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Whole-mount in situ hybridization (WISH) is a useful method for detecting specific gene expression patterns at their site of action during embryonic development. Traditional WISH methods are costly and suitable only for mouse embryos younger than 11.5 days. We present here an economical and practical in situ hybridization method using DIG-labeled RNA probes. We changed the conditions in several steps to make the WISH method suitable for whole mouse embryos from embryonic days 9.5 to 12.5 and for older stage mouse embryonic organs. We performed all steps in one microcentrifuge tube up to the staining steps to avoid losing or damaging the mouse embryos. We re-used the solutions and materials to make the method more economical and suitable for less sophisticated laboratories. We also performed β-galactosidase staining on Tb × 18 Cre/Rosa26/LacZ mouse embryos; the results agreed with the in situ hybridization results. Finally, we sectioned the specimens after hybridization and β-galactosidase staining; the results agreed with the literature. [ABSTRACT FROM AUTHOR]

Metabolic reprogramming precedes most alterations during pathological cardiac hypertrophy and heart failure (HF). Recent studies have revealed that Phosphofructokinase, platelet (PFKP) has a wealth of metabolic and non-metabolic functions. In this study, we explored the role of PFKP in cardiac hypertrophic growth and HF. The expression level of PFKP was elevated both in pathological cardiac remodeling mouse model challenged by transverse aortic constriction (TAC) surgery and in the neonatal rat cardiomyocytes (NRCMs) stimulated by phenylephrine (PE). In global PFKP knockout (PFKP-KO) mice, cardiac hypertrophy was ameliorated under TAC surgery, while overexpression of PFKP by intravenous injection of adeno-associated virus 9 (AAV9) under the cardiac troponin T (cTnT) promoter worsened myocardial hypertrophy and fibrosis. In NRCMs, small interfering RNA (SiRNA) knockdown or adenovirus (Adv) overexpression of PFKP was employed and the intervention of PFKP showed a similar phenotype. Mechanistically, immunoprecipitation combined with liquid chromatography-tandem mass spectrometry (IP-MS/MS) analysis was used to identify the interacting proteins of PFKP. Eukaryotic translation initiation factor 2 subunit beta (EIF2S2) was identified as the downstream target of PFKP. In the PE-stimulated NRCM hypertrophy model and mouse TAC model, knocking down EIF2S2 after PFKP overexpression reduced the synthesis of new proteins and alleviated the hypertrophy phenotype. Our findings illuminate that PFKP participates in pathological cardiac hypertrophy partly by regulating protein synthesis through EIF2S2, which provides a new clue for the involvement of metabolic intermediates in signal transduction., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

Objective: To investigate the effect of 20/4Hz transcutaneous auricular vagus nerve stimulation (taVNS) on anxiety symptoms in Parkinson's disease (PD) and the potential neural mechanism., Methods: In the current randomized, double-blind, sham-controlled trial, 30 PD patients with anxiety (PD-A), 30 PD patients without anxiety (PD-nA), and 30 healthy controls (HCs) were enrolled. PD-A patients were randomly (1:1) allotted to real taVNS stimulation group (RS) or sham stimulation group (SS) to explore the efficacy of a two-week treatment of taVNS to promote anxiety recovery. Simultaneously, all participants were measured activation in the bilateral prefrontal cortex during verbal fluency task (VFT) using functional near-infrared spectroscopy., Results: PD-A patients showed significantly decreased oxyhemoglobin in the left triangle part of the inferior frontal gyrus (IFG) during VFT, which was negatively related to the severity of anxiety symptoms. After two-week treatment of taVNS, the interaction of group and time had significant effect on HAMA scores (F = 18.476, p < 0.001, η 2  = 0.398). In RS group, compared with baseline, HAMA scores decreased significantly in the post-treatment and follow-up condition (both p < 0.001). Meanwhile, in RS group, HAMA scores were lower than those in SS group in the post-treatment and follow-up condition (p = 0.006, <0.001, respectively). Furthermore, the 20/4Hz taVNS remarkably ameliorated anxiety symptoms in PD patients, directly correlated with the increased activation of the left triangle part of the IFG during VFT in RS group., Conclusion: Our results depicted that taVNS could ameliorate the anxiety symptoms of PD-A patients and regulated the function of the left triangle part of the IFG., Competing Interests: Declaration of competing interest Authors declare no conflict of interest., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Camellia crapnelliana Tutch., belonging to the Theaceae family, is an excellent landscape tree species with high ornamental values. It is particularly an important woody oil-bearing plant species with high ecological, economic, and medicinal values. Here, we first report the chromosome-scale reference genome of C. crapnelliana with integrated technologies of SMRT, Hi-C and Illumina sequencing platforms. The genome assembly had a total length of ~2.94 Gb with contig N50 of ~67.5 Mb, and ~96.34% of contigs were assigned to 15 chromosomes. In total, we predicted 37,390 protein-coding genes, ~99.00% of which could be functionally annotated. The chromosome-scale genome of C. crapnelliana will become valuable resources for understanding the genetic basis of the fatty acid biosynthesis, and greatly facilitate the exploration and conservation of C. crapnelliana., (© 2024. The Author(s).)

AP2 / ERF transcription factor family plays an important role in plant development and stress responses. Previous studies have shed light on the evolutionary trajectory of the AP2 and DREB subfamilies. However, knowledge about the evolutionary history of the ERF subfamily in angiosperms still remains limited. In this study, we performed a comprehensive analysis of the ERF subfamily from 107 representative angiosperm species by combining phylogenomic and synteny network approaches. We observed that the expansion of the ERF subfamily was driven not only by whole-genome duplication (WGD) but also by tandem duplication (TD) and transposition duplication events. We also found multiple transposition events in Poaceae, Brassicaceae, Poales, Brassicales, and Commelinids. These events may have had notable impacts on copy number variation and subsequent functional divergence of the ERF subfamily. Moreover, we observed a number of ancient tandem duplications occurred in the ERF subfamily across angiosperms, e.g., in Subgroup IX, IXb originated from ancient tandem duplication events within IXa. These findings together provide novel insights into the evolution of this important transcription factor family.

The pentatricopeptide repeat ( PPR ) gene family is one of the largest gene families in land plants. However, current knowledge about the evolution of the PPR gene family remains largely limited. In this study, we performed a comparative genomic analysis of the PPR gene family in O. sativa and its wild progenitor, O. rufipogon , and outlined a comprehensive landscape of gene duplications. Our findings suggest that the majority of PPR genes originated from dispersed duplications. Although segmental duplications have only expanded approximately 11.30% and 13.57% of the PPR gene families in the O. sativa and O. rufipogon genomes, we interestingly obtained evidence that segmental duplication promotes the structural diversity of PPR genes through incomplete gene duplications. In the O. sativa and O. rufipogon genomes, 10 (~33.33%) and 22 pairs of gene duplications (~45.83%) had non- PPR paralogous genes through incomplete gene duplication. Segmental duplications leading to incomplete gene duplications might result in the acquisition of domains, thus promoting functional innovation and structural diversification of PPR genes. This study offers a unique perspective on the evolution of PPR gene structures and underscores the potential role of segmental duplications in PPR gene structural diversity.

