Piwi-interacting RNAs (piRNAs) are important for repressing transposable elements (TEs) and modulating gene expression in germ cells, thereby maintaining genome stability and germ cell function. Although they are also important for maintaining germline stem cells (GSCs) in the Drosophila ovary by repressing TEs and preventing DNA damage, piRNA expression has not been investigated in GSCs or their early progeny. Here, we show that the canonical piRNA clusters are more active in GSCs and their early progeny than late germ cells and also identify more than 3,000 new piRNA clusters from deep sequencing data. The increase in piRNAs in GSCs and early progeny can be attributed to both canonical and newly identified piRNA clusters. As expected, piRNA clusters in GSCs, but not those in somatic support cells (SCs), exhibit ping-pong signatures. Surprisingly, GSCs and early progeny express more TE transcripts than late germ cells, suggesting that the increase in piRNA levels may be related to the higher levels of TE transcripts in GSCs and early progeny. GSCs also have higher piRNA levels and lower TE levels than SCs. Furthermore, the 3′ UTRs of 171 mRNA transcripts may produce sense, antisense, or dual-stranded piRNAs. Finally, we show that alternative promoter usage and splicing are frequently used to modulate gene function in GSCs and SCs. Overall, this study has provided important insight into piRNA production and TE repression in GSCs and SCs. The rich information provided by this study will be a beneficial resource to the fields of piRNA biology and germ cell development.

Acacia koa A. Gray, an economically important timber-wood tree growing in the Hawaiian Islands, is affected by many environmental stresses, including drought, strong wind, heavy rain, and infection by fungal pathogens. Previous studies have shown that some morphological and biochemical changes that take place as a result of environmental stresses in plants can be also induced by mechanical stresses such as touching and bending. We studied morphological and biochemical changes and levels of gene transcription in A. koa plants due to mechanical stress. For a mechanical stress treatment, A. koa seedlings were gently bent in four cardinal directions daily for 2–6 months, after which morphological and biochemical changes were quantified. The stressed A. koa had significantly increased stem diameter, number of xylem cells, and anthocyanin and lignin contents and significantly reduced stem length. The gene expression analyses showed that 53 genes, including the genes for calcium signaling, ethylene biosynthesis, abscisic acid degradation, stress-related transcriptional regulation, and disease resistance, were induced more than twofold within 10–60 min following mechanical stress. The observation that the genes for disease resistance such as NBS-LRR can be induced by mechanical stress suggests that strong wind and rain in the natural forest may also induce disease resistance in trees.

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Acacia koa is a leguminous timber tree endemic to the Hawaiian Islands. For breeding projects involved in improving wood quality of A. koa, understanding of genes influencing wood quality is crucial. Therefore, the objective of this study was to identify A. koa genes in the monolignol biosynthesis pathway, which is involved in wood formation and development. In this study, whole transcritpome sequencing of A. koa seedlings was performed through Illumina-based sequencing and over 88 million high-quality paired-end raw reads were generated. Trinity de novo assembly of those reads yielded 85,533 unigenes with an average length of 641 bp. Based on sequence similarity search with known proteins, we annotated 47,038 of the unigenes. Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 149 unigenes were assigned to ortholog groups of enzymes involved in the monolignol biosynthesis pathway. In addition, we identified complete coding sequences of genes for all the ten identified enzymes of the pathway. Future studies on expression levels of these genes in A. koa with different wood qualities will provide a tool for selection of desirable types. Comprehensive sequence resources of A. koa generated through this study will contribute to genomic studies and improvement programs for this tree.

Leucaena leucocephala (leucaena) is a fast-growing tree legume highly tolerant to various abiotic and biotic stresses. Because of its abilities to withstand high temperature and prolonged drought and to grow as a disease-free plant, it is an interesting model plant to investigate genetics of stress resistance. The high-level stress resistance may be correlated with higher expression of certain genes in the root, which is the primary site for nutrient and water uptake and also infection by soil-borne pathogens. The objectives of this study were to characterize the transcriptome of leucaena and to identify root-specific genes that may be involved in drought tolerance and disease resistance. Transcriptomes of leucaena were analyzed through Illumina-based sequencing and de novo assembly, which generated 62,299 and 61,591 unigenes (≥500 bp) from the root and shoot, respectively. Through a 4 x 180k microarray analysis, the expression of 10,435 unigenes were compared between the root and shoot. Upregulated sequences in the root were mostly represented by unigenes that were related to secondary metabolism, while in the shoot, upregulated sequences were mostly represented by unigenes that were involved in carbohydrate and lipid metabolism. The unigenes sharing homology with terpenoid biosynthesis genes and a nicotianamine synthase gene were upregulated more than 100-fold in the root, which indicates that these genes may have important roles in high stress tolerance of leucaena. Cataloging of actively transcribed sequences in the root and shoot will lead to identification of genes for drought tolerance and disease resistance in leucaena.