901
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Xia M, Zhang F, Rao H, Chi X, Khan G, Zhang Y, Yu J, Chen S. Complete chloroplast genome sequence of Parnassia brevistyla (Celastraceae) and phylogenetic analysis with related species. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:1187-1188. [PMID: 33474459 PMCID: PMC7800561 DOI: 10.1080/23802359.2018.1524725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The taxonomic status of Parnassia has been widely discussed, which has been placed in more than five families, Parnassiaceae, Droseraceae, Saxifragaceae, and Celastraceae. Due to the lack of reliable genetic data, we sequenced and analyzed P. brevistyla chloroplast genome for future genetic study. The complete chloroplast genomes of Parnassia brevistyla was sequenced with NovaSeq 6000. The full length of P. brevistyla chloroplast genomes is 151,728 bp. A total of 114 unique genes, including 30 tRNA genes, four rRNA genes, and 80 protein-coding genes were found in the chloroplast genome. Using the whole chloroplast genome sequences alignment of 10 species from Celastraceae and Saxifragaceae, the phylogenetic relationship was built. The phylogenetic position of P. brevistyla was closely clustered with Celastraceae. The complete chloroplast genome of P. brevistyla provides utility information for further research of phylogenetic relationship and taxonomic status of Parnassia.
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Affiliation(s)
- Mingze Xia
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Faqi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, China
| | - Hua Rao
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaofeng Chi
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Gulzar Khan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Yu Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingya Yu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shilong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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902
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Liu S, Huang S, Chen F, Zhao L, Yuan Y, Francis SS, Fang L, Li Z, Lin L, Liu R, Zhang Y, Xu H, Li S, Zhou Y, Davies RW, Liu Q, Walters RG, Lin K, Ju J, Korneliussen T, Yang MA, Fu Q, Wang J, Zhou L, Krogh A, Zhang H, Wang W, Chen Z, Cai Z, Yin Y, Yang H, Mao M, Shendure J, Wang J, Albrechtsen A, Jin X, Nielsen R, Xu X. Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History. Cell 2018; 175:347-359.e14. [DOI: 10.1016/j.cell.2018.08.016] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/12/2018] [Accepted: 08/08/2018] [Indexed: 02/06/2023]
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903
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Li B, Kremling KAG, Wu P, Bukowski R, Romay MC, Xie E, Buckler ES, Chen M. Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation. Genome Res 2018; 28:1555-1565. [PMID: 30166407 PMCID: PMC6169892 DOI: 10.1101/gr.229716.117] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 08/29/2018] [Indexed: 12/16/2022]
Abstract
Ribosomal repeats occupy 5% of a plant genome, yet there has been little study of their diversity in the modern age of genomics. Ribosomal copy number and expression variation present an opportunity to tap a novel source of diversity. In the present study, we estimated the ribosomal DNA (rDNA) copy number and ribosomal RNA (rRNA) expression for a population of maize inbred lines and investigated the potential role of rDNA and rRNA dosage in regulating global gene expression. Extensive variation was found in both ribosomal DNA copy number and ribosomal RNA expression among maize inbred lines. However, rRNA abundance was not consistent with the copy number of the rDNA. We have not found that the rDNA gene dosage has a regulatory role in gene expression; however, thousands of genes are identified to be coregulated with rRNA expression, including genes participating in ribosome biogenesis and other functionally relevant pathways. We further investigated the potential roles of copy number and the expression level of rDNA on agronomic traits and found that both correlated with flowering time but through different regulatory mechanisms. This comprehensive analysis suggested that rRNA expression variation is a valuable source of functional diversity that affects gene expression variation and field-based phenotypic changes.
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Affiliation(s)
- Bo Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China 100101
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
| | - Karl A G Kremling
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Penghao Wu
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- College of Agronomy, Xinjiang Agriculture University, Urumqi, China 830052
| | - Robert Bukowski
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York 14853, USA
| | - Maria C Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
| | - En Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China 100101
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
- US Department of Agriculture-Agricultural Research Service (USDA-ARS), Ithaca, New York 14853, USA
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China 100101
- University of Chinese Academy of Sciences, Beijing, China 100049
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904
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Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. BIOINFORMATICS (OXFORD, ENGLAND) 2018. [PMID: 30423086 DOI: 10.1093/bioinformatics/bty560%j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
MOTIVATION Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. RESULTS We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2-5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. AVAILABILITY AND IMPLEMENTATION The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.