Cyclin-dependent kinase 12 (CDK12) has been found to regulate tumor progression. However, its function in gastric carcinoma (GC) remains controversial. This work aimed to explore the exact effect of CDK12 on GC progression. We detected the expression of CDK12 in GC cells and normal gastric mucosal epithelial cells. Then CDK12 function on GC cell proliferation, migration, and angiogenesis was researched by colony formation experiment, Transwell experiment, and angiogenesis assay. Moreover, CDK12 effect on the PI3K/AKT/mTOR pathway activity was explored by western blot. Further, we used LY294002 (10 μM) to treat GC cells to verify whether CDK12 regulates GC progression by activating the PI3K/AKT/mTOR pathway. Additionally, CDK12 effect on the expression of prognostic factors of GC was detected by western blot, including alkaline phosphatase (ALP) and Ki67. Quantitative real-time polymerase chain reaction and western blot were utilized to evaluate the expression of mRNAs and proteins. As a result, CDK12 was upregulated in GC cells. CDK12 overexpression facilitated the proliferation, migration, and angiogenesis of GC cells. However, CDK12 silencing showed an opposite result. CDK12 overexpression activated the PI3K/AKT/mTOR pathway, but CDK12 silencing inactivated it in GC cells. The blockage of the PI3K/AKT/mTOR pathway induced by LY294002 treatment counteracted the promotion of CDK12 on the proliferation, migration, and angiogenesis of GC. Further, CDK12 silencing suppressed the expression of ALP and Ki67 proteins in GC cells. Taken together, CDK12 promotes the proliferation, migration, and angiogenesis of GC by activating the PI3K/AKT/mTOR pathway. It may be a novel target for GC treatment., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Background: Biologists have long debated the drivers of the genome size evolution and variation ever since Darwin. Assumptions for the adaptive or maladaptive consequences of the associations between genome sizes and environmental factors have been proposed, but the significance of these hypotheses remains controversial. Eragrostis is a large genus in the grass family and is often used as crop or forage during the dry seasons. The wide range and complex ploidy levels make Eragrostis an excellent model for investigating how the genome size variation and evolution is associated with environmental factors and how these changes can ben interpreted., Methods: We reconstructed the Eragrostis phylogeny and estimated genome sizes through flow cytometric analyses. Phylogenetic comparative analyses were performed to explore how genome size variation and evolution is related to their climatic niches and geographical ranges. The genome size evolution and environmental factors were examined using different models to study the phylogenetic signal, mode and tempo throughout evolutionary history., Results: Our results support the monophyly of Eragrostis . The genome sizes in Eragrostis ranged from ~0.66 pg to ~3.80 pg. We found that a moderate phylogenetic conservatism existed in terms of the genome sizes but was absent from environmental factors. In addition, phylogeny-based associations revealed close correlations between genome sizes and precipitation-related variables, indicating that the genome size variation mainly caused by polyploidization may have evolved as an adaptation to various environments in the genus Eragrostis ., Conclusion: This is the first study to take a global perspective on the genome size variation and evolution in the genus Eragrostis . Our results suggest that the adaptation and conservatism are manifested in the genome size variation, allowing the arid species of Eragrostis to spread the xeric area throughout the world., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Hutang, Tong, Zhu and Gao.)

Genome size variation and evolutionary forces behind have been long pursued in flowering plants. The genus Oryza , consisting of approximately 25 wild species and two cultivated rice, harbors eleven extant genome types, six of which are diploid (AA, BB, CC, EE, FF, and GG) and five of which are tetraploid (BBCC, CCDD, HHJJ, HHKK, and KKLL). To obtain the most comprehensive knowledge of genome size variation in the genus Oryza , we performed flow cytometry experiments and estimated genome sizes of 166 accessions belonging to 16 non-AA genome Oryza species. k -mer analyses were followed to verify the experimental results of the two accessions for each species. Our results showed that genome sizes largely varied fourfold in the genus Oryza , ranging from 279 Mb in Oryza brachyantha (FF) to 1,203 Mb in Oryza ridleyi (HHJJ). There was a 2-fold variation (ranging from 570 to 1,203 Mb) in genome size among the tetraploid species, while the diploid species had 3-fold variation, ranging from 279 Mb in Oryza brachyantha (FF) to 905 Mb in Oryza australiensis (EE). The genome sizes of the tetraploid species were not always two times larger than those of the diploid species, and some diploid species even had larger genome sizes than those of tetraploids. Nevertheless, we found that genome sizes of newly formed allotetraploids (BBCC-) were almost equal to totaling genome sizes of their parental progenitors. Our results showed that the species belonging to the same genome types had similar genome sizes, while genome sizes exhibited a gradually decreased trend during the evolutionary process in the clade with AA, BB, CC, and EE genome types. Comparative genomic analyses further showed that the species with different rice genome types may had experienced dissimilar amplification histories of retrotransposons, resulting in remarkably different genome sizes. On the other hand, the closely related rice species may have experienced similar amplification history. We observed that the contents of transposable elements, long terminal repeats (LTR) retrotransposons, and particularly LTR/ Gypsy retrotransposons varied largely but were significantly correlated with genome sizes. Therefore, this study demonstrated that LTR retrotransposons act as an active driver of genome size variation in the genus Oryza ., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Dai, Zhu, Hutang, Li, Tian, Jiang, Zhang and Gao.)

Rosaceae comprises numerous types of economically important fruits, ornamentals, and timber. The lack of plastome characteristics has blocked our understanding of the evolution of plastome and plastid genes of Rosaceae crops. Using comparative genomics and phylogenomics, we analyzed 121 Rosaceae plastomes of 54 taxa from 13 genera, predominantly including Cerasus (true cherry) and its relatives. To our knowledge, we generated the first comprehensive map of genomic variation across Rosaceae plastomes. Contraction/expansion of inverted repeat regions and sequence losses of the two single-copy regions underlie large genomic variations in size among Rosaceae plastomes. Plastid protein-coding genes were characterized with a high proportion (over 50%) of synonymous variants and insertion-deletions with multiple triplets. Five photosynthesis-related genes were specially selected in perennial woody trees. Comparative genomic analyses implied divergent evolutionary patterns between pomaceous and drupaceous trees. Across all examined plastomes, unique and divergent evolution was detected in Cerasus plastomes. Phylogenomic analyses and molecular dating highlighted the relatively distant phylogenetic relationship between Cerasus and relatives ( Microcerasus , Amygdalus , Prunus , and Armeniaca ), which strongly supported treating the monophyletic true cherry group as a separate genus excluding dwarf cherry. High genetic differentiation and distinct phylogenetic relationships implied independent origins and domestication between fruiting cherries, particularly between Prunus pseudocerasus ( Cerasus pseudocerasus ) and P. avium ( C. avium ). Well-resolved maternal phylogeny suggested that cultivated P. pseudocerasus originated from Longmenshan Fault zone, the eastern edge of Himalaya-Hengduan Mountains, where it was subjected to frequent genomic introgression between its presumed wild ancestors and relatives., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Zhang, Wang, Chen, Chen, Wang, Liu, Wang, Xie, He, Li, Liu, Yang, Li, Lin, Zhang, Zhang, Luo, Tang, Gao and Wang.)

