BackgroundmicroRNA166 (miR166) is a highly conserved family of miRNAs implicated in a wide range of cellular and physiological processes in plants. miR166 family generally comprises multiple miR166 members in plants, which might exhibit functional redundancy and specificity. The soybean miR166 family consists of 21 members according to the miRBase database. However, the evolutionary conservation and functional diversification of miR166 family members in soybean remain poorly understood.ResultsWe identified five novel miR166s in soybean by data mining approach, thus enlarging the size of miR166 family from 21 to 26 members. Phylogenetic analyses of the 26 miR166s and their precursors indicated that soybean miR166 family exhibited both evolutionary conservation and diversification, and ten pairs of miR166 precursors with high sequence identity were individually grouped into a discrete clade in the phylogenetic tree. The analysis of genomic organization and evolution of MIR166 gene family revealed that eight segmental duplications and four tandem duplications might occur during evolution of the miR166 family in soybean. The cis-elements in promoters of MIR166 family genes and their putative targets pointed to their possible contributions to the functional conservation and diversification. The targets of soybean miR166s were predicted, and the cleavage of ATHB14-LIKE transcript was experimentally validated by RACE PCR. Further, the expression patterns of the five newly identified MIR166s and 12 target genes were examined during seed development and in response to abiotic stresses, which provided important clues for dissecting their functions and isoform specificity.ConclusionThis study enlarged the size of soybean miR166 family from 21 to 26 members, and the 26 soybean miR166s exhibited evolutionary conservation and diversification. These findings have laid a foundation for elucidating functional conservation and diversification of miR166 family members, especially during seed development or under abiotic stresses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-017-0983-9) contains supplementary material, which is available to authorized users.

SUMMARY SPLAYED (SYD) is a SWItch/Sucrose Non‐Fermentable (SWI/SNF)‐type chromatin remodeler identified in Arabidopsis thaliana (Arabidopsis). It is believed to play both redundant and differential roles with its closest homolog BRAHMA (BRM) in diverse plant growth and development processes. To better understand how SYD functions, we profiled the genome‐wide occupancy of SYD and its impact on the global transcriptome and trimethylation of histone H3 on lysine 27 (H3K27me3). To map the global occupancy of SYD, we generated a GFP‐tagged transgenic line and used it for chromatin immunoprecipitation experiments followed by next‐generation sequencing, by which more than 6000 SYD target genes were identified. Through integrating SYD occupancy and transcriptome profiles, we found that SYD preferentially targets to nucleosome‐free regions of expressed genes. Further analysis revealed that SYD occupancy peaks exhibit five distinct patterns, which were also shared by BRM and BAF60, a conserved SWI/SNF complex component, indicating the common target sites of these SWI/SNF chromatin remodelers and the functional relevance of such distinct patterns. To investigate the interplay between SYD and Polycomb‐group (PcG) proteins, we performed a genome‐wide analysis of H3K27me3 in syd‐5. We observed both increases and decreases in H3K27me3 levels at a few hundred genes in syd‐5 compared to wild type. Our results imply that SYD can act antagonistically or synergistically with PcG at specific genes. Together, our SYD genome‐wide occupancy data and the transcriptome and H3K27me3 profiles provide a much‐needed resource for dissecting SYD’s crucial roles in the regulation of plant growth and development.

Color change is an important event during fruit maturation in blueberry, usually depending on chlorophyll degradation and anthocyanin accumulation. miR156/SPL modules are an important group of regulatory hubs involved in the regulation of anthocyanin biosynthesis. However, little is known regarding the roles of miR156/SPLs in blueberry and chlorophyll metabolism during color change. In this study, a MIR156 gene (VcMIR156a) was experimentally identified in blueberry. Overexpression of VcMIR156a in tomato enhanced anthocyanin biosynthesis and chlorophyll degradation in the stem via altering pigment-associated gene expression. Further investigation indicated that the VcSPL12 transcript could be targeted by miR156, and they showed the reverse accumulation patterns during blueberry fruit development and maturation. Noticeably, VcSPL12 was highly expressed at green fruit stages, while VcMIR156a transcripts mainly accumulated at the white fruit stage when VcSPL12 was dramatically decreased, implying that VcMIR156a/VcSPL12 is a key regulatory hub during fruit coloration. Moreover, VcSPL12 decreased the expression of several anthocyanin biosynthetic and regulatory genes, and a Y2H assay indicated that VcSPL12 interacted with VcMYBPA1. Intriguingly, VcSPL12 significantly enhanced chlorophyll accumulation and altered the expression of several chlorophyll-associated genes. Additionally, the chloroplast ultrastructure was altered by VcMIR156a and VcSPL12. These findings provide a novel insight into the functional roles of miR156/SPLs in plants, especially blueberry fruit coloration.