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Affiliation(s)
- Shifu Chen
- Department of Bioinformatics, HaploX Biotechnology, Shenzhen, China
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yanqing Zhou
- Department of Bioinformatics, HaploX Biotechnology, Shenzhen, China
| | - Yaru Chen
- Department of Bioinformatics, HaploX Biotechnology, Shenzhen, China
| | - Jia Gu
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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905
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Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. BIOINFORMATICS (OXFORD, ENGLAND) 2018; 34:i884-i890. [PMID: 30423086 DOI: 10.1101/274100] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
MOTIVATION Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. RESULTS We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2-5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. AVAILABILITY AND IMPLEMENTATION The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.
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Affiliation(s)
- Shifu Chen
- Department of Bioinformatics, HaploX Biotechnology, Shenzhen, China
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yanqing Zhou
- Department of Bioinformatics, HaploX Biotechnology, Shenzhen, China
| | - Yaru Chen
- Department of Bioinformatics, HaploX Biotechnology, Shenzhen, China
| | - Jia Gu
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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906
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Zhao H, Wang S, Wang J, Chen C, Hao S, Chen L, Fei B, Han K, Li R, Shi C, Sun H, Wang S, Xu H, Yang K, Xu X, Shan X, Shi J, Feng A, Fan G, Liu X, Zhao S, Zhang C, Gao Q, Gao Z, Jiang Z. The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana). Gigascience 2018; 7:5067873. [PMID: 30101322 PMCID: PMC6117794 DOI: 10.1093/gigascience/giy097] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/03/2018] [Accepted: 07/26/2018] [Indexed: 01/22/2023] Open
Abstract
Background Calamus simplicifolius and Daemonorops jenkinsiana are two representative rattans, the most significant material sources for the rattan industry. However, the lack of reference genome sequences is a major obstacle for basic and applied biology on rattan. Findings We produced two chromosome-level genome assemblies of C. simplicifolius and D. jenkinsiana using Illumina, Pacific Biosciences, and Hi-C sequencing data. A total of ∼730 Gb and ∼682 Gb of raw data covered the predicted genome lengths (∼1.98 Gb of C. simplicifolius and ∼1.61 Gb of D. jenkinsiana) to ∼372 × and ∼426 × read depths, respectively. The two de novo genome assemblies, ∼1.94 Gb and ∼1.58 Gb, were generated with scaffold N50s of ∼160 Mb and ∼119 Mb in C. simplicifolius and D. jenkinsiana, respectively. The C. simplicifolius and D. jenkinsiana genomes were predicted to harbor 51,235 and 53,342 intact protein-coding gene models, respectively. Benchmarking Universal Single-Copy Orthologs evaluation demonstrated that genome completeness reached 96.4% and 91.3% in the C. simplicifolius and D. jenkinsiana genomes, respectively. Genome evolution showed that four Arecaceae plants clustered together, and the divergence time between the two rattans was ∼19.3 million years ago. Additionally, we identified 193 and 172 genes involved in the lignin biosynthesis pathway in the C. simplicifolius and D. jenkinsiana genomes, respectively. Conclusions We present the first de novo assemblies of two rattan genomes (C. simplicifolius and D. jenkinsiana). These data will not only provide a fundamental resource for functional genomics, particularly in promoting germplasm utilization for breeding, but also serve as reference genomes for comparative studies between and among different species.
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Affiliation(s)
- Hansheng Zhao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District, Beijing 100102, China
| | - Songbo Wang
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, No. 7, Pengfei Road, Dapeng District, Shenzhen 518120, China
| | - Jiongliang Wang
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District, Beijing 100102, China
| | - Chunhai Chen
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Shijie Hao
- BGI-Qingdao, No. 2877, Tuanjie Road, Sino-German Ecopark, Qingdao, Shandong 266555, China
| | - Lianfu Chen
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District, Beijing 100102, China
| | - Benhua Fei
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District, Beijing 100102, China
| | - Kai Han
- BGI-Qingdao, No. 2877, Tuanjie Road, Sino-German Ecopark, Qingdao, Shandong 266555, China
| | - Rongsheng Li
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangshanyi Rd, Tianhe District, Guangzhou 510000, China
| | - Chengcheng Shi
- BGI-Qingdao, No. 2877, Tuanjie Road, Sino-German Ecopark, Qingdao, Shandong 266555, China
| | - Huayu Sun
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District, Beijing 100102, China