Photoperiod sensitivity is a dominant determinant for the phase transition in cereal crops. CCT ( CONSTANS, CO-like, and TOC1 ) transcription factors (TFs) are involved in many physiological functions including the regulation of the photoperiodic flowering. However, the functional roles of CCT TFs have not been elucidated in the wild progenitors of crops. In this study, we identified 41 CCT TFs, including 19 CMF , 17 COL , and five PRR TFs in Oryza rufipogon , the presumed wild ancestor of Asian cultivated rice. There are thirty-eight orthologous CCT genes in Oryza sativa , of which ten pairs of duplicated CCT TFs are shared with O. rufipogon . We investigated daily expression patterns, showing that 36 OrCCT genes exhibited circadian rhythmic expression. A total of thirteen OrCCT genes were identified as putative flowering suppressors in O. rufipogon based on rhythmic and developmental expression patterns and transgenic phenotypes. We propose that OrCCT08 , OrCCT24 , and OrCCT26 are the strong functional alleles of rice DTH2 , Ghd7 , and OsPRR37 , respectively. The SD treatment at 80 DAG stimulated flowering of the LD-grown O. rufipogon plants. Our results further showed that the nine OrCCT genes were significantly downregulated under the treatment. Our findings would provide valuable information for the construction of photoperiodic flowering regulatory network and functional characterization of the CCT TFs in both O. rufipogon and O. sativa ., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Peng, Tun, Dai, Li, Zhang, Yin, Yoon, Cho, An and Gao.)

The ultimate goal of genome assembly is a high-accuracy gapless genome. Here, we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui 63. The resulting 397.71-Mb final assembly is composed of 12 contigs with a contig N50 size of 31.93 Mb. Each chromosome is represented by a single contig and the genomic sequences of all chromosomes are gapless. Quality evaluation of this gapless genome assembly showed that gene regions in our assembly have the highest completeness compared with the other 15 reported high-quality rice genomes. Further comparison with the japonica rice genome revealed that the gapless indica genome assembly contains more transposable elements (TEs) and segmental duplications (SDs), the latter of which produce many duplicated genes that can affect agronomic traits through dose effect or sub-/neo-functionalization. The insertion of TEs can also affect the expression of duplicated genes, which may drive the evolution of these genes. Furthermore, we found the expansion of nucleotide-binding site with leucine-rich repeat disease-resistance genes and cis-zeatin-O-glucosyltransferase growth-related genes in SDs in the gapless indica genome assembly, suggesting that SDs contribute to the adaptive evolution of rice disease resistance and developmental processes. Collectively, our findings suggest that active TEs and SDs synergistically contribute to rice genome evolution., (Copyright © 2021 The Author. Published by Elsevier Inc. All rights reserved.)

Bromus catharticus Vahl. belongs to the Pooideae subfamily of Poaceae. In this study, we sequenced and assembled the complete chloroplast genome of B. catharticus. The complete chloroplast genome was 134,718 bp in size, including a large single-copy region of 80,540 bp, a small single-copy region of 11,806 bp and a pair of reverse repeats of 21,186 bp in size. The annotation of B. catharticus indicates that it contained 89 protein-coding genes, 47 tRNA genes and eight rRNA genes. Our phylogenetic analysis of all protein-coding genes of the 36 grass complete chroloplast genomes using Cyperus rotundus as outgroup showed that B. catharticus is closely related to the Koeleria and Avena species to form the Pooideae lineage of the grass family., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Arundo formosana Hack. belongs to the Arundionideae subfamily of Poaceae. In this study, we sequenced and assembled the complete chloroplast genome of A. formosana. The complete chloroplast genome was 136,919 bp in size, including a large single copy region of 82,039 bp, a small single-copy region of 12,108 bp and a pair of reverse repeats of 21,386 bp in size. The annotation of A. formosana indicates that it contained 81 protein-coding genes, 47 tRNA and 8 rRNA. Our phylogenetic analysis of the 36 grass complete chroloplast genomes of protein-coding genes using Cyperus rotundus as outgroup showed that A. formosana is closely related to Crinipes species to form the Arundionideae lineage of the grass family., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Eleusine coracana (L.) Gaertn. is a kind of highly adaptable cereal crop with a high nutritional value with the reputation of 'black pearl'. In this study, we sequenced, assembled and characterized the complete chloroplast genome of the grass species. The circular genome of E. coracana was 135,137 bp in length, which comprised two inverted repeat (IRa and IRb) regions of 20,919 bp in length separated by a large single copy (LSC) region of 80,663 bp and a small single copy (SSC) region of 12,636 bp. The total GC content of the E. coracana chloroplast genome was ∼38.13%. A total of 108 functional genes were predicted, including 76 protein-coding genes, 28 tRNA genes, and four rRNA genes. Our phylogenomic analysis of all protein-coding genes further revealed that E. coracana is closely related to Bouteloua curtipendula and B. gracilis , and they are together positioned in the subfamily Chloridoideae clade of the grass family., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Bonia amplexicaulis (L.C.Chia, H.L.Fung & Y.L.Yang) N.H.Xia is a member of the Bambusoideae subfamily in Poaceae. In this study, we sequenced, assembled and characterized the complete chloroplast genome of B. amplexicaulis. The complete chloroplast genome was 139,935 bp in size, including a large single copy region of 83,453 bp, a small single-copy region of 12,860 bp and a pair of reverse repeats of 21,811 bp in size. The annotation of the B. amplexicaulis chloroplast genome indicates that it contained 83 protein-coding genes, 36 tRNA genes and 8 rRNA genes. Our phylogenetic analysis of all protein-coding genes from the 36 complete chroloplast grass genomes using Cyperus rotundus as outgroup showed that B. amplexicaulis is closely related to Otatea glauca and Pariana campestris to form the Bambusoideae lineage of the grass family., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Bamboos are important nontimber forest plants widely distributed in the tropical and subtropical regions of Asia, Africa, America, and Pacific islands. They comprise the Bambusoideae in the grass family (Poaceae), including approximately 1700 described species in 127 genera. In spite of the widespread uses of bamboo for food, construction, and bioenergy, the gene repertoire of bamboo still remains largely unexplored. Raddia distichophylla (Schrad. ex Nees) Chase, belonging to the tribe Olyreae (Bambusoideae, Poaceae), is a diploid herbaceous bamboo with only slightly lignified stems. In this study, we report a draft genome assembly of the ∼589 Mb whole-genome sequence of R. distichophylla with a contig N50 length of 86.36 Kb. Repeat sequences account for ∼49.08% of the genome assembly, of which LTR retrotransposons occupy ∼35.99% of the whole genome. A total of 30,763 protein-coding genes were annotated in the R. distichophylla genome with an average transcript size of 2887 bp. Access to this herbaceous bamboo genome sequence will provide novel insights into biochemistry, molecular marker-assisted breeding programs, and germplasm conservation for bamboo species worldwide., (© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.)

