The complete chloroplast genome of Castanopsis hystrix Hook. f. & Thomson ex A. DC. 1863 (Fagaceae).

Castanopsis hystrix Hook. f. & Thomson ex A. DC. 1863 (Fagaceae) is an evergreen broad-leaved tree with high economic and ecological value. In this study, the complete chloroplast genome of C. hystrix was sequenced, assembled and annotated. The plastome (plastid genome) of C. hystrix was 160,624 bp in size, consisting of a pair of inverted repeats (IRs, 25,699 bp), a large-single-copy (LSC, 90,276 bp) region, and a small-single-copy (SSC, 18,950 bp). The overall GC content of C. hystrix was 36.8%. A total of 133 genes were annotated, including 88 protein-coding genes (PCG), 37 transfer RNA genes (tRNA), and eight ribosomal RNA genes (rRNA). A maximum likelihood analysis showed that the Castanopsis species form a monophyletic clade. C. hystrix is most closely related to C. tibetana with 100% bootstrap support value. The result enriches the genomic data for the genus Castanopsis, which will contribute to future studies in phylogenetics and evolution.

The complete chloroplast genome sequence and phylogenetic analysis of Nanhaia speciosa (Fabaceae).

Nanhaia speciosa (Fabaceae) is a woody perennial vine used as an important traditionally Chinese medicine. In this study, the complete chloroplast genome of Nanhaia speciosa was sequenced and assembled. The chloroplast genome of N. speciosa was 132,551bp in length including only one copy of the inverted repeat (IR). It encoded a total of 110 genes, containing 76 protein-coding genes, 30 tRNA and 4 rRNA. The overall GC content was 34.1%. Phylogenetic analysis using a matrix of 69 protein-coding genes illustrated that N. speciosa is most closely related to Wisteriopsis reticulata of tribe Wisterieae.

The complete chloroplast genome sequence of chaya (Cnidoscolus aconitifolius) and phylogenetic analysis.

Cnidoscolus aconitifolius is a leafy green heathy vegetable and medicinal plant belongs to the family Euphorbiaceae. In the present study, we sequenced the complete chloroplast genome of C. aconitifolius, which is 158,658 bp in length and consisted of two copies of inverted repeat (IR) of 26,982 bp separated by a large single copy (LSC) of 87,022 bp and a small single copy (SSC) of 17,672 bp. The GC content of C. aconitifolius was 36.3%. A total of 130 genes were predicted, including 86 protein-coding genes, 36 tRNAs and 8 rRNAs. The plastid phylogenomic analysis support C. aconitifolius is closely related to Manihot esculenta.

Characterization of the complete chloroplast genome of the Taiwan alder Alnus formosana (Betulaceae) based on next-generation sequencing technology.

Alnus formosana (Betulaceae) is an important ecological and economic deciduous tree species widely distributed throughout subtropical regions of Taiwan province, China. At the present study, the complete chloroplast genome of A. formosana was assumbled using next-generation sequencing technology. The complete chloroplast sequence is 161,029 bp in length, which consisted of a large single copy (LSC, 89,720 bp) and a small single copy (SSC; 19,205 bp) separated a pair of inverted repeats (IRs; 26,052 bp). The overall guanine-cytosine (GC) content was 36.4%. A total of 131 genes were annotated, including 85 protein-coding genes, 37 tRNAs, eight rRNAs and one pseudogene (ψycf1). The phylogenetic analysis fully resolved A. formosana in a clade with A. japonica. The plastome of A. formosana will provide informative genomic resources for further phylogenetic application and genetic improvement.

Identification of binding domains and key amino acids involved in the interaction between BmLARK and G4 structure in the BmPOUM2 promoter in Bombyx mori.

It has been found that the non-B form DNA structures, like G-quadruplex (G4) and i-motif, are involved in many important biological processes. Our previous study showed that the silkworm transcription factor BmLARK binds to the G4 structure in the promoter of the transcription factor BmPOUM2 and regulates its promoter activity. However, the binding mechanism between BmLARK and BmPOUM2 G4 structure remains unclear. In this study, binding domains and key amino acid residues involved in the interaction between BmLARK and BmPOUM2 G4 were studied. The electrophoretic mobility shift assay results indicated that the two RNA-recognition motifs (RRM) of BmLARK are simultaneously required for the binding with the G4 structure. Either RRM1 or RRM2 alone could not bind with the G4 structure. The zinc-finger motif was not involved in the binding. A series of mutant proteins with specific amino acid mutations were expressed and used to identify the key amino acid residues involving the interaction. The results indicated that ß sheets, especially the ß1 and ß3 sheets, in the RRM domains of BmLARK played critical roles in the binding with the G4 structure. Several amino acid mutations of RRM1/2 in ribonucleoprotein domain 1 (RNP1) (motif in ß3 strand) and RNP2 (motif in ß1 strand) caused loss of binding ability, indicating that these amino acids are the key sites for the binding. All the results suggest that RRM domains, particularly their the RNP1 and RNP2 motifs, play important roles not only in RNA recognition, but also in the G4 structure binding.

