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Shanghai, China

Cui L.,Shanghai Normal University | Huang F.,Shanghai Normal University | Zhang D.,Chinese Academy of Sciences | Lin Y.,University of California at Berkeley | And 3 more authors.
Molecular Genetics and Genomics

Tropane alkaloids (TAs) such as anisodamine, anisodine, hyoscyamine and scopolamine are extensively used in clinical practice as anticholinergic agents. Anisodus acutangulus produces TAs in root tissue, and although several genes involved in scopolamine biosynthesis have been cloned, yet the biosynthetic pathway of TAs remains poorly understood. To further understand TAs biosynthesis mechanism, transcriptome analysis with deep RNA sequencing in A. acutangulus roots was performed in this study; 48 unigenes related to tropane, piperidine and pyridine alkaloid biosynthesis, 145 linked to the distribution of arginine to TAs biosynthesis, and 86 categorized to terpenoid backbone biosynthesis have been identified in pathway enrichment analyses with eukaryotic orthologous groups (KOG) and Kyoto encyclopedia of genes and genomes. Additionally, 82 unigenes annotated as cytochrome P450 family members seemed to be involved in secondary metabolism. Genes encoding littorine mutase/monooxygenase (CYP80F1), diamine oxidase (DAO), alcohol dehydrogenase (ADH) and aromatic amino acid aminotransferase (ArAT) may also play roles in TAs biosynthetic pathways. Furthermore, over 1,000 unigenes were identified as potential transcription factors of WRKY, AP2/ERF, MYB and bHLH families, which would be helpful to understand transcriptional regulation of secondary metabolite biosynthesis. These data enable novel insights into A. acutangulus transcriptome, updating the knowledge of TAs biosynthetic mechanism at molecular level. © 2015, Springer-Verlag Berlin Heidelberg. Source

Lu Y.,Shanghai JiaoTong University | Cui X.,Shanghai JiaoTong University | Li R.,Shanghai JiaoTong University | Huang P.,Shanghai JiaoTong University | And 5 more authors.
Journal of Integrative Plant Biology

DNA markers play important roles in plant breeding and genetics. The Insertion/Deletion (InDel) marker is one kind of co-dominant DNA markers widely used due to its low cost and high precision. However, the canonical way of searching for InDel markers is time-consuming and labor-intensive. We developed an end-to-end computational solution (InDel Markers Development Platform, IMDP) to identify genome-wide InDel markers under a graphic pipeline environment. IMDP constitutes assembled genome sequences alignment pipeline (AGA-pipe) and next-generation re-sequencing data mapping pipeline (NGS-pipe). With AGA-pipe we are able to identify 12,944 markers between the genome of rice cultivars Nipponbare and 93-11. Using NGS-pipe, we reported 34,794 InDels from re-sequencing data of rice cultivars Wu-Yun-Geng7 and Guang-Lu-Ai4. Combining AGA-pipe and NGS-pipe, we developed 205,659 InDels in eight japonica and nine indica cultivars and 2,681 InDels showed a subgroup-specific pattern. Polymerase chain reaction (PCR) analysis of subgroup-specific markers indicated that the precision reached 90% (86 of 95). Finally, to make them available to the public, we have integrated the InDels/markers information into a website (Rice InDel Marker Database, RIMD, The application of IMDP in rice will facilitate efficiency for development of genome-wide InDel markers, in addition it can be used in other species with reference genome sequences and NGS data. © 2015 Institute of Botany, Chinese Academy of Sciences. Source

Fan W.,Shanghai JiaoTong University | Zong J.,Novel Bioinformatics Co. | Luo Z.,Shanghai JiaoTong University | Chen M.,Shanghai JiaoTong University | And 7 more authors.