Panax notoginseng is one of the most widely used traditional Chinese herbs with particularly valued roots. Triterpenoid saponins are mainly specialized secondary metabolites, which medically act as bioactive components. Knowledge of the ginsenoside biosynthesis in P. notoginseng, which is of great importance in the industrial biosynthesis and genetic breeding program, remains largely undetermined. Here we combined single molecular real time (SMRT) and Second-Generation Sequencing (SGS) technologies to generate a widespread transcriptome atlas of P. notoginseng. We mapped 2,383 full-length non-chimeric (FLNC) reads to adjacently annotated genes, corrected 1,925 mis-annotated genes and merged into 927 new genes. We identified 8,111 novel transcript isoforms that have improved the annotation of the current genome assembly, of which we found 2,664 novel lncRNAs. We characterized more alternative splicing (AS) events from SMRT reads (20,015 AS in 6,324 genes) than Illumina reads (18,498 AS in 9,550 genes), which contained a number of AS events associated with the ginsenoside biosynthesis. The comprehensive transcriptome landscape reveals that the ginsenoside biosynthesis predominantly occurs in flowers compared to leaves and roots, substantiated by levels of gene expression, which is supported by tissue-specific abundance of isoforms in flowers compared to roots and rhizomes. Comparative metabolic analyses further show that a total of 17 characteristic ginsenosides increasingly accumulated, and roots contained the most ginsenosides with variable contents, which are extraordinarily abundant in roots of the three-year old plants. We observed that roots were rich in protopanaxatriol- and protopanaxadiol-type saponins, whereas protopanaxadiol-type saponins predominated in aerial parts (leaves, stems and flowers). The obtained results will greatly enhance our understanding about the ginsenoside biosynthetic machinery in the genus Panax.

Morchella conica Pers. is a highly-prized mushroom for its edible and medical values. In this study, we determined the complete mitochondrial genome of M. conica combining both PacBio and Illumina sequencing technologies. The complete mitochondrial genome is 280,763 bp in length with a GC content of 39.88%. We identified a total of 14 core conserved protein-coding genes, 127 non-conserved open reading frames (ncORFs) and 30 tRNA genes in the M. conica mitogenome. However, no large or small rRNA subunits (rnl or rns) were identified in this mitogenome. In addition, we detected two mitochondrial RNase P (rnpB) genes and one ribosomal protein genes (rps3). Phylogenetic analysis was performed among M. conica and 18 other representative fungi from Ascomycota, Basidiomycota and Mucoromycota. Our results showed that M. conica was most closely related to M. importuna . The availability of the M. conica mitochondrial genome will form the basis of genetic breeding program and enhance our understanding of the evolution of this species., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Oryza rufipogon and O. longistaminata are important wild relatives of cultivated rice, harboring a promising source of novel genes for rice breeding programs. Here, we present de novo assembled draft genomes and annotation of O. rufipogon and O. longistaminata . Our analysis reveals a considerable number of lineage-specific gene families associated with the self-incompatibility (SI) and formation of reproductive separation. We show how lineage-specific expansion or contraction of gene families with functional enrichment of the recognition of pollen, thus enlightening their reproductive diversification. We documented a large number of lineage-specific gene families enriched in salt stress, antifungal response, and disease resistance. Our comparative analysis further shows a genome-wide expansion of genes encoding NBS-LRR proteins in these two outcrossing wild species in contrast to six other selfing rice species. Conserved noncoding sequences (CNSs) in the two wild rice genomes rapidly evolve relative to selfing rice species, resulting in the reduction of genomic variation owing to shifts of mating systems. We find that numerous genes related to these rapidly evolving CNSs are enriched in reproductive structure development, flower development, and postembryonic development, which may associate with SI in O. rufipogon and O. longistaminata ., Competing Interests: The authors declare no conflict of interest., (© 2020 The Authors. Plant Direct published by American Society of Plant Biologists, Society for Experimental Biology and John Wiley & Sons Ltd.)

Nanozymes have been widely applied in bio-assays in the field of biotechnology and biomedicines. However, the physicochemical basis of nanozyme catalytic activity remains elusive. To test whether nanozymes exhibit an inactivation effect similar to that of natural enzymes, we used guanidine chloride (GuHCl) to disturb the iron oxide nanozyme (IONzyme) and observed that GuHCl induced IONzyme aggregation and that the peroxidase-like activity of IONzyme significantly decreased in the presence of GuHCl. However, the aggregation appeared to be unrelated to the quick process of inactivation, as GuHCl acted as a reversible inhibitor of IONzyme instead of a solo denaturant. Inhibition kinetic analysis showed that GuHCl binds to IONzyme competitively with H 2 O 2 but non-competitively with tetramethylbenzidine. In addition, electron spin resonance spectroscopy showed that increasing GuHCl level of GuHCl induced a correlated pattern of changes in the activity and the state of the unpaired electrons of the IONzymes. This result indicates that GuHCl probably directly interacts with the iron atoms of IONzyme and affects the electron density of iron, which may then induce IONzyme inactivation. These findings not only contribute to understanding the essence of nanozyme catalytic activity but also suggest a practically feasible method to regulate the catalytic activity of IONzyme., (Copyright © 2020 Mo, Yu, Gao, Liu, Wei and He.)

Premise: Camellia reticulata , which is native to southwestern China, is an economically important plant belonging to the family Theaceae. We developed expressed sequence tag-simple sequence repeat (EST-SSR) markers for C. reticulata , which can be used to investigate its genetic diversity, population structure, and evolutionary history., Methods and Results: We detected 4780 SSRs in C. reticulata from Camellia RNA-Seq data deposited in the National Center for Biotechnology Information's expressed sequence tags database (dbEST). Primer pairs for 70 SSR loci were designed and used for PCR amplification using 90 individuals from four populations of C. reticulata . Of these loci, 50 microsatellite markers were successfully identified, including 11 polymorphic markers. The allele number per locus ranged from two to seven (mean = 4.182), and the levels of observed and expected heterozygosity ranged from 0.044 to 0.567 and from 0.166 to 0.642, respectively. Eleven primer pairs amplified PCR products in three other species of Camellia ( C. saluenensis , C. pitardii , and C. yunnanensis )., Conclusions: The set of microsatellite markers developed here can be used to study the genetic variation and population structure of C. reticulata and related species and thereby help to develop conservation strategies for this species., (© 2020 Tong and Gao. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.)