Genomics- and Peptidomics-Based Discovery of Conserved and Novel Neuropeptides in the American Cockroach.

As a model hemimetabolous insect species and an invasive urban pest that is globally distributed, the American cockroach, Periplaneta americana, is of great interest in both basic and applied research. Previous studies on P. americana neuropeptide identification have been based on biochemical isolation and molecular cloning. In the present study, an integrated approach of genomics- and peptidomics-based discovery was performed for neuropeptide identification in this insect species. First, 67 conserved neuropeptide or neurohormone precursor genes were predicted via an in silico analysis of the P. americana genome and transcriptome. Using a large-scale peptidomic analysis of peptide extracts from four different tissues (the central nervous system, corpora cardiac and corpora allata complex, midgut, and male accessory gland), 35 conserved (predicted) neuropeptides and a potential (novel) neuropeptide were then identified. Subsequent experiments revealed the tissue distribution, sex difference, and developmental patterns of two conserved neuropeptides (allatostatin B and short neuropeptide F) and a novel neuropeptide (PaOGS36577). Our study shows a comprehensive neuropeptidome and detailed spatiotemporal distribution patterns, providing a solid basis for future functional studies of neuropeptides in the American cockroach (data are available via ProteomeXchange with identifier PXD021660).

Effects of ADAM10 deletion on Notch-1 signaling pathway and neuronal maintenance in adult mouse brain.

A disintegrin and metalloproteinase 10 (ADAM10) has been demonstrated to regulate embryonic brain development by initiating Notch signaling. However, it is still unclear whether ADAM10 is required to activate the Notch signaling pathway in adult brain. To investigate the physiological role of ADAM10, we generated conditional knockout (cKO) mice lacking the Adam10 gene primarily in the cortex and hippocampus. We found that conditional disruption of ADAM10 resulted in a prominent decrease in the number of proliferating neuronal progenitor cells in the subgranular zone (SGZ), and a significant increase in the number of adult-generated postmitotic neurons in the hippocampal dentate gyrus (DG) due to premature neuronal differentiation. Moreover, the mutant mice also displayed an age-dependent reduction in the number of granule neurons in the hippocampal DG. It was further showed that the activation of Notch-1 and its downstream target genes Hes1, Hes5, Hey1, and Hey2 was impaired in ADAM10-deficient hippocampal tissues. Finally, Adam10 cKO mice had impaired learning and memory in the Morris water-maze. Thus, we provided experimental evidence to demonstrate that ADAM10 plays an essential role in the activation of Notch-1 signaling and has a remarkable effect on neuronal maintenance in adult mouse brain.

[Generation and characterization of the adult neuron-specific ADAM10 knock-out mice].

A disintegrin and metalloproteinase 10 (ADAM10) is a major sheddase for over 30 different membrane proteins and gets involved in such physiological processes and pathogenesis as embryonic development, cell adhesion, signal transduction, immune reaction, cancer, and Alzheimer's disease. Both ADAM10 knock-out mice and the neural progenitor cell-specific ADAM10 knock-out mice having been reported so far died in the embryonic or perinatal stage, respectively, thus resulting in the failure to investigate ADAM10 function in the adult mouse brain. Through a series of tests, we have succeeded in generating and characterizing the CaMKIIα-Cre/ADAM10(loxP/loxP) mice surviving until adulthood by means of crossing ADAM10(loxP/loxP) mice with newly generated CaMKIIα-Cre transgenic mice. PCR analysis of genomic DNAs from different regions of the ADAM10 cKO mouse brain shows that the deleted ADAM10 alleles are mainly found in the cortex and hippocampus. Real-time RT-PCR findings further confirm that ADAM10 mRNAs decrease in the cortex and hippocampus by 55.7% and 60.8%, respectively. Western-blotting analysis demonstrates 63% and 84.8% loss of mature ADAM10 proteins from the cortex and hippocampus. Immunohistochemical tests show that there is significantly less ADAM10- positive staining in the cortical and hippocampal neurons but not gliocytes of ADAM10 cKO mice compared with control mice. In summary, we established the adult neuron-specific ADAM10 knock-out (cKO) mice for the first time, which prevented ADAM10(-/-) mice from the embryonic and perinatal mortality and laid a firm foundation for the further study of ADAM10 function in the brain of adult mice in vivo.