Rapid and accurate genome-wide marker detection is essential to the marker-assisted breeding and functional genomics studies. In this work, we developed an integrated software, AgroMarker Finder (AMF: http://erp.novelbio.com/AMF), for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. By application of AMF, a total of 90,743 high-quality markers (82,878 SNPs and 7,865 InDels) were detected between rice varieties JP69 and Jiaoyuan5A. The density of the identified markers is 0.2 per Kb for SNP markers, and 0.02 per Kb for InDel markers. Sequencing validation revealed that the accuracy of genomewide marker detection by AMF is 93%. In addition, a validated subset of 82 SNPs and 31 InDels were found to be closely linked to 117 important agronomic trait genes, providing a basis for subsequent marker-assisted selection (MAS) and variety identification. Furthermore, we selected 12 markers from 31 validated InDel markers to identify seed authenticity of variety Jiaoyuanyou69, and we also identified 10 markers closely linked to the fragrant gene BADH2 to minimize linkage drag for Wuxiang075 (BADH2 donor)/Jiachang1 recombinants selection. Therefore, this software provides an efficient approach for marker identification from RAD-seq data, and it would be a valuable tool for plant MAS and variety protection. © 2016 Fan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Source

Xu W.-W.,CAS Kunming Institute of Zoology | Xu W.-W.,University of Chinese Academy of Sciences | Han M.-J.,CAS Kunming Institute of Zoology | Han M.-J.,University of Chinese Academy of Sciences | And 7 more authors.
BMC Medical Genomics

Background: Upon co-stimulation with CD3/CD28 antibodies, activated CD4 + T cells were found to lose their susceptibility to HIV-1 infection, exhibiting an induced resistant phenotype. This rather unexpected phenomenon has been repeatedly confirmed but the underlying cell and molecular mechanisms are still unknown. Methods. We first replicated the reported system using the specified Dynal beads with PHA/IL-2-stimulated and un-stimulated cells as controls. Genome-wide expression and analysis were then performed by using Agilent whole genome microarrays and established bioinformatics tools. Results: We showed that following CD3/CD28 co-stimulation, a homogeneous population emerged with uniform expression of activation markers CD25 and CD69 as well as a memory marker CD45RO at high levels. These cells differentially expressed 7,824 genes when compared with the controls on microarrays. Series-Cluster analysis identified 6 distinct expression profiles containing 1,345 genes as the representative signatures in the permissive and resistant cells. Of them, 245 (101 potentially permissive and 144 potentially resistant) were significant in gene ontology categories related to immune response, cell adhesion and metabolism. Co-expression networks analysis identified 137 "key regulatory" genes (84 potentially permissive and 53 potentially resistant), holding hub positions in the gene interactions. By mapping these genes on KEGG pathways, the predominance of actin cytoskeleton functions, proteasomes, and cell cycle arrest in induced resistance emerged. We also revealed an entire set of previously unreported novel genes for further mining and functional validation. Conclusions: This initial microarray study will stimulate renewed interest in exploring this system and open new avenues for research into HIV-1 susceptibility and its reversal in target cells, serving as a foundation for the development of novel therapeutic and clinical treatments. © 2013 Xu et al.; licensee BioMed Central Ltd. Source

Zhang H.,Shanghai JiaoTong University | Xu C.,Shanghai JiaoTong University | He Y.,Shanghai JiaoTong University | Zong J.,Novel Bioinformatics Co. | And 6 more authors.
Proceedings of the National Academy of Sciences of the United States of America

Rice is a major staple food worldwide. Making hybrid rice has proved to be an effective strategy to significantly increase grain yield. Current hybrid rice technologies rely on male sterile lines and have been used predominantly in indica cultivars. However, intrinsic problems exist in the implementation of these technologies, such as limited germplasms and unpredictable conversions from sterility to fertility in the field. Here, we describe a photoperiod-controlled male sterile line, carbon starved anther (csa), which contains a mutation in an R2R3 MYB transcription regulator of pollen development. This mutation was introduced into indica and japonica rice, and it rendered male sterility under short-day conditions and male fertility under long-day conditions in both lines. Furthermore, F1 plants of csa and a restorer line JP69 exhibited heterosis (hybrid vigor), suggesting the feasibility of using this mutation to create hybrid rice. The csa-based photoperiod-sensitive male sterile line allows the establishment of a stable two-line hybrid system, which promises to have a significant impact on agriculture. Source

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