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The endosperm provides nutrients and growth regulators to the embryo during seed development. LEAFY COTYLEDON1 (LEC1) has long been known to be essential for embryo maturation. LEC1 is expressed in both the embryo and the endosperm; however, the functional relevance of the endosperm-expressed LEC1 for seed development is unclear. Here, we provide genetic and transgenic evidence demonstrating that endosperm-expressed LEC1 is necessary and sufficient for embryo maturation. We show that endosperm-synthesized LEC1 is capable of orchestrating full seed maturation in the absence of embryo-expressed LEC1. Inversely, without LEC1 expression in the endosperm, embryo development arrests even in the presence of functional LEC1 alleles in the embryo. We further reveal that LEC1 expression in the endosperm begins at the zygote stage and the LEC1 protein is then trafficked to the embryo to activate processes of seed maturation. Our findings thus establish a key role for endosperm in regulating embryo development.

Porcine epidemic diarrhea virus (PEDV), which re-emerged in China since 2010, has swept across the whole country leading to tremendous economic losses. In this study, a total of 645 diarrhea samples collected from 156 pig farms in Sichuan and Guizhou province during 2014-2018 were tested for PEDV. We found that samples from 47.66% (84/156) of the farms were positive for PEDV with an overall detection rate of 35.81% (231/645). Fifty-two strains were selected for full-length S gene analyses, and these strains were classified into three subgroups, an S-INDEL subgroup (G1c), and two non-S-INDEL subgroups (G2b, AJ1102-like and G2c), accounting for 15.38% (8/52), 23.08% (12/52) and 59.62% (31/52) of the total analysed strains, respectively. We found these three subgroups of PEDV coexisted in Sichuan province, and the S-INDEL strain was detected in Guizhou. Further antigenic variation analysis of the neutralizing epitopes (S10, COE, SS2, SS6 and 2C10) on the spike protein revealed that the S-INDEL and non-S-INDEL strains shared similar variation features in COE and SS6, but exhibited distinct variation patterns in the S10 domain. Unique variation patterns on N-glycosylation sites in the S protein were also observed for the S-INDEL and non-S-INDEL strains. Moreover, nine strains (three from each subgroup) were subjected to full-genome characterization.Complete genome phylogeny showed an inconsistent tree topology for genotyping, with two G2c strains grouped into the GII-b (AH2012-like) genogroup and the remaining seven strains including three S-INDEL strains grouped into the GII-c genogroup. Further recombination analyses indicated that six of the GII-c strains probably originated from intra-genogroup recombinations. Notably, three newly emerged S-INDEL strains with novel recombination patterns were first identified. Together, our data revealed a new status of PEDV in southwest China, which can increase understanding of the prevalence, genetic characteristics and evolutionary profiles of circulating PEDV strains in China.

Aux/IAA genes are an important class of players in diverse developmental processes in plants, which generally exert their functions through the auxin signaling pathway. Blueberry is an economically and nutritionally important berry-bearing crop. However, Aux/IAA genes remain unknown in blueberry. In the present study, an Aux/IAA gene (VcIAA27) was identified and characterized in blueberry, and it is most closely related to IAA27 in other plant species. Expression analysis indicated that VcIAA27 transcripts accumulate highly in shoot, flower and fruit. Interestingly, VcIAA27 was highly expressed at early fruit developmental stages, and dramatically decreased from the onset of fruit ripening, implying that VcIAA27 possibly plays important roles during fruit enlargement. Meanwhile, the analysis of promoter activity in Arabidopsis showed that strong GUS signal was detected in the trichome and hydathodes of leaves, receptacle of silique, and lateral roots of seedling. Overexpression of VcIAA27 in Arabidopsis leads to auxin-related defects such as downward-curled leaves, short or sterile siliques, shorter stature, and more shoot branches. Moreover, qPCR analysis indicated that VcIAA27 is able to alter the expression patterns of the auxin-related genes BRU6, SAG13, SAUR26 in Arabidopsis, suggesting that VcIAA27 might be negatively involved in the auxin signaling pathway. The findings will greatly contribute to future investigation of Aux/IAA-mediated mechanisms that control blueberry development, especially fruit development and ripening.

Members of the Mi14-3-3 gene family interact with target proteins that are widely involved in plant hormone signal transduction and physiology-related metabolism and play important roles in plant growth, development and stress responses. In this study, 14-3-3s family members are identified by the bioinformatic analysis of the mango (Mangifera indica L.) genome. The gene structures, chromosomal distributions, genetic evolution, and expression patterns of these genes and the physical and chemical properties and conserved motifs of their proteins are analysed systematically. The results identified 16 members of the 14-3-3 genes family in the mango genome. The members were not evenly distributed across the chromosomes, and the gene structure analysis showed that the gene sequence length and intron number varied greatly among the different members. Protein sequence analysis showed that the Mi14-3-3 proteins had similar physical and chemical properties and secondary and tertiary structures, and protein subcellular localization showed that the Mi14-3-3 family proteins were localized to the nucleus. The sequence analysis of the Mi14-3-3s showed that all Mi14-3-3 proteins contain a typical conserved PFAM00244 domain, and promoter sequence analysis showed that the Mi14-3-3 promoters contain multiple hormone-, stress-, and light-responsive cis-regulatory elements. Expression analysis showed that the 14-3-3 genes were expressed in all tissues of mango, but that their expression patterns were different. Drought, salt and low temperature stresses affected the expression levels of 14-3-3 genes, and different 14-3-3 genes had different responses to these stresses. This study provides a reference for further studies on the function and regulation of Mi14-3-3 family members.