Artemisinin has a significant role in treatment of malaria, as well as effective anti-inflammatory and anti-cancer activities. However, such problems as poor water solubility and easy recrystallization limit its application. In this study, polyethylene glycol, a solvent which is widely used in pharmaceutics, was introduced to prepare an artemisinin dissolution. Under the action of hydrogen bonding in 12% polyethylene glycol 4000 solvent, the maximum solubility of artemisinin could reach up to 1 mg/mL. Meanwhile, biological functions of such artemisinin solution were evaluated. The obtained artemisinin solution had a significant inhibitory effect on Gram-positive bacteria, Gram-negative bacteria and fungi. As for the anti-inflammatory property, 0.031 mg/mL artemisinin solution had an obvious inhibitory effect on nitric oxide release in inflammatory cells, and the survival rate of cells was greater than 50%. Low concentration of the obtained artemisinin solution (0.031 mg/mL) had no significant cytotoxicity, while it displayed selective inhibition in cancer cells. IC50 for human hepatoma cells BEL-7404, SMMC7721 and Hep G2 is 0.0016 mg/mL, 0.0084 mg/mL and 0.0541 mg/mL, respectively. In conclusion, the 12% PEG4000-assisted artemisinin solution has a good biological effect and it can be further applied in pharmaceutics, biomaterials and medicine.

Exploiting novel gene sources from wild relatives has proven to be an efficient approach to advance crop genetic breeding efforts. Oryza granulata, with the GG genome type, occupies the basal position of the Oryza phylogeny and has the second largest genome (~882 Mb). As an upland wild rice species, it possesses renowned traits that distinguish it from other Oryza species, such as tolerance to shade and drought, immunity to bacterial blight and resistance to the brown planthopper. Here, we generated a 736.66-Mb genome assembly of O. granulata with 40,131 predicted protein-coding genes. With Hi-C data, for the first time, we anchored ~98.2% of the genome assembly to the twelve pseudo-chromosomes. This chromosome-length genome assembly of O. granulata will provide novel insights into rice genome evolution, enhance our efforts to search for new genes for future rice breeding programmes and facilitate the conservation of germplasm of this endangered wild rice species.

Asian cultivated rice is believed to have been domesticated from a wild progenitor, Oryza rufipogon, offering promising sources of alleles for world rice improvement. Here we first present a high-quality chromosome-scale genome of the typical O. rufipogon. Comparative genomic analyses of O. sativa and its two wild progenitors, O. nivara and O. rufipogon, identified many dispensable genes functionally enriched in the reproductive process. We detected millions of genomic variants, of which large-effect mutations could affect agronomically relevant traits. We demonstrate how lineage-specific expansion of gene families may have contributed to the formation of reproduction isolation. We document thousands of genes with signatures of positive selection that are mainly involved in the reproduction and response to biotic- and abiotic stresses. We show that selection pressures may serve as forces to govern substantial genomic alterations that form the genetic basis of rapid evolution of mating and reproductive systems under diverse habitats.

African wild rice Oryza longistaminata, one of the eight AA- genome species in the genus Oryza, possesses highly valued traits, such as the rhizomatousness for perennial rice breeding, strong tolerance to biotic and abiotic stresses, and high biomass production on poor soils. To obtain the high-quality reference genome for O. longistaminata we employed a hybrid assembly approach through incorporating Illumina and PacBio sequencing datasets. The final genome assembly comprised only 107 scaffolds and was approximately ∼363.5 Mb, representing ∼92.7% of the estimated African wild rice genome (∼392 Mb). The N50 lengths of the assembled contigs and scaffolds were ∼46.49 Kb and ∼6.83 Mb, indicating ∼3.72-fold and ∼18.8-fold improvement in length compared to the earlier released assembly (∼12.5 Kb and 364 Kb, respectively). Aided with Hi-C data and syntenic relationship with O. sativa, these assembled scaffolds were anchored into 12 pseudo-chromosomes. Genome annotation and comparative genomic analysis reveal that lineage-specific expansion of gene families that respond to biotic- and abiotic stresses are of great potential for mining novel alleles to overcome major diseases and abiotic adaptation in rice breeding programs. This reference genome of African wild rice will greatly enlarge the existing database of rice genome resources and unquestionably form a solid base to understand genomic basis underlying highly valued phenotypic traits and search for novel gene sources in O. longistaminata for the future rice breeding programs., (© 2020 The Authors. The Plant Genome published by Wiley Periodicals, Inc. on behalf of Crop Science Society of America.)

The rubber tree, Hevea brasiliensis, produces natural rubber that serves as an essential industrial raw material. Here, we present a high-quality reference genome for a rubber tree cultivar GT1 using single-molecule real-time sequencing (SMRT) and Hi-C technologies to anchor the ∼1.47-Gb genome assembly into 18 pseudochromosomes. The chromosome-based genome analysis enabled us to establish a model of spurge chromosome evolution, since the common paleopolyploid event occurred before the split of Hevea and Manihot. We show recent and rapid bursts of the three Hevea-specific LTR-retrotransposon families during the last 10 million years, leading to the massive expansion by ∼65.88% (∼970 Mbp) of the whole rubber tree genome since the divergence from Manihot. We identify large-scale expansion of genes associated with whole rubber biosynthesis processes, such as basal metabolic processes, ethylene biosynthesis, and the activation of polysaccharide and glycoprotein lectin, which are important properties for latex production. A map of genomic variation between the cultivated and wild rubber trees was obtained, which contains ∼15.7 million high-quality single-nucleotide polymorphisms. We identified hundreds of candidate domestication genes with drastically lowered genomic diversity in the cultivated but not wild rubber trees despite a relatively short domestication history of rubber tree, some of which are involved in rubber biosynthesis. This genome assembly represents key resources for future rubber tree research and breeding, providing novel targets for improving plant biotic and abiotic tolerance and rubber production., (Copyright © 2019 The Author. Published by Elsevier Inc. All rights reserved.)

The aim of this retrospective analysis is to explore whether growth hormone (GH) pretreatment is beneficial for patients with poor ovarian reserve undertaking in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) treatment. Poor ovarian reserve patients with anti-Mullerian hormone (AMH) <1.2 ng/mL were recruited and divided into the GH adjuvant group (GH+ group) and the counterpart without GH pretreatment (GH- group). One-to-one case-control matching was performed to adjust essential confounding factors between the GH+ group and GH- group. A total of 676 cycles were included in the present study with 338 cycles in each group. Conventional ovarian stimulation protocols were applied for ART treatment. Patients were further divided into POSEIDON group 3 (PG3, age <35 years) and POSEIDON group 4 (PG4, age ≥35 years), based on POSEIDON criteria. The demographic data, cycle characteristics, and clinical outcomes between the GH+ group and GH- group, as well as in the further stratified analysis of PG3 and PG4 were compared. GH adjuvant showed a beneficial effect on the ovarian response and live birth rate in poor ovarian reserve patients. Further stratification revealed that in PG4, there was a significantly increased number of good-quality embryos in the GH+ group compared to the GH- group (1.58 ± 1.71 vs. 1.25 ± 1.55, P = 0.032), accompanied by a reduced miscarriage rate and a greatly improved live birth rate (29.89 vs. 17.65%, P = 0.028). GH adjuvant failed to promote the live birth rate in PG3. In conclusion, GH pretreatment is advantageous by elevating ovarian response and correlated with an improved live birth rate and reduced miscarriage rate in POSEIDON poor ovarian reserve patients older than 35., (Copyright © 2019 Cai, Gao, Liang, Fang, Wu and Yang.)

