Chromosome‐level genome assembly of an important pine defoliator,Dendrolimus punctatus (Lepidoptera; Lasiocampidae)

Dendrolimus spp. are important destructive pests of conifer forests, and Dendrolimus punctatus Walker (Lepidoptera; Lasiocampidae) is the most widely distributed Dendrolimus species. During periodic outbreaks, this species is said to make “fire without smoke” because large areas of pine forest can be quickly and heavily damaged. Yet, little is known about the molecular mechanisms that underlie the unique ecological characteristics of this forest insect. Here, we combined Pacific Biosciences (PacBio) RSII single‐molecule long reads and high‐throughput chromosome conformation capture (Hi‐C) genomics‐linked reads to produce a high‐quality, chromosome‐level reference genome for D. punctatus. The final assembly was 614 Mb with contig and scaffold N50 values of 1.39 and 22.15 Mb, respectively, and 96.96% of the contigs anchored onto 30 chromosomes. Based on the prediction, this genome contained 17,593 protein‐coding genes and 56.16% repetitive sequences. Phylogenetic analyses indicated that D. punctatus diverged from the common ancestor of Hyphantria cunea, Spodoptera litura and Thaumetopoea pityocampa ~ 108.91 million years ago. Many gene families that were expanded in the D. punctatus genome were significantly enriched for the xenobiotic biodegradation system, especially the cytochrome P450 gene family. This high‐quality, chromosome‐level reference genome will be a valuable resource for understanding mechanisms of D. punctatus outbreak and host resistance adaption. Because this is the first Lasiocampidae insect genome to be sequenced, it also will serve as a reference for further comparative genomics.     

Cell-type action specificity of auxin on Arabidopsis root growth

The plant hormone auxin plays a critical role in root growth and development; however, the contributions or specific roles of cell-type auxin signals in root growth and development are not well understood. Here, we mapped tissue and cell types that are important for auxin-mediated root growth and development by manipulating the local response and synthesis of auxin. Repressing auxin signaling in the epidermis, cortex, endodermis, pericycle or stele strongly inhibited root growth, with the largest effect observed in the endodermis. Enhancing auxin signaling in the epidermis, cortex, endodermis, pericycle or stele also caused reduced root growth, albeit to a lesser extent. Moreover, we established that root growth was inhibited by enhancement of auxin synthesis in specific cell types of the epidermis, cortex and endodermis, whereas increased auxin synthesis in the pericycle and stele had only minor effects on root growth. Our study thus establishes an association between cellular identity and cell type-specific auxin signaling that guides root growth and development.     

Congestive heart failure in COX2 deficient rats

Non-steroidal anti-inflammatory drugs (NSAIDs) inhibit prostaglandin (PG) formation by targeting cyclooxygenase (COX) 1 and 2.Long-term use of NSAIDs that selectively inhibit COX2 increases the risk for thrombotic events,cardiac failure,and hypertension.However,the underlying mechanisms remain unclear.In this study,COX1- and COX2-deficient rats were created via Cas9/RNA-mediated gene targeting.DNA genotyping and Western blot analysis confirmed successful generation of COX1~(-/-)and COX2~(-/-)rats.Adult COX1~(-/-)rats grew normally,while more than 70%of COX2~(-/-)rats after wean died within 2 months.Echocardiography showed markedly reduced left ventricular ejection fraction and fractional shortening in adult COX2~(-/-)rats compared to those in wildtype (WT) controls.Histological analysis revealed accumulation of inflammatory cells and severe interstitial and perivascular fibrosis in COX2~(-/-)cardiac tissues.Moreover,cardiac ATP and acetyl-Co A production was dramatically decreased in COX2~(-/-)rats.Consistently,the expression of genes related to mitochondrial oxidation,such as those that encode for subunits of pyruvate dehydrogenase complex and acyl Co A dehydrogenases,were downregulated,while glycolytic hexokinase 1 (HK1) was upregulated in COX2~(-/-)heart tissues.These observations indicate that COX2-deficient rats developed spontaneously heart failure,likely as a result of dysregulated cardiac energy metabolism.     

Extensive profiling of the expressions of tRNAs and tRNA-derived fragments (tRFs) reveals the complexities of tRNA and tRF populations in plants

Evidence is emerging that t RNA-derived fragments(t RFs) are regulatory molecules. Studies of t RFs in plants have been based on conventional small RNA sequencing, and focused on profiling of t RF-5 and t RF-3 species. A more comprehensive and quantitative analysis of the entire t RF population is highly necessary. Here, we employ t RNA-seq and YAMAT-seq, and develop a bioinformatics tool to comprehensively profile the expressions of t RNAs and t RFs in plants. We show that in Arabidopsis,approximately half of t RNA genes are extremely weakly expressed, accounting for only 1% of total t RNA abundance, while～12% of t RNA genes contribute to ～80% of t RNA abundance. Our t RNA sequencings in various plants reveal that t RNA expression profiles exhibit a cross-species conserved pattern. By characterizing the composition of a highly heterogeneous t RF population, we show that t RNA halves and previously unnoticed 10–16-nt tiny t RFs represent substantial portions. The highly accumulated 13-nt and 16-nt tiny t RFs in Arabidopsis indicate that tiny t RFs are not random t RNA degradation products. Finally,we provide a user-friendly database for displaying the dynamic spatiotemporal expressions of t RNAs and t RFs in the model plants Arabidopsis and rice.