Aquilaria sinensis (Lour.) Gilg is an important medicinal woody plant producing agarwood, which is widely used in traditional Chinese medicine. High-throughput sequencing of chloroplast (cp) genomes enhanced the understanding about evolutionary relationships within plant families. In this study, we determined the complete cp genome sequences for A. sinensis. The size of the A. sinensis cp genome was 159,565 bp. This genome included a large single-copy region of 87,482 bp, a small single-copy region of 19,857 bp, and a pair of inverted repeats (IRa and IRb) of 26,113 bp each. The GC content of the genome was 37.11%. The A. sinensis cp genome encoded 113 functional genes, including 82 protein-coding genes, 27 tRNA genes, and 4 rRNA genes. Seven genes were duplicated in the protein-coding genes, whereas 11 genes were duplicated in the RNA genes. A total of 45 polymorphic simple-sequence repeat loci and 60 pairs of large repeats were identified. Most simple-sequence repeats were located in the noncoding sections of the large single-copy/small single-copy region and exhibited high A/T content. Moreover, 33 pairs of large repeat sequences were located in the protein-coding genes, whereas 27 pairs were located in the intergenic regions. Aquilaria sinensis cp genome bias ended with A/T on the basis of codon usage. The distribution of codon usage in A. sinensis cp genome was most similar to that in the Gonystylus bancanus cp genome. Comparative results of 82 protein-coding genes from 29 species of cp genomes demonstrated that A. sinensis was a sister species to G. bancanus within the Malvales order. Aquilaria sinensis cp genome presented the highest sequence similarity of >90% with the G. bancanus cp genome by using CGView Comparison Tool. This finding strongly supports the placement of A. sinensis as a sister to G. bancanus within the Malvales order. The complete A. sinensis cp genome information will be highly beneficial for further studies on this traditional medicinal plant. Moreover, the results will enhance our understanding about the evolution of cp genomes of the Malvales order, particularly with regard to the role of A. sinensis in plant systematics and evolution.

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Background Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few late SE-related genes have been identified and the molecular regulation mechanisms of late SE are still not well understood. Results In this study, the transcriptomes of embryogenic callus (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, 85.92% of them were mapped to the rubber tree genome. The de novo assembly generated 36,937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs were mainly involved in the phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors (AUX-like1, GH3.1, SAUR32-like, IAA9-like, IAA14-like, IAA27-like, IAA28-like and ARF5-like). The transcription factors including WRKY40, WRKY70, MYBS3-like, MYB1R1-like, AIL6 and bHLH93-like were characterized as molecular markers for rubber tree late SE. CML13, CML36, CAM-7, SERK1 and LEAD-29-like were also related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE. Conclusions This study provides important information to elucidate the molecular regulation during rubber tree late SE.

Lychee is rich in a 22-kDa VSP with trypsin inhibitor activity. The VSP plays an important role in nitrogen storage while its possible defensive function remains to be elucidated.

It was generally assumed that the accumulation of vegetative storage protein (VSP) in poplar trees and/or temperate hardwoods did not occur in spring. To test this assumption, the accumulation of the 32-kDa VSP and the differential expression of a gene encoding for the protein in poplars were investigated using light and electron microscopy, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and reverse transcription-polymerase chain reaction (RT-PCR). We report, for the first time, that poplar trees initiated VSP accumulation in new shoots during the development of new shoots in spring under conditions of high temperature and long days. The amount of 32-kDa VSP increased gradually in the stem of new shoots and in two-year-old branches, but there were no detectable changes in its abundance in the bark tissues of trunks during new shoot development. Based on the presence of a 286-bp DNA fragment that is identical to the VSP gene bspA, encoding for the 32-kDa VSP in Populus deltoids Bartr. ex Marsh., the differential expression of the 32-kDa VSP gene in P. canadensis Moench was revealed by RT-PCR. The results indicated that the 32-kDa VSP gene was expressed strongly in new shoots, relative weakly in twoyear-old branches and was not expressed in the trunk during new shoot development. This pattern of VSP accumulation and VSP gene space-time differential expression may be an important mechanism by which stored nitrogen compounds are used preferentially to exogenously available nitrogen and, in addition, the dynamic pattern may also have a role in the regulation of nitrogen metabolism, especially nitrogen uptake by the roots.