Tea is the most popular non-alcoholic caffeine-containing and the oldest beverage in the world. In this study, we de novo assembled the chloroplast (cp) and mitochondrial (mt) genomes of C. sinensis var. assamica cv. Yunkang10 into a circular contig of 157,100 bp and two complete circular scaffolds (701719 bp and 177329 bp), respectively. We correspondingly annotated a total of 141 cp genes and 71 mt genes. Comparative analysis suggests repeat-rich nature of the mt genome compared to the cp genome, for example, with the characterization of 37,878 bp and 149 bp of long repeat sequences and 665 and 214 SSRs, respectively. We also detected 478 RNA-editing sites in 42 protein-coding mt genes, which are ~4.4-fold more than 54 RNA-editing sites detected in 21 protein-coding cp genes. The high-quality cp and mt genomes of C. sinensis var. assamica presented in this study will become an important resource for a range of genetic, functional, evolutionary and comparative genomic studies in tea tree and other Camellia species of the Theaceae family.

The course, tempo and mode of chloroplast genome evolution remain largely unknown, resulting in limited knowledge about how plant plastome gene and genome evolve during the process of recent plant speciation. Here, we report the complete plastomes of 22 closely related Oryza species in chronologically ordered stages and generate the first precise map of genomic structural variation, to our knowledge. The occurrence rapidity was estimated on average to be ~7 insertions and ~15 deletions per Myr. Relatively fewer deletions than insertions result in an increased repeat density that causes the observed growth of Oryza chloroplast genome sizes. Genome-wide scanning identified 14 positively selected genes that are relevant to photosynthesis system, eight of which were found independently in shade-tolerant or sun-loving rice species. psaA seemed positively selected in both shade-tolerant and sun-loving rice species. The results show that adaptive evolution of chloroplast genes makes rice species adapt to diverse ecological habitats related to sunlight preferences., Competing Interests: Competing interestsThe authors declare no competing interests.

The primary bile acids (BAs) synthesized from cholesterol in the liver are converted to secondary BAs by gut microbiota. It was recently disclosed that the major secondary BA, deoxycholate (DCA) species, is stereoselectively oxidized to tertiary BAs exclusively by CYP3A enzymes. This work subsequently investigated the in vitro oxidation kinetics of DCA at C-1 β , C-3 β , C-4 β , C-5 β , C-6 α , C-6 β , and C-19 in recombinant CYP3A enzymes and naive enzymes in human liver microsomes (HLMs). The stereoselective oxidation of DCA fit well with Hill kinetics at 1-300 μ M in both recombinant CYP3A enzymes and pooled HLMs. With no contributions or trace contributions from CYP3A5, CYP3A7 favors oxidation at C-19, C-4 β , C-6 α , C-3 β , and C-1 β , whereas CYP3A4 favors the oxidation at C-5 β and C-6 β compared with each other. Correlation between DCA oxidation and testosterone 6 β -hydroxylation in 14 adult single-donor HLMs provided proof-of-concept evidence that DCA 19-hydroxylation is an in vitro marker reaction for CYP3A7 activity, whereas oxidation at other sites represents mixed indicators for CYP3A4 and CYP3A7 activities. Deactivation caused by DCA-induced cytochrome P450-cytochrome P420 conversion, as shown by the spectral titrations of isolated CYP3A proteins, was observed when DCA levels were near or higher than the critical micelle concentration (about 1500 μ M). Unlike CYP3A4, CYP3A7 showed abnormally elevated activities at 500 and 750 μ M, which might be associated with an altered affinity for DCA multimers. The disclosed kinetic and functional roles of CYP3A isoforms in disposing of the gut bacteria-derived DCA may help in understanding the structural and functional mechanisms of CYP3A., (Copyright © 2019 by The American Society for Pharmacology and Experimental Therapeutics.)

The WRKY gene family plays a vital role in plant development and environment response. Although previous studies suggested that the WRKY genes in carrot (Kuroda type) involved in biotic and abiotic stress responses, the information of WRKY genes in the latest version of the carrot genome ( Daucus carota v2.0, Nantes type carrot) and their response to hormone and injury stresses have not been reported. In this study, we performed a genome-wide analysis of WRKY s using a chromosome-scale genome assembly of carrot ( Daucus carota subsp. sativus L.). We identified a total of 67 WRKY genes, which were further classified into the three groups. These WRKY genes are unevenly distributed on carrot chromosomes. We found that more than half of them were derived from whole-genome duplication (WGD) events, suggesting that WGDs have played a major role during the evolution of the WRKY gene family. We experimentally ascertained the expression divergence existed between WGD-derived WRKY duplicated gene pairs, which is indicative of functional differentiation between duplicated genes. Our analysis of cis -acting elements indicated that WRKY genes were transcriptionally regulated upon hormone and mechanic injury stresses. Gene expression analyses by qRT-PCR further presented that WRKY genes were involved in hormone and mechanic injury stresses.

The gut microbiota modifies endogenous primary bile acids (BAs) to produce exogenous secondary BAs, which may be further metabolized by cytochrome P450 enzymes (P450s). Our primary aim was to examine how the host adapts to the stress of microbe-derived secondary BAs by P450-mediated oxidative modifications on the steroid nucleus. Five unconjugated tri-hydroxyl BAs that were structurally and/or biologically associated with deoxycholate (DCA) were determined in human biologic samples by liquid chromatography-tandem mass spectrometry in combination with enzyme-digestion techniques. They were identified as DCA-19-ol, DCA-6 β -ol, DCA-5 β -ol, DCA-6 α -ol, DCA-1 β -ol, and DCA-4 β -ol based on matching in-laboratory synthesized standards. Metabolic inhibition assays in human liver microsomes and recombinant P450 assays revealed that CYP3A4 and CYP3A7 were responsible for the regioselective oxidations of both DCA and its conjugated forms, glycodeoxycholate (GDCA) and taurodeoxycholate (TDCA). The modification of secondary BAs to tertiary BAs defines a host liver (primary BAs)-gut microbiota (secondary BAs)-host liver (tertiary BAs) axis. The regioselective oxidations of DCA, GDCA, and TDCA by CYP3A4 and CYP3A7 may help eliminate host-toxic DCA species. The 19- and 4 β -hydroxylation of DCA species demonstrated outstanding CYP3A7 selectivity and may be useful as indicators of CYP3A7 activity., (Copyright © 2019 by The American Society for Pharmacology and Experimental Therapeutics.)