| | - Sining Wang
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District, Beijing 100102, China
| | - Hao Xu
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District, Beijing 100102, China
| | - Kebin Yang
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District, Beijing 100102, China
| | - Xiurong Xu
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District, Beijing 100102, China
| | - Xuemeng Shan
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District, Beijing 100102, China
| | - Jingjing Shi
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District, Beijing 100102, China
| | - Aiqin Feng
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Guangyi Fan
- BGI-Qingdao, No. 2877, Tuanjie Road, Sino-German Ecopark, Qingdao, Shandong 266555, China
| | - Xin Liu
- BGI-Qingdao, No. 2877, Tuanjie Road, Sino-German Ecopark, Qingdao, Shandong 266555, China
- BGI-Fuyang, Floor 3, Jinshan Building, Qinghe East Road, Yingzhou District, Fuyang 236009, China
| | - Shancen Zhao
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, No. 7, Pengfei Road, Dapeng District, Shenzhen 518120, China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, No. 7, Pengfei Road, Dapeng District, Shenzhen 518120, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Zhimin Gao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District, Beijing 100102, China
| | - Zehui Jiang
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District, Beijing 100102, China
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907
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Tai Y, Liu C, Yu S, Yang H, Sun J, Guo C, Huang B, Liu Z, Yuan Y, Xia E, Wei C, Wan X. Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis). BMC Genomics 2018; 19:616. [PMID: 30111282 PMCID: PMC6094456 DOI: 10.1186/s12864-018-4999-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 08/08/2018] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The leaves of tea plants (Camellia sinensis) are used to produce tea, which is one of the most popular beverages consumed worldwide. The nutritional value and health benefits of tea are mainly related to three abundant characteristic metabolites; catechins, theanine and caffeine. Weighted gene co-expression network analysis (WGCNA) is a powerful system for investigating correlations between genes, identifying modules among highly correlated genes, and relating modules to phenotypic traits based on gene expression profiling. Currently, relatively little is known about the regulatory mechanisms and correlations between these three secondary metabolic pathways at the omics level in tea. RESULTS In this study, levels of the three secondary metabolites in ten different tissues of tea plants were determined, 87,319 high-quality unigenes were assembled, and 55,607 differentially expressed genes (DEGs) were identified by pairwise comparison. The resultant co-expression network included 35 co-expression modules, of which 20 modules were significantly associated with the biosynthesis of catechins, theanine and caffeine. Furthermore, we identified several hub genes related to these three metabolic pathways, and analysed their regulatory relationships using RNA-Seq data. The results showed that these hub genes are regulated by genes involved in all three metabolic pathways, and they regulate the biosynthesis of all three metabolites. It is notable that light was identified as an important regulator for the biosynthesis of catechins. CONCLUSION Our integrated omics-level WGCNA analysis provides novel insights into the potential regulatory mechanisms of catechins, theanine and caffeine metabolism, and the identified hub genes provide an important reference for further research on the molecular biology of tea plants.
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Affiliation(s)
- Yuling Tai
- School of Life Science, Anhui Agricultural University, Hefei, 230036 China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Chun Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Shuwei Yu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Hua Yang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Jiameng Sun
- School of Life Science, Anhui Agricultural University, Hefei, 230036 China
| | - Chunxiao Guo
- School of Life Science, Anhui Agricultural University, Hefei, 230036 China
| | - Bei Huang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Zhaoye Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Yi Yuan
- School of Life Science, Anhui Agricultural University, Hefei, 230036 China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
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908
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Zhao H, Zhang M, Zhong W, Zhang J, Huang W, Zhang Y, Li W, Jia P, Zhang T, Liu Z, Lin J, Chen F. A novel IRF6 mutation causing non-syndromic cleft lip with or without cleft palate in a pedigree. Mutagenesis 2018; 33:195-202. [PMID: 30053123 DOI: 10.1093/mutage/gey012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/06/2018] [Indexed: 12/11/2022] Open
