2 Journal of Environmental Entomology bp SOLiD Solexa 454 NIH SOLiD PCR Sanger 70 bp ABI SOLiD Illumina Solexa Roche 454 PacBio

Size: px

Start display at page:

Download "2 Journal of Environmental Entomology bp SOLiD Solexa 454 NIH SOLiD PCR Sanger 70 bp ABI SOLiD Illumina Solexa Roche 454 PacBio"

枯佟焚穆
5 years ago
Views:

2017 39 1 1-18 http hjkcxb. alljournals. net Journal of Environmental Entomology doi 10. 3969 /j. issn. 1674-0858. 2017. 01. 1 Invited Review. J. 2017 39 1 1-18.

1 http hjkcxb. alljournals. net Journal of Environmental Entomology doi /j. issn Invited Review. J * NCBI Q963 S43 A The progress of insecg genomic research and the gene database YIN Chuan-Lin LI Mei-Zhen HE Kang DING Si-Min GUO Dian-Hao XI Yu LI Fei * Institute of Inesct Science Zhejiang University Hangzhou China Abstract With huge amount of insect genome sequencing data was generated entomology has entered a new era of systematic biology. Up to now 467 insect genome projects have been registered on NCBI among which 225 have submitted with sequencing raw reads 215 have been assemblied 65 have been annotated and 43 have been published. Here we reviewed the development of different sequence technologies methods and problems of genome assembly genome annotation and analysis and important achievements in the field of insect genome projects. In addition we summarized the development of insect genome databases. Insect genomics is now a hotspot of scientific study which has wide applications in pest control and utilization of the resource insects. Key words Insect genome genome database big DATA biological databases % Robinson et al % Robinson et al YFC E - mail yincl2013@ 126. com * Author for correspondence E - mail lifei18@ zju. edu. cn Received Accepted

2 2 Journal of Environmental Entomology bp SOLiD Solexa 454 NIH SOLiD PCR Sanger 70 bp ABI SOLiD Illumina Solexa Roche 454 PacBio SMRT Oxford Nanopore Heather et al Illunima Solexa 1975 Sanger Coulson Sanger et al Maxam Gilbert PacBio SMRT Maxam et al Oxford Nanopore Technologies X Sanger et al % Solexa bp PCR PCR 2001 Sanger Venter et al Adams et al Mb Whole Geome Shotgun WGS Sanger

3 1期尹传林等昆虫基因组及数据库研究进展算机科学和信息科学等多学科的理论与技术产生和创造生物数据管理和存储生物数据以及图1 Fig. 1 3 挖掘和分析生物数据揭示生物数据蕴含的生物学意义近年来生物信息学得到了空前的充分测序技术的发展和昆虫基因组测序历程 The process of technology development and insect genome sequencing

4 4 Journal of Environmental Entomology 39 Shorty Edena Celera Sanger Celera De Bruijn Graph DBG SOAPdenovo Euler Velvet Ouzounis et al k-mer 3 Greey graph alogorithms 1 SSAKE SHARCGS VCAKE Wajid et al CABOG Miller et al SOAPdenove Luo et al ALLPATH-LG Butler et al ABySS Simpson et al SOAPdenove k-mer bp 200X SOAPdenove K-mer DNA DNA Richards et al et al De novo assembly comparative 1 assembly Wajid et al reads reads reads K-mer 2 overlap / layout / Consensus OLC CABOG Newbler ALLPATH-LG Wajid

5 1 5 pairedend mate-pair RNA 3 N50 RNA trna rrna pirna N50 mirna snorna rasirna RNA mirdeep N50 Friedlander et al RNAstructure contigs scaffolds N50 Bellaousov et al TripletSVM Xue et al. 4 CEGMA CEGMA Parra et al Rfam mirbase Kozomara et al snornabase CEG Scaffold CEG CEG CEG CEG 5 BUSCO BUSCO Simao et al CEGMA BUSCO CEGMA 2647 Glean Elsik et al Evigan Liu et al al jigsaw Allen et al RNA 1 4 Repeatmasker Tarailo-Graovac et al Blast MITEs LTR Recon Bao NCBI et al Piler Edgar et al Non-redundant protein sequences NR Repeatscout Price et al LTR-finder Xu RNA RNA 2005 RNA RNAdb Pang et al NONCODE Zhao et al. 3 PASA Xu et al MAKER Cantarel et refseq protein SWISS-PROT et al. 2007

