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Main conclusion: This study compared the plastomes of Ulmaceae allowing analyses of the dynamic evolution, including genome structure, codon usage bias, repeat sequences, molecular mutation rates, and phylogenetic inferences. Ulmaceae is a small family in the order Rosales. This family consists of seven genera, including Ulmus, Zelkova, Planera, Hemiptelea, Phyllostylon, Ampelocera, and Holoptelea. Ulmaceae is an interesting lineage from plant biogeographic, systematic, evolutionary, and paleobotanic perspectives. It is also a good model to investigate the evolution of the plastomes in woody plants. In this study, we sequenced and assembled the complete plastomes of the six Ulmaceae genera to compare genomic structures and reveal the molecular evolutionary patterns. The size of the quadripartite plastomes ranged from 158,290 bp to 161,886 bp. The genomes contained 131 genes, including 87 coding genes, 36 tRNA, and 8 rRNA. The gene number, gene content, and genomic structure were highly consistent among the Ulmaceae genera. Nine variable regions including ndhA intron, ndhF-rpl32, ycf1, psbK-trnS,rps16-trnQ, trnT-trnL, trnT-psbD, trnS-trnG, and rpl32-trnL, were identified in Ulmaceae plastomes according to the nucleotide diversity values. Condon usage was biased among the genes and showed consistent trends in the seven genera. Molecular evolution analyses revealed that most of the genes and all gene groups were under widespread purifying selection. Twelve genes (ccsA, matK, psbH, psbK, rbcL, rpl22, rpl32, rpoA, rps12, rps15, rps16, and ycf2) were under positive selection. Phylogenetic analyses supported that Ulmaceae should be divided into two main clades, such as the temperate clade, including Ulmus, Zelkova, Planera, and Hemiptelea and the tropical clade, including Phyllostylon, Ampelocera and Holoptelea. This study reports the structure and evolutionary characteristics of the Elm family. These new genomic data will benefit assessments of genomic evolution and provide information to elucidate the phylogenetic relationships among Ulmaceae species. [ABSTRACT FROM AUTHOR]

As a specialized seed appendage, the aril is a noteworthy and taxonomically important feature of Celastrus orbiculatus; the aril also has important ornamental value and biological functions. To better understand the mechanism of aril development, paraffin sections were used to examine its morphogenesis, and RNA-sequencing (RNA-seq) technology was employed for transcriptional profiling of the developing aril. Our results revealed that the aril of C. orbiculatus was formed by the cells of the exostomal region of the outer integument. By analyzing global changes in the transcriptome, 41,560,806, 42,789,340, and 44,496,748 clean reads from three cDNA libraries were generated and assembled into 87,600 unigenes with N50 of 1328 bp, in which 31,971 (36.49%) were annotated to Nr database. Furthermore, a total of 25,914 (29.79%), 14,394 (16.4%) and 11,957 (13.65%) genes were successfully annotated with hierarchical 48 GO terms, 26 KOGs and 32 KEGG pathways. Totally, 104, 1887 and 1967 differently expressed genes were identified in CO-F2 versus CO-F3, CO-F2 versus CO-YF1 and CO-F3 versus CO-YF1, respectively. GO and KEGG pathway analyses of DEGs involved in cell-cell communication and plant hormone signal transduction contributed to aril development were identified. Furthermore, we found putative key target genes of WRKY, Aux/IAA, ARF and MADS-box family's transcription factors related to aril development. Real-time qPCR was performed on eight genes randomly selected from important transcription factors to validate the expression profiles obtained by RNA-seq. This work provides a platform for future genetic and functional genomics research on the molecular mechanisms of aril structure, and expands our understanding of the molecular mechanism and evolutionary analysis of aril development in other members of the Celastraceae. [ABSTRACT FROM AUTHOR]