. Seventeen conserved microsynteny regions were detected in Chinese pear genome, suggested that these PbrOFP genes might be considered to have originated from the large-scale duplication events., indicating these PbrOFP genes might contain specialized regulatory mechanisms in these tissues, such as flower, ovary and fruit. Remarkably, two PbrOFP genes (Pbr010426.1 and Pbr010427.1) were up-regulated under Venturia nashicola treatment, and five PbrOFP genes were up-regulated under PEG treatment, suggesting that these genes might play crucial roles in defence to environmental stresses. Our data presented a systematic analysis and might aid in the selection of appropriate PbrOFPs for further functional studies in Chinese pear, especially in response to the mechanism of biotic and abiotic stresses.