Affiliation(s)
- Huaxiang Zhao
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Mengqi Zhang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Wenjie Zhong
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Jieni Zhang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Wenbin Huang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Yunfan Zhang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Weiran Li
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Peizeng Jia
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Taowen Zhang
- Department of Orthodontics, Yantai Stomatology Hospital, Shandong, PR China
| | - Zhonghao Liu
- Department of Oral Implantology, Yantai Stomatology Hospital, Shandong, PR China
| | - Jiuxiang Lin
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Feng Chen
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, PR China
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909
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Li FN, Liao S, Guo M, Tuo L, Yan X, Li W, Jin T, Lee SMY, Sun CH. Mangrovicella endophytica gen. nov., sp. nov., a new member of the family Aurantimonadaceae isolated from Aegiceras corniculatum. Int J Syst Evol Microbiol 2018; 68:2838-2845. [PMID: 30010526 DOI: 10.1099/ijsem.0.002907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic, motile and short-rod-shaped bacterium, designated strain 5T4P-12-1T, was isolated from a piece of surface-sterilized bark of Aegiceras corniculatum collected from Cotai Ecological Zones in Macao, China and tested by a polyphasic approach to clarify its taxonomic position. Strain 5T4P-12-1T grew optimally with 0-1 % (w/v) NaCl at 30 °C and at pH 7.0-8.0. The 16S rRNA gene sequence of strain 5T4P-12-1T had the highest similarity (96.7 %) to Aureimonas altamirensis DSM 21988T. Phylogenic analysis based on 16S rRNA gene sequences and coding sequences of 98 protein clusters showed that the strain represented a novel genus of the family Aurantimonadaceae. The predominant quinone system of strain 5T4P-12-1T was ubiquinone 10. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmethylethanolamine, an unidentified aminophospholipid, three unidentified aminolipids, three unidentified phospholipids and three unidentified lipids. The major fatty acids (>10 % of total fatty acids) were C18 : 1ω7c (55.4 %) and C18 : 1 2-OH (15.6 %). The DNA G+C content of strain 5T4P-12-1T was 66.5 mol%. Based on the phylogenic, phenotypic and chemotaxonomic features, strain 5T4P-12-1T is considered to represent a novel species of a new genus in the family Aurantimonadaceae, for which the name Mangrovicella endophytica gen. nov., sp. nov. is proposed. The type strain is 5T4P-12-1T (=KCTC 62053T=CGMCC 1.16279 T).
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Affiliation(s)
- Fei-Na Li
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Shuilin Liao
- 2BGI-Shenzhen, Beishan, Industrial Zone, Shenzhen 518083, PR China
- 3China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, PR China
- 4BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, PR China
| | - Min Guo
- 5State Key Laboratory of Quality Research of Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, PR China
| | - Li Tuo
- 6Research Center for Medicine and Biology, Zunyi Medical University, Zunyi 563003, PR China
| | - Xinyu Yan
- 7China Pharmaceutical University, Nanjing 210009, PR China
| | - Wenlian Li
- 7China Pharmaceutical University, Nanjing 210009, PR China
| | - Tao Jin
- 2BGI-Shenzhen, Beishan, Industrial Zone, Shenzhen 518083, PR China
- 3China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, PR China
| | - Simon Ming-Yuen Lee
- 5State Key Laboratory of Quality Research of Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, PR China
| | - Cheng-Hang Sun
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
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910
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Li FW, Brouwer P, Carretero-Paulet L, Cheng S, de Vries J, Delaux PM, Eily A, Koppers N, Kuo LY, Li Z, Simenc M, Small I, Wafula E, Angarita S, Barker MS, Bräutigam A, dePamphilis C, Gould S, Hosmani PS, Huang YM, Huettel B, Kato Y, Liu X, Maere S, McDowell R, Mueller LA, Nierop KGJ, Rensing SA, Robison T, Rothfels CJ, Sigel EM, Song Y, Timilsena PR, Van de Peer Y, Wang H, Wilhelmsson PKI, Wolf PG, Xu X, Der JP, Schluepmann H, Wong GKS, Pryer KM. Fern genomes elucidate land plant evolution and cyanobacterial symbioses. NATURE PLANTS 2018; 4:460-472. [PMID: 29967517 PMCID: PMC6786969 DOI: 10.1038/s41477-018-0188-8] [Citation(s) in RCA: 250] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/24/2018] [Indexed: 05/18/2023]
Abstract
Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns-one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.
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Affiliation(s)
- Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA.
- Plant Biology Section, Cornell University, Ithaca, NY, USA.
