微生物基因组研究现状.pptx

嗜盐古菌基因组研究现状,报告人,目录,CONTENTS,Background,PART ONE,Current situation,PART TWO,Paper,PART THREE,Reference,PART FOUR,Thanks,End,,,,,,Background,PART ONE,,,测序技术简史,,,1950,1960,1970,1980,1990,2000,2010,Development of Sanger Sequencing (1977),Invention of Automated Fluorescent Sequencer (1985),Invention of Capillary Sequencer (1996),Invention of Applied Biosystems Solid System (2007),Invention of Illumina Genome Analyzer System (2006),Invention of 454 GS 20 Sequencer (2005),chemical degradation method by Maxam-Gilbert method (1977),Chemical degradation method by Whitfield (1954),Invention of Heliscope single molecular sequencer,Invention of Single molecule real time(SMRT) DNA sequencing,Invention of Nanopore single molecular sequencing (Oxford Nanopore corporation),Invention of personal genome machine,Invention of optical mappingsystem,人类基因组计划的研究概况,1986年,,1988年,1988年美国能源部和国家卫生研究院率先在美国开展人类基因组计划，并经国会批准由政府给予资助。此后，成立了一个国际间的合作机构——人类基因组织 (Human Genome Organization)，由多个国家筹集资金和科研力量，积极参加这一国际性研究计划。,,1990年,1989年，美国国立卫生研究院成立了人类染色体研究中心，沃森出任第一任主任。,1989年,1990年，美国国会批准了“人类基因组计划”，并于10月1日正式启动，由多国科学家参加、被称为“生命科学阿波罗计划”的人类基因组计划正式启动。预计用15年时间，投资30亿美元，完成 30 亿对碱基的测序，并对所有基因进行绘图和排序。美国承担了全部任务的54%，英国33%，日本7%，法国2.8%，德国2.2%。 中国于1999年9月加入人类基因组计划并承担了 1% 的测序任务。,2000年,2000年6月26日，美国国家人类基因组研究所所长弗朗西斯·柯林斯、塞莱拉公司的董事长兼首席科学家克莱格·文特尔、美国总统克林顿、英国首相布莱尔联合宣布人类基因组工作草图绘制成功。此后，人类基因组研究进入绘制“完成图”的阶段。与“框架图”相比， “完成图”的覆盖率从90％扩展到100％，准确率从99％上升到99.99％。,2001年,2001年2月12日，参加绘制人类基因组图谱的美、英、日、法、德、中6国科学家公布了更加准确、清晰、完整的人类基因组图谱，并指出人类基因总数只有 3 ~ 3.5万个,编码序列占2%。 2001年7月10日，中国“人类基因组计划”重大项目秘书长杨焕明教授宣布：在人类基因组完成图的绘制工作中，中国已率先超额（1.13%）完成所承担的任务。,1998年,1998年，生产DNA测序仪的最大厂家Perkin-Elmer(简称PE)公司与文特尔领导的基因研究所合作成立了塞莱拉（Celera）遗传信息公司，并宣布他们将利用最新技术在3年内完成人类基因组的测序工作，这使得该计划处于一种公私竞争的状态，从而加快了人类基因组的研究步伐。,“想搞清楚微生物如何影响人和地球的健康，需要启动一个《国际微生物组计划》”2015年10月29日的《自然》周刊刊登了德国、美国和中国的三位科学家的建议，他们分别是德国马普海洋研究所的 Nicole Dubilier教授、美国夏威夷大学的Margaret McFall-Ngai教授和中国上海交通大学的赵立平教授。,白宫科学与技术政策办公室（OSTP）在5月14日表示，在多家国立机构的帮助下，这项斥资1.21亿美元的“国家微生物组计划”（NMI, National Microbiome Initiative ）将尝试在未来两年中绘制并研究这些微生物的组合。 未来几年中，除联邦机构外，美国数十所大学与研究机构也将加入NMI，它们在当天白宫召开的微生物组计划会议上承诺，将在这个领域投入4亿美元。在4年的时间里对发展中国家的营养和病虫害防治项目进行研究，还有一些研究机构将聚焦微生物在癌症治疗和海洋微生物学等科目中所扮演的角色。,Current situation,PART TWO,,,132,,,,Paper,PART THREE,,,1,2,3,4,5,6,,Main point,· Endolithic communities harbor low diversity because of the extreme nature of their natural environment and, as such, provide unique model systems to investigate the ecology of native microbial assemblages,Doubt from introduction,· What kind of role does each genus play? How to identify? · How to cooperate? How to accomplish carbon cycling? · What change does it make to adapt hyper-arid and hyperhaline environment?,Background information/ aim of work,· These endolithic communities are typically composed of primary producers, mostly Cyanobacteria, interacting with diverse heterotrophic bacteria and/or archaea and sometimes eukaryotes (Wierzchos et al., 2012a; Chan et al., 2013;Robinson et al.2015).,· The assortment of colonized rock habitats discovered so far shows that life has found innovative ways to adapt to extreme water stress (Pointing and Belnap, 2012; Wierzchos et al., 2012a).,· In the most arid deserts on Earth, microorganisms find refuge inside rock substrates as a survival strategy (Pointing and Belnap, 2012;Wierzchos et al., 2012a).,Between rainfall events and extremely low air relative humidity (RH) (mean year -1 values <35%)for decades.,Halite nodule interior in the Yungay area of the hyper-arid core remained wet for 5362 h year-1 (Wierzchos et al., 2012b),Background information/ aim of work,· Sequenced the pooled metagenome of a microbial community associated with halite nodules,· To unravel the community functional adaptations and the interactions between community members,Key finding/ Data from figures,1、Halite metagenome taxonomic and functional analyses,Key finding/Data from figures,A community dominated by Archaea (71%) and also composed of Bacteria (27%) and Eukarya (1%).,Halobacteria represented the majority ，Archaea (90%) with a small representation of Nanohaloarchaea (2%). Most bacteria belonged to the Salinibacter genera (63%) and Cyanobacteria constituted 15% of bacteria,Key finding/Data from figures,Reconstruction of 16S rRNA gene sequences from the metagenomic dataset,Key finding/Data from figures,The functional composition of the halite metagenome,,Key finding/Data from figures,Of the genes involved in carbon metabolism, only 8% were allocated to autotrophic CO2 fixation,Calvin–Benson cycle (CB) was the only pathway for autotrophic CO2 fixation,Key finding/Data from figures,Majority of the assigned RubisCO type I genes (> 91%) were attributed to members of the Cyanobacteria,RubisCO type III genes and those were all from members of the Halobacteriaceae,Sequences(99%) of key enzymes in CB pathway belonged to Cyanobacteria,,Key finding/Data from figures,PSI and PSII major proteins and for light harvesting complexes, belonged to Cyanobacteria with only a small fraction assigned to green algae,24 to 26% of all sequences were not given a taxonomic rank and 3% of PSII sequences were assigned to unclassified viruses,Key finding/Data from figures,Phototrophy was also supported via light-driven proton pumps that belong to a number of heterotrophs including Roseiflexus (proteorhodopsin), Salinibacter (xanthorhodopsin) and Halobacteriaceae (bacteriorhodopsin),Key finding/Data from figures,No nitrogenase (nif) genes were detected,Key finding/ Data from figures,2、Osmotic adaptation of the algae from the halite community,Key finding/Data from figures,Key finding/Data from figures,The alga clustered with other members of the Chlorophyta ,grouping consistently with the Micromonas and Ostreococcus species,Key finding/Data from figures,Halite alga (blue),Micromonas sp. RCC299 (red),Ostreococcus tauri (purple) and Dunaliella salina (orange),Using a paired one-sided Wilcoxon t-testhad significantly lower pI when paired using BLASTP with O. tauri homologues (difference of means: 0.55) and with Micromonas sp. RCC299 homologues (difference of means: 0.24).,Key finding/ Data from figures,Bayesian model comparison: reported that the probability that the proteins of the halite alga had a lower mean pI (difference of means less than 0) than that of Micromonas sp. RCC299 was 97.9%. This analysis predicted that the halite alga might have one of the lowest protein pI distributions of any reported eukaryote,Key finding/ Data from figures,The halite metagenome also contained a number of genes from algal organelles. Predicted proteins for the organelles had mean pI values above 8, which may indicate different environmental conditions in the organelle than in the intracellular space,Key finding/ Data from figures,3、The complete genome sequence for a novel nanohaloarchaeon,,Key finding/Data from figures,Genome assembly produced a nanohaloarchaeon genome of 1.1 Mbp long, encoding for 1292 genes and with a G+C content of 46.4% (referred to as SG9),,Key finding/Data from figures,Isoelectric point distributions for all predicted proteins in three “salt-in” species,Haloarcula hispanica ATCC (red), Candidatus Nanopetramus SG9 (orange), Salinibacter ruber M8 (blue), and one non salt-in species, Halothece PCC 7418 (green).,Key finding/ Data from figures,The SG9 genome was highly reduced and mostly composed of protein encoding genes 79% of predicted proteins could not be assigned to known function. The evidence including rhodopsin biosynthesis, carbohydrate metabolism, PTS,PPP,3 potassium uptake systems, (Trk, Ktr