6 6 Journal of Environmental Entomology i5k i5k National Center for Biotechnology synteny NCBI 43. 5% 15 2A Strepsiptera Odonata Blattodea Orthoptera Trichoptera 2. 6 Phthiraptera Thysanoptera Plecoptera Isoptera Zootermopsis nevadensis Ephemeroptera Coleoptera Hemiptera Lepidoptera Hymenoptera Diptera gene cluster % % % 9. 30% 4. 18% % 3. 1 i5k i5k Gene Robinson Information NCBI BioProject 2B 215 Science

7 Fig. 2 2 The statistics of insect genomes have been released 3 Dazao Mb contig N kb scaffold N kb moricin cecropins lysozymes hemolin lectins prophenoloxidases 2008 NCBI contig N kb scaffold N Mb 87% scaffold LINEs SINEs 14. 5% 13. 3% Gly Ala Ser trna trna Ser1 Ser2 Ser3 D-AB1 DNJ Bomyx mori 2004 Xia et al. 2004

8 8 Journal of Environmental Entomology 39 1 Table 1 The published insect genomes Species Mb N50 Sequencing Chromosome Genome size Kb platform scaffolds Gene numbe References Drosophila melanogaster Anopheles gambiae Bombyx mori Apis mellifera Aedes aegypti Tribolium castaneum Culex quinquefasciatus ~ 180 Sanger Sanger Sanger Sanger Sanger Applied Biosystems FLX Science Science Science Nature Science Nature Science FLX Camponotus floridanus Harpegnathos saltator FLX Science Acyrthosiphon pisum 525 Sanger PLoS Biol e Pediculus humanus FLX PNAS Nasonia vitripennis Acromyrmex echinatior FLX FLX Science Genome Res Linepithema humile FLX Titanium PNAS Pogonomyrmex barbatus XLR PNAS Atta cephalotes 309 Roche PLoS Genetics e Solenopsis invicta 343 Roche PNAS Danaus plexippus FLX /titanium platform Cell Heliconius melpomene and Illumina Nature 2012

9 1 9 Species Mb N50 Sequencing Chromosome Genome size Kb platform scaffolds Gene number References Dendroctonus ponderosae Lasioglossum albipes Plutella xylostella Ceratosolen solmsi 246 Illumina Hiseq Illumina Illumina Hiseq Illumina Hiseq Genome Biol R27 Genome Biol R142 Nature Genetics Genome Biol R141 Antarctic midge 99 Illumina Nat. Commun Illumina Hiseq Cerapachys biroi Curr Biol Musca domestica Stick insect 728 Illumina Illumina Genome Biol Science Zootermopsis nevadensis Locusta migratoria 472 Illumina Hiseq Nat. Commun Illumina Hiseq Nat. Commun Nilaparvata lugens Spodoptera frugiperda Diuraphis noxia 1324 Illumina Hiseq Illumina Illumina Hiseq Genome Biol Genomics BMC Genomics Hypothenemus hampei 163 Illumina Hiseq Rep Lucilia cuprina 458 Illumina - ALLPATHS - LG Nat. Commun Operophtera brumata 638 Illumina Miseq Genome Biol. Evol Cimex lectularius 650 Illumina - ALLPATHS - LG Nat. Commun Ceratitis capitata 479 Illumina Genome Biol

10 10 Journal of Environmental Entomology Apis mellifera The Honeybee 517 Mb 464 Genome Sequencing Consortium 2006 contig N kb scaffold N kb contig N kb 41 kb scaffold N kb kb 236 Mb % AT-rich 67% mirna Drosophila melanogaster 58% 56% AT Buchnera aphidicola 10% 85% dynamin DNA Dnmt1 Dnmt2 Dnmt3 DNA Sanger contigs Consortium Mb Pediculus humanus 2010 N. giraulti and N. longicornis Sanger 108 Mb Illumina N. scaffold N kb vitripennis 62% and 57 micrornas 62. 6% reads N. vitripennis 84. 7% 86. 3% N. vitripennis Riesia 52 mirna Riesia DNA DNA Riesia Dnmt1 3 N. vitripennis Toll N. vitripennis yellow /major royal jelly Kirkness N. vitripennis Wolbachia et al IMD hexamerin Nasonia vitripennis 2010 N50 = kb 6181 Scaffolds N50 = 709 kb Acyrthosiphon pisum