| | - Paul Brouwer
- Molecular Plant Physiology Department, Utrecht University, Utrecht, the Netherlands
| | - Lorenzo Carretero-Paulet
- Bioinformatics Institute Ghent and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Shifeng Cheng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet Tolosan, France
| | - Ariana Eily
- Department of Biology, Duke University, Durham, NC, USA
| | - Nils Koppers
- Department of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Dusseldorf, Germany
| | | | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Mathew Simenc
- Department of Biological Science, California State University, Fullerton, CA, USA
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Eric Wafula
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Stephany Angarita
- Department of Biological Science, California State University, Fullerton, CA, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | - Claude dePamphilis
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Sven Gould
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Dusseldorf, Germany
| | | | | | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding, Cologne, Germany
| | - Yoichiro Kato
- Institute for Sustainable Agro-ecosystem Services, University of Tokyo, Tokyo, Japan
| | - Xin Liu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Steven Maere
- Bioinformatics Institute Ghent and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Rose McDowell
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | | | - Klaas G J Nierop
- Geolab, Faculty of Geosciences, Utrecht University, Utrecht, the Netherlands
| | | | - Tanner Robison
- Department of Biology, Utah State University, Logan, UT, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Erin M Sigel
- Department of Biology, University of Louisiana, Lafayette, LA, USA
| | - Yue Song
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Prakash R Timilsena
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Yves Van de Peer
- Bioinformatics Institute Ghent and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Hongli Wang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | | | - Paul G Wolf
- Department of Biology, Utah State University, Logan, UT, USA
| | - Xun Xu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Joshua P Der
- Department of Biological Science, California State University, Fullerton, CA, USA
| | | | - Gane K-S Wong
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Department of Biological Sciences, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
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911
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Draft Genome Sequence of Mycobacterium virginiense Strain GF75, Isolated from the Mud of a Swine Farm in Japan. GENOME ANNOUNCEMENTS 2018; 6:6/17/e00362-18. [PMID: 29700164 PMCID: PMC5920169 DOI: 10.1128/genomea.00362-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mycobacterium virginiense, a newly described species of the Mycobacterium terrae complex, is a cause of tenosynovitis and osteomyelitis in the United States. Here, we report the 4,849,424-bp draft genome sequence of M. virginiense strain GF75, isolated from a mud sample taken from a Japanese swine farm.
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912
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Zhang L, Xu P, Cai Y, Ma L, Li S, Li S, Xie W, Song J, Peng L, Yan H, Zou L, Ma Y, Zhang C, Gao Q, Wang J. The draft genome assembly of Rhododendron delavayi Franch. var. delavayi. Gigascience 2017; 6:1-11. [PMID: 29020749 PMCID: PMC5632301 DOI: 10.1093/gigascience/gix076] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/28/2017] [Accepted: 08/04/2017] [Indexed: 01/16/2023] Open
Abstract
Rhododendron delavayi Franch. is globally famous as an ornamental plant. Its distribution in southwest China covers several different habitats and environments. However, not much research had been conducted on Rhododendron spp. at the molecular level, which hinders understanding of its evolution, speciation, and synthesis of secondary metabolites, as well as its wide adaptability to different environments. Here, we report the genome assembly and gene annotation of R. delavayi var. delavayi (the second genome sequenced in the Ericaceae), which will facilitate the study of the family. The genome assembly will have further applications in genome-assisted cultivar breeding. The final size of the assembled R. delavayi var. delavayi genome (695.09 Mb) was close to the 697.94 Mb, estimated by k-mer analysis. A total of 336.83 gigabases (Gb) of raw Illumina HiSeq 2000 reads were generated from 9 libraries (with insert sizes ranging from 170 bp to 40 kb), achieving a raw sequencing depth of ×482.6. After quality filtering, 246.06 Gb of clean reads were obtained, giving ×352.55 coverage depth. Assembly using Platanus gave a total scaffold length of 695.09 Mb, with a contig N50 of 61.8 kb and a scaffold N50 of 637.83 kb. Gene prediction resulted in the annotation of 32 938 protein-coding genes. The genome completeness was evaluated by CEGMA and BUSCO and reached 95.97% and 92.8%, respectively. The gene annotation completeness was also evaluated by CEGMA and BUSCO and reached 97.01% and 87.4%, respectively. Genome annotation revealed that 51.77% of the R. delavayi genome is composed of transposable elements, and 37.48% of long terminal repeat elements (LTRs). The de novo assembled genome of R. delavayi var. delavayi (hereinafter referred to as R. delavayi) is the second genomic resource of the family Ericaceae and will provide a valuable resource for research on future comparative genomic studies in Rhododendron species. The availability of the R. delavayi genome sequence will hopefully provide a tool for scientists to tackle open questions regarding molecular mechanisms underlying environmental interactions in the genus Rhododendron, more accurately understand the evolutionary processes and systematics of the genus, facilitate the identification of genes encoding pharmaceutically important compounds, and accelerate molecular breeding to release elite varieties.
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Affiliation(s)
- Lu Zhang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Pengwei Xu
- BGI-Shenzhen, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Yanfei Cai
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Lulin Ma
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Shifeng Li
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Shufa Li
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Weijia Xie
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Jie Song
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Lvchun Peng
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Huijun Yan
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Ling Zou
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Yongpeng Ma
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei Road, Panlong District, Kunming, Yunnan 650201, China
| | - Chengjun Zhang
- Germplasm Bank of Wild species, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei Road, Panlong District, Kunming, Yunnan 650201, China
| | - Qiang Gao
- BGI-Shenzhen, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Jihua Wang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
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