and HKT) archaeal flagellar proteins, photolyase, archaeal-like nucleotide excision repair pathways etc, all typically found in archaea,,Key finding/Data from figures,The 16S rRNA gene sequence of SG9 was 91% identical to that of Candidatus Haloredivivus and 90% and 88% identical to Candidatus Nanosalina and Candidatus Nanosalinarum,,Key finding/Data from figures,Lower G+C content indicates CRISPR system via horizontal gene transfer (HGT),Locus was acquired from Methanobacteria or Halobacteria rather than the phylogenetically closer Nanoarchaeota, Halobacteria genomes have high G+C%, as a result, it comes from halophilic methanogen, Methanohalophilus,Spacer 22 was the most recently added spacer to the CRISPR array,Key finding/ Data from figures,4、Halite community viral diversity,,Key finding/Data from figures,Phage similarity networks. (weighted network by the proportion and percent identity of predicted proteins they shared),Protein–protein similarity networks.,Viruses are coloured according to network communities predicted by the Walktrap community finding algorithm,,Key finding/Data from figures,Identification of over 30 complete or near complete viral or proviral genomes in the halite metagenome,For they shared few to no genes with others, making a phylogenetic or tree-based analysis impractical,,Key finding/Data from figures,Cat1: most confident; cat2: likely prediction; cat3: possible prediction,,Main conclusion,· CO2 fixation via the CB pathway by Cyanobacteria as the major primary producers, and Halothece is likely responsible for most of the CO2 fixed in the community. A number of organisms in the halite community encoded light-driven proton pumps in their genomes with the potential to carry out photoheterotrophy. · The pI of the alga predicted proteins was one of the lowest pI reported for any eukaryote. A low median isoelectric point (pI) suggesting a ‘salt-in’ strategy for osmotic balance.,,Main conclusion,· As the first nanohaloarchaeon genome , SG9 has a photoheterotrophic life-style and uses the ‘salt-in’ strategy for low proteome PI. Adaptive immunity against viruses is also a feature of nanohaloarchaeal and SG9 acquired its CRISPR system via HGT. · Viruses infecting haloarchaea come in a variety of virion morphotypes with majority is head-tail structure. Haloviruses genomes have rather high G+C content , also characteristic of haloarchaea.,,Discussion/gaps in work,· CRISPR sequences found in the newly described SG9 genome where also present on a partial viral genome, providing a direct connection between virus and host. · Further understanding of the major taxonomic groups and essential metabolic pathways underlying the functioning of this unique community will require a combination of field-based measurements of metabolic activity coupled with meta-transcriptomics, to capture gene expression levels for specific function and taxonomic groups,Reference,PART FOUR,,,Crits‐Christoph A, Gelsinger D R, Ma B, et al. Functional interactions of archaea, bacteria, and viruses in a hypersaline endolithic community[J]. Environmental Microbiology, 2016, 18(6). Anderson R E, Sogin M L, Baross J A. Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents[J]. Fems Microbiology Ecology, 2014, 91(1):1-11. Andrade K, Logemann J, Heidelberg K B, et al. Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem.[J]. Isme Journal, 2015, 9(12). Atanasova N S, Roine E, Oren A, et al. Global network of specific virus–host interactions in hypersaline environments[J]. Environmental Microbiology, 2012, 14(2):426–440. Becker E A, Seitzer P M, Tritt A, et al. Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response.[J]. Plos Genetics, 2014, 10(11):e1004784-e1004784.,Reference,Thanks for listening,End,,,