The interfacial compatibility between compact TiO 2 and perovskite layers is critical for the performance of planar heterojunction perovskite solar cells (PSCs). A compact TiO 2 film employed as an electron-transport layer (ETL) was modified using 3-aminopropyl trimethoxy silane (APMS) hydrolysate. The power conversion efficiency (PCE) of PSCs composed of an APMS-hydrolysate-modified TiO 2 layer increased from 13.45 to 15.79%, which was associated with a significant enhancement in the fill factor (FF) from 62.23 to 68.04%. The results indicate that APMS hydrolysate can enhance the wettability of γ-butyrolactone (GBL) on the TiO 2 surface, form a perfect CH 3 NH 3 PbI 3 film, and increase the recombination resistance at the interface. This work demonstrates a simple but efficient method to improve the TiO 2 /perovskite interface that can be greatly beneficial for developing high-performance PSCs., Competing Interests: The authors declare no competing interests.

Camellia sasanqua is one of the most famous horticultural plants in Camellia (Theaceae) due to its aesthetic appeal as landscape plant. Knowledge regarding the genetic basis of flowering time, floral aroma and color in C. sasanqua is limited, but is essential to breed new varieties with desired floral traits. Here, we described the de novo transcriptome of young leaves, flower buds and flowers of C. sasanqua. A total of 60,127 unigenes were functionally annotated based on the sequence similarity. After analysis, we found that two floral integrator genes, SOC1 and AP1, in flowering time pathway showed evidence of gene family expansion. Compared with 1-deoxy-D-xylulose-5-phosphate pathway, some genes in the mevalonate pathway were most highly expressed, suggesting that this might represent the major pathway for terpenoid biosynthesis related to floral aroma in C. sasanqua. In flavonoid biosynthesis pathway, PAL, CHI, DFR and ANS showing significantly higher expression levels in flowers and flower buds might have important role in regulation of floral color. The top five most transcription factors (TFs) families in C. sasanqua transcriptome were MYB, MIKC, C3H, FAR1 and HD-ZIP, many of which have a direct relationship with floral traits. In addition, we also identified 33,540 simple sequence repeats (SSRs) in the C. sasanqua transcriptome. Collectively, the C. sasanqua transcriptome dataset generated from this study along with the SSR markers provide a new resource for the identification of novel regulatory transcripts and will accelerate the genetic improvement of C. sasanqua breeding programs., (Copyright © 2017. Published by Elsevier Masson SAS.)

Recent studies have shown that high miR-155 expression was associated with poor prognosis in patients with acute myelogeneous leukemia (AML). Furthermore, targeting miR-155 results in monocytic differentiation and apoptosis. However, the exact role and mechanisms of miR-155 in human AML remains speculative. HL-60 cells were treated with anti-miR-155 for 72 h. Cell growth and apoptosis in vitro were detected by MTT, BrdU proliferation, colony formation and flow cytometry assay. The effect of anti-miR-155 on growth of HL-60 cells was also evaluated in a leukemia mouse model. Slug cDNA and PUMA siRNA trannsfection was used to assess the signal pathway. Different protein expression was detected by western blot assay and quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) assay. The results shown that targeting miR-155 resulted in a 24-fold decrease of miR-155 expression compared to negative control in the HL-60 cells. Targeting miR-155 significantly downregulated Slug and upregulated PUMA expression, and decreased HL-60 cell growth by 70% , impaired colony formation by approximately 60%, and increased HL-60 cell apoptosis by 45%. Targeting PUMA reversed miR-155 sliencing-induced proliferation and apoptosis of HL-60 cells. Restoration of Slug decreased PUMA expression. In murine engraftment models of HL-60 cells, we showed that targeting miR-155 was able to reduce tumor growth. This was accompanied with decreased Slug expression and increased PUMA expression in these tumors. Collectively, our findings strongly suggest targeting miR-155 exhibited in vivo and in vitro antileukemic activities in AML through a novel mechanism resulting in inhibition of Slug expression and increase of PUMA expression.

Genome duplication and repeat multiplication contribute to genome evolution in plants. Our previous work identified a recent allotetraploidization event and five high-copy LTR retrotransposon (LTR-RT) families PgDel, PgTat, PgAthila, PgTork, and PgOryco in Panax ginseng. Here, using whole-genome sequences, we quantified major repeats in five Panax species and investigated their role in genome evolution. The diploids P. japonicus, P. vietnamensis, and P. notoginseng and the tetraploids P. ginseng and P. quinquefolius were analyzed alongside their relative Aralia elata. These species possess 0.8-4.9 Gb haploid genomes. The PgDel, PgTat, PgAthila, and PgTork LTR-RT superfamilies accounted for 39-52% of the Panax species genomes and 17% of the A. elata genome. PgDel included six subfamily members, each with a distinct genome distribution. In particular, the PgDel1 subfamily occupied 23-35% of the Panax genomes and accounted for much of their genome size variation. PgDel1 occupied 22.6% (0.8 Gb of 3.6 Gb) and 34.5% (1.7 Gb of 4.9 Gb) of the P. ginseng and P. quinquefolius genomes, respectively. Our findings indicate that the P. quinquefolius genome may have expanded due to rapid PgDel1 amplification over the last million years as a result of environmental adaptation following migration from Asia to North America.

The dynamics of long terminal repeat (LTR) retrotransposons and their contribution to genome evolution during plant speciation have remained largely unanswered. Here, we perform a genome-wide comparison of all eight Oryza AA-genome species, and identify 3911 intact LTR retrotransposons classified into 790 families. The top 44 most abundant LTR retrotransposon families show patterns of rapid and distinct diversification since the species split over the last ∼4.8 MY (million years). Phylogenetic and read depth analyses of 11 representative retrotransposon families further provide a comprehensive evolutionary landscape of these changes. Compared with Ty1- copia , independent bursts of Ty3- gypsy retrotransposon expansions have occurred with the three largest showing signatures of lineage-specific evolution. The estimated insertion times of 2213 complete retrotransposons from the top 23 most abundant families reveal divergent life histories marked by speedy accumulation, decline, and extinction that differed radically between species. We hypothesize that this rapid evolution of LTR retrotransposons not only divergently shaped the architecture of rice genomes but also contributed to the process of speciation and diversification of rice., (Copyright © 2017 Zhang and Gao.)

