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Shenzhen, China

Zhang Y.-H.,Yunnan Normal University | Zhang S.-D.,CAS Kunming Institute of Botany | Ling L.-Z.,BGI Yunnan
Plant Gene | Year: 2015

Stellera chamaejasme L. is a well-recognized traditional medicine in China and can synthesizes various secondary metabolites including a group of flavonoids. However, little is known about the molecular mechanisms underlying flavonoid biosynthesis. In this study, large-scale RNA sequencing on flower of S. chamaejasme produced a de novo transcriptome consisting of 32,216 unigenes with a N50 length of 1745 bp. Among all unigenes, 21,355 unigenes were identified as putative homologs of annotated sequences in the public protein databases. Further functional classification revealed that the active genes in flower are predominately involved in metabolic process and biosynthesis of secondary metabolite pathways. A total of 19 candidate genes encoding 11 structural enzymes involved in flavonoid biosynthesis were identified in the unigene dataset by targeted searches of their annotations. In addition, a number of regulatory genes including MYB, basic helix-loop-helix (bHLH), and WD40 repeat proteins were discovered based on transcriptome dataset. Therefore, this study presents the first survey of transcriptome on the flower of S. chamaejasme to discover the major candidate genes involved in flavonoid biosynthesis pathway. These results will promote an understanding of the genetic mechanism of flavonoid biosynthesis in S. chamaejasme. At the same time, this transcriptome dataset can serve as an important public information platform for gene expression, genomic and functional genomic studies in this species. © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Zhang S.-D.,Germplasm Bank of Wild Species | Ling L.-Z.,BGI Yunnan | Zhang Q.-F.,Shandong Academy of Agricultural Sciences | Xu J.-D.,Shandong Academy of Agricultural Sciences | Cheng L.,BGI Yunnan
PLoS ONE | Year: 2015

A complete picture of the evolution of miRNA combinatorial regulation requires the synthesis of information on all miRNAs and their targets. MiR156 and miR529 are two combinatorial regulators of squamosa promoter binding protein-like (SBP-box) genes. Previous studies have clarified the evolutionary dynamics of their targets; however, there have been no reports on the evolutionary patterns of two miRNA regulators themselves to date. In this study, we investigated the evolutionary differences between these two miRNA families in extant land plants. Our work found that miR529 precursor, especially of its mature miRNA sequence, has a higher evolutionary rate. Such accelerating evolution of miR529 has significantly effects on its structural stability, and sequence conservation against existence of itself. By contrast, miR156 evolves more rapidly in loop region of the stable secondary structure, which may contribute to its functional diversity. Moreover, miR156 and miR529 genes have distinct rates of loss after identical duplication events. MiR529 genes have a higher average loss rate and asymmetric loss rate in duplicated gene pairs, indicating preferred miR529 gene losses become another predominant mode of inactivation, that are implicated in the contraction of this family. On the contrary, duplicated miR156 genes have a low loss rate, and could serve as another new source for functional diversity. Taken together, these results provide better insight into understanding the evolutionary divergence of miR156 and miR529 family in miRNA combinational regulation network. © 2015 Zhang et al.

Zhang L.,Shanxi Medical University | Zhou Y.,BGI Shenzhen | Cheng C.,Shanxi Medical University | Cui H.,Shanxi Medical University | And 61 more authors.
American Journal of Human Genetics | Year: 2015

Esophageal squamous cell carcinoma (ESCC) is one of the most common cancers worldwide and the fourth most lethal cancer in China. However, although genomic studies have identified some mutations associated with ESCC, we know little of the mutational processes responsible. To identify genome-wide mutational signatures, we performed either whole-genome sequencing (WGS) or whole-exome sequencing (WES) on 104 ESCC individuals and combined our data with those of 88 previously reported samples. An APOBEC-mediated mutational signature in 47% of 192 tumors suggests that APOBEC-catalyzed deamination provides a source of DNA damage in ESCC. Moreover, PIK3CA hotspot mutations (c.1624G>A [p.Glu542Lys] and c.1633G>A [p.Glu545Lys]) were enriched in APOBEC-signature tumors, and no smoking-associated signature was observed in ESCC. In the samples analyzed by WGS, we identified focal (<100 kb) amplifications of CBX4 and CBX8. In our combined cohort, we identified frequent inactivating mutations in AJUBA, ZNF750, and PTCH1 and the chromatin-remodeling genes CREBBP and BAP1, in addition to known mutations. Functional analyses suggest roles for several genes (CBX4, CBX8, AJUBA, and ZNF750) in ESCC. Notably, high activity of hedgehog signaling and the PI3K pathway in approximately 60% of 104 ESCC tumors indicates that therapies targeting these pathways might be particularly promising strategies for ESCC. Collectively, our data provide comprehensive insights into the mutational signatures of ESCC and identify markers for early diagnosis and potential therapeutic targets. © 2015 The Authors.

Zhang S.-D.,CAS Kunming Institute of Botany | Ling L.-Z.,BGI Yunnan | Yi T.-S.,CAS Kunming Institute of Botany
BMC Genomics | Year: 2015

Background: Squamosa promoter binding protein (SBP)-box family genes encode plant-specific transcription factors that control many important biological functions, including phase transition, inflorescence branching, fruit ripening, and copper homeostasis. Nevertheless, the evolutionary patterns of SBP-box genes and evolutionary forces driving them are still not well understood. Methods: 104 SBP-box gene candidates of five representative land plants were obtained from Phytozome database (v10.3). Phylogenetic combined with gene structure analyses were used to identify SBP-box gene lineages in land plants. Gene copy number and the sequence and structure features were then compared among these different SBP-box lineages. Selection analysis, relative rate tests and expression divergence were finally used to interpret the evolutionary relationships and divergence of SBP-box genes in land plants. Results: We investigated 104 SBP-box genes from moss, Arabidopsis, poplar, rice, and maize. These genes are divided into group I and II, and the latter is further divided into two subgroups (subgroup II-1 and II-2) based on phylogenetic analysis. Interestingly, subgroup II-1 genes have similar sequence and structural features to group I genes, whereas subgroup II-2 genes exhibit intrinsic differences on these features, including high copy numbers and the presence of miR156/miR529 regulation. Further analyses indicate that subgroup II-1 genes are constrained by stronger purifying selection and evolve at a lower substitution rate than II-2 genes, just as group I genes do when compared to II genes. Among subgroup II-2 genes, miR156 targets evolve more rapidly than miR529 targets and experience comparatively relaxed purifying selection. These results suggest that group I and subgroup II-1 genes under strong selective constraint are conserved. By contrast, subgroup II-2 genes evolve under relaxed purifying selection and have diversified through gene copy duplications and changes in miR156/529 regulation, which might contribute to morphological diversifications of land plants. Conclusions: Our results indicate that different evolutionary rates and selection strengths lead to differing evolutionary patterns in SBP-box genes in land plants, providing a guide for future functional diversity analyses of these genes. © 2015 Zhang et al.

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