BGI Yunnan

Kunming, China

BGI Yunnan

Kunming, China
SEARCH FILTERS
Time filter
Source Type

Zhang S.-D.,CAS Kunming Institute of Botany | Ling L.-Z.,BGI Yunnan
Agri Gene | Year: 2017

The fresh fleshy peduncles of Hovenia acerba have been used as a food supplement and traditional herbal medicine (i.e. immunostimulatory and antialcoholism) for a long time. However, little is known about the genetic factors underlying peduncle development. Here, we presented the first transcriptome-wide peduncle development research at two developmental stages using Illumina's Genome Analyzer. Our results indicated that a total of 146,206 unigenes were identified and their functional annotation and classification revealed that the unigenes involved in energy catabolism and genetic information processing were necessary to the developing of peduncle in H. acerba. The comparison of Gene Ontology (GO) annotation between two developmental stages indicated that the term of oxidation-reduction process exhibited the big difference in unigene number, in which the possible relative transcription factors were identified. However, we found that these transcription factors were partly involved in oxidation-reduction process and most of them were involved in regulation of transcription. The metabolic process was classified into the second different GO term when compared unigene number between two stages. Combined with the KEGG pathway annotation, we found that carbohydrate metabolism showed the major difference in unigene number, which might contribute to the biosynthesis of polysaccharides as immunostimulatory agent. Finally, 54 candidate genes encoding 14 enzymes were found to biosynthesize flavonoid that has the antialcoholism effect. This study is the first report on transcriptome information in H. acerba and will promote to understand the genetic mechanism of peduncle development. © 2016 Elsevier Inc.


PubMed | Shandong Academy of Agricultural Sciences, Germplasm Bank of Wild Species and BGI Yunnan
Type: Journal Article | Journal: 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.


PubMed | BGI Yunnan, BGI Shenzhen, Hubei University of Education, CAS East China Sea Fisheries Research Institute and 2 more.
Type: | Journal: Scientific reports | Year: 2015

The desert is a harsh habitat for flora and microbial life due to its aridness and strong radiation. In this study, we constructed the first complete and deeply annotated genome of the genus Pontibacter (Pontibacter korlensis X14-1(T)= CCTCC AB 206081(T), X14-1). Reconstruction of the sugar metabolism process indicated that strain X14-1 can utilize diverse sugars, including cellulose, starch and sucrose; this result is consistent with previous experiments. Strain X14-1 is also able to resist desiccation and radiation in the desert through well-armed systems related to DNA repair, radical oxygen species (ROS) detoxification and the OstAB and TreYZ pathways for trehalose synthesis. A comparative transcriptomic analysis under gamma radiation revealed that strain X14-1 presents high-efficacy operating responses to radiation, including the robust expression of catalase and the manganese transport protein. Evaluation of 73 novel genes that are differentially expressed showed that some of these genes may contribute to the strains adaptation to radiation and desiccation through ferric transport and preservation.


PubMed | Shanxi Provincial Peoples Hospital, Shanxi Cancer Hospital, Shantou University, Henan Cancer Hospital and 4 more.
Type: Journal Article | Journal: 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 indicatesthat 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.


PubMed | BGI Shenzhen, Kunming University of Science and Technology, Yunnan University, The First Peoples Hospital of Yunnan Province and BGI Yunnan
Type: | Journal: Genetics in medicine : official journal of the American College of Medical Genetics | Year: 2017

Thalassemia is one of the most common monogenic diseases in southwestern China, especially among the Dai ethnic group. Here, we explore the feasibility of a next-generation sequencing (NGS) screening method specifically for the Dai people.Blood samples were obtained from Dai people for premarital screening. Double-blind, parallel hemoglobinopathy screening was conducted using both traditional hematological methods (red cell indexes and hemoglobin electrophoresis, then DNA sequencing) and an NGS approach.Among 951 tested individuals, we found a thalassemia carrier rate of 49.5% (471/951) using the NGS screen, in contrast to 22.0% (209/951) found using traditional methods. Almost 74.8% (217/290) of -thalassemia carriers and 30.5% (25/82) of composite - and -thalassemia carriers were missed by traditional screens. The proportion of such - and -thalassemia carriers among the Dai people is 8.6% (82/951). For -thalassemia carriers, the high ratio (66/99) of CD26 mutations may suggest a correlation between CD26 and the environmental adaption of the Dai people.Methodological comparisons demonstrate the superiority of NGS for both sensitivity and specificity, provide a comprehensive assessment of thalassemia screening strategies, and indicate that NGS is a competitive screening method, especially among populations with a high prevalence of disease.Genet Med advance online publication 26 January 2017Genetics in Medicine (2017); doi:10.1038/gim.2016.218.


Kapron C.M.,Trent University | Cheng L.,BGI Yunnan
Birth Defects Research Part A - Clinical and Molecular Teratology | Year: 2015

Background: While it is known that cadmium-exposed embryonic cells have increased activation of c-Jun N-terminal kinase (JNK), the role of this stress signaling pathway in the embryotoxic response is not clear. Thus, the effects of modification of the transcription factor c-Jun, one of the downstream targets of JNK, on cadmium-induced embryotoxicity were investigated in primary cultures of mouse embryo limb bud cells. Methods: Cultures of limb bud cells harvested on day 11 of gestation were pretreated with antisense oligonucleotides (ASO) to c-Jun to reduce its expression, and then incubated with cadmium in the form of cadmium chloride. Toxicity was measured through assessments of cell proliferation and differentiation, while the effectiveness of the ASO in reducing c-Jun was assessed through Western blotting using phosphorylation-specific antibodies. Results: When cells were treated with ASO c-Jun, the total amounts of c-Jun and also cadmium-induced c-Jun activation were diminished. Cadmium-induced cytotoxicity, indicated by reduced cell numbers and differentiation, was found to decrease when cells were exposed to the antisense oligonucleotides to c-Jun. In addition, limb cell numbers and differentiation were also enhanced by exposure to ASO in the absence of cadmium. Conclusion: The JNK pathway, and particularly the downstream effector c-Jun, appears to play an important role in regulating cell survival and differentiation in mouse embryo limb bud cells both in the presence and absence of the toxic metal cadmium. Birth Defects Research (Part A) 103:1039-1045, 2015. © 2015 Wiley Periodicals, Inc.


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.,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.


PubMed | CAS Kunming Institute of Botany and BGI Yunnan
Type: | Journal: BMC genomics | Year: 2015

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.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.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.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.

Loading BGI Yunnan collaborators
Loading BGI Yunnan collaborators