Tea is the world's oldest and most popular caffeine-containing beverage with immense economic, medicinal, and cultural importance. Here, we present the first high-quality nucleotide sequence of the repeat-rich (80.9%), 3.02-Gb genome of the cultivated tea tree Camellia sinensis. We show that an extraordinarily large genome size of tea tree is resulted from the slow, steady, and long-term amplification of a few LTR retrotransposon families. In addition to a recent whole-genome duplication event, lineage-specific expansions of genes associated with flavonoid metabolic biosynthesis were discovered, which enhance catechin production, terpene enzyme activation, and stress tolerance, important features for tea flavor and adaptation. We demonstrate an independent and rapid evolution of the tea caffeine synthesis pathway relative to cacao and coffee. A comparative study among 25 Camellia species revealed that higher expression levels of most flavonoid- and caffeine- but not theanine-related genes contribute to the increased production of catechins and caffeine and thus enhance tea-processing suitability and tea quality. These novel findings pave the way for further metabolomic and functional genomic refinement of characteristic biosynthesis pathways and will help develop a more diversified set of tea flavors that would eventually satisfy and attract more tea drinkers worldwide., (Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.)

Trident maple Acer buergerianum Miq., belonging to the family of Aceraceae, is an important ornamental tree. Here, we report the complete chloroplast genome sequence of A. buergerianum . The circular genome was 156,477 bp in size, and comprised a pair of inverted repeat (IR) regions of 26,090 bp, a large single-copy (LSC) region of 86,246 bp and a small single-copy (SSC) region of 18,062 bp. It contained 134 genes, including 89 protein-coding genes, 40 transfer RNA genes, and 8 ribosomal genes. Maximum likelihood phylogenomic analysis shows that A. buergerianum is closely related to other Acer species, including A. miaotaiense , A. morrisonense , and A. davidii ., Competing Interests: The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper., (© 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

To understand the potential genetic basis of highland adaptation of fungal pathogenicity, we present here the ~116 Mb de novo assembled high-quality genome of Ophiocordyceps sinensis endemic to the Qinghai-Tibetan Plateau. Compared with other plain-dwelling fungi, we find about 3.4-fold inflation of the O. sinensis genome due to a rapid amplification of long terminal repeat retrotransposons that occurred ~38 million years ago in concert with the uplift of the plateau. We also observe massive removal of thousands of genes related to the transport process and energy metabolism. O. sinensis displays considerable lineage-specific expansion of gene families functionally enriched in the adaptability of low-temperature of cold tolerance, fungal pathogenicity and specialized host infection. We detect signals of positive selection for genes involved in peroxidase and hypoxia to enable its highland adaptation. Resequencing and analyzing 31 whole genomes of O. sinensis, representing nearly all of its geographic range, exhibits latitude-based population divergence and nature selection for population inhabitation towards higher altitudes on the Qinghai-Tibetan Plateau.

Morchella species are well known world-round as popular and prized edible fungi due to their unique culinary flavor. Recently, several species have been successfully cultivated in China. However, their reproductive modes are still unknown, and their basic biology needs to be elucidated. Here, we use the morel genome information to investigate mating systems and life cycles of fourteen black morel species. Mating type-specific primers were developed to screen and genotype ascospores, hymenia and stipes from 223 ascocarps of the 14 species from Asia and Europe. Our data indicated that they are all heterothallic and their life cycles are predominantly haploid, but sterile haploid fruiting also exists. Ascospores in all species are mostly haploid, homokaryotic, and multinuclear, whereas aborted ascospores without any nuclei were also detected. Interestingly, we monitored divergent spatial distribution of both mating types in natural morel populations and cultivated sites, where the fertile tissue of fruiting bodies usually harbored both mating types, whereas sterile tissue of wild morels constantly had one MAT allele, while the sterile tissue of cultivated strains always exhibited both MAT alleles. Furthermore, MAT1-1-1 was detected significantly more commonly than MAT1-2-1 in natural populations, which strongly suggested a competitive advantage for MAT1-1 strains.

The dysfunction of endothelial cells (ECs) plays crucial roles in vascular remodeling during hypertension. Researches suggested that ECs are regulated by the circulating platelets in vivo, which may participate in abnormal EC apoptosis in hypertension. However the molecular mechanism in this process is still unclear. Here we focused on the microRNAs (miRs) in platelets, and detected the potential role and delivery mechanism of platelet-derived miRs in ECs. Using microarray, the differentially expressed profile of miRs between platelets and ECs was detected. The results revealed that compared with ECs, 67 miRs highly expressed in platelets including the most significant one- miR-142-3p. Since platelets are activated by thrombin in hypertension, we detected the miR-142-3p transferring mechanism of activated platelet, and proved that platelet-derived microparticles (PMPs), but not platelets directly, delivered miR-142-3p into ECs via cellular adherent. Furthermore, BCL2L1, an important molecule in cell apoptosis, was predicted to be a putative target of miR-142-3p by multiple algorithms. Dual luciferase reporter assays, as well as miR-142-3p mimics treatment were used to confirm the interplay between miR-142-3p and BCL2L1. Meanwhile, using in vivo hypertensive rat model, our results showed that the expression of platelet-derived miR-142-3p and the apoptosis were both significantly increased in ECs during hypertension. The present results suggested that platelet-derived miR-142-3p is delivered into ECs via PMPs, and may modulate the expression of target molecule- BCL2L1, which may subsequently display a negative function by modulating EC apoptosis in hypertension.

The amplification and recombination of long terminal repeat (LTR) retrotransposons have proven to determine the size, organization, function, and evolution of most host genomes, especially very large plant genomes. However, the limitation of tools for an efficient discovery of structural complexity of LTR retrotransposons and the nested insertions is a great challenge to confront ever-growing amount of genomic sequences for many organisms. Here we developed a novel software, called as LTRtype, to characterize different types of structurally complex LTR retrotransposon elements as well as nested events. This system is capable of rapidly scanning large-scale genomic sequences and appropriately characterizing the five complex types of LTR retrotransposon elements. After testing on the Arabidopsis thaliana genome, we found that this program is able to properly annotate a large number of structurally complex elements as well as the nested insertions. Thus, LTRtype can be employed as an automatic and efficient tool that will help to reconstruct the evolutionary history of LTR retrotransposons and better understand the evolution of host genomes. LTRtype is publicly available at: http://www.plantkingdomgdb.com/LTRtype/index.html.

Here, we report the complete mitochondrial genome sequence of North Island brown kiwi( Apteryx mantelli ). The genome is found to be 16,694 bp in length and has a base composition of A (30.74%), G (13.46%), C (26.50%), and T (29.30%). Similar to other Apteryx species, it contains a typically conserved structure including 13 protein-coding genes, 2 rRNA genes, 1 control region (D-loop), and 22tRNA genes. The proportion of coding sequences with a total length of 11,431 bp is 68.47%, which encodes 3776 amino acids. All protein-coding genes started with Met, and ND2 , COX2 , and COX3 ended by TAA as a stop codon. The lengths of 12S ribosomal RNA and 16S ribosomal RNA are 973 bp and 1596 bp, respectively. The length of control region is 1112 bp, ranging from 15,583 bp to 16,694 bp. The complete mitochondrial genome sequence provided here would be useful for further understanding the evolution of ratite and conservation genetics of A. mantelli ., Competing Interests: The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper., (© 2016 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)