11 1 11 Werren et al Mb Danaus plexippus Cell Illumina Genome Analyzer IIx HiSeq2000 Fosmid-to-Fosmid WGS 1819 scaffold N kb ncrna Gb Illumina reads 273 Mb GSS GSS 1 SUMF P450 GST COE ABC CRY2 CRY Ceratosolen solmsi mir-1 mir-7 mir mirna P 2013 Ors Grs IRs 278 Mb scaffold 7397 AT % 9. 85% scaffold N Mb 5 Mb 21 kb 3 Collagen IV α ORs GRs DPOGS IR OBPs CSPs Zhan et al You et al P450s GSTs CCEs Toll imd Plutella xylostella JAK /STAT JNK

12 12 Journal of Environmental Entomology Mb Scaffold N kb Toll imd JAK /STAT JNK 12 Xiao et al P450s 11 P450 pseudogenes 33 GSTs 92 Locusta migratoria Gb scaffold N kb Scott et al % Contig 5003 N kb CEGMA 25 Dnmt1 Dnmt2 Dnmt3 DNA % OBP perilipins fatty-acidbinding protein Prdx6s sigma GST enoyl-coa hydratase acetyl-coa acyltransferase 2 Nilapavata lugens OBPs ORs GRs IRs 2014 HiSeq2000 UGTs carboxyl /choline esterases Gb CysLGIC Belgica antarctica Mb Kelley et al Scaffold N kb Musca domestica

13 1 13 OR GR walbacia 805 P450 GST alpha- CHS2 Benoit et al YLS A. nilaparvatae YLS A. nilaparvatae 479 Mb 10 YLS Illumina YLS HiSeq2000 DNA contig N50 YLS 3. 1 kb kb Scaffold N kb 4. 1 Mb YLS CDS 14 A nilaparvatae B Xue et al Cimex lectularius Medflymic scaffold scaffold X Illumina Solexa Mb 1402 scaffold scaffold Ceratitis capitata 1608 / N Mb MAKER IR GR P450 CYP6 Toll sp tzle TWDL CPLCA CRY1 JET ceratotoxin opsin RHG reaper grim SFP SIT AQP Papanicolaou et al P450 -S- Baxevanis et al Stephens ABC CPR et al. 2015

14 14 Journal of Environmental Entomology i5k NAL Poelchau et al InsectBase Yin et al i5k Workspace@ NAL i5k Workspace@ NAL NCBI EBI 46 DDBJ HMMER CLUSTAL Poelchau et al i5k VectorBase Giraldo-Calderon et al i5k Workspace@ NAL i5k NAL Hymenoptera Genome Database 4. 2 InsectBase Munoz-Torres et al InsectBase Agripestbase DBM-DB Tang et al KONAGAbase Jouraku et al MonarchBase Zhan et al APHIDBASE Legeai et al Yin et al SilkDB Duan et al Wang et al KAIKObase Shimomura et al G InsectBase Heliconius Genome Project ChiloDB Yin et al WaspAtlas Official Gene Set OGS Davies et al i5k Workspace@ NAL InsectBase http / / www. insect-genome. com / EST mirna NCBI 215 pirna Ensemble UTR CDS 61 OGS NCBI InsectBase 36 NCBI OrthoMCL InsectBase

15 1 15 PubMed ifacebook InsectBase % Table 2 2 Insects genome database statistics Database Genome with Species Gene Sets URL NCBI GeneBank & Refseq http / /www. ncbi. nlm. nih. gov Ensembl http / /metazoa. ensembl. org Flybase http / /flybase. org / i5kworkspace http / /i5k. nal. usda. gov / VectorBase https / /www. VectorBase. org / HymenopteraMine http / /hymenopteragenome. org /hymenopteramine Hymenoptera Genome Database BeeBase 1 1 http / /hymenopteragenome. org /beebase / NasoniaBase 1 1 http / /hymenopteragenome. org /nasonia Ant Genomes Portal 8 8 http / /hymenopteragenome. org /ant_genomes Hessian Fly Base 1 1 http / /agripestbase. org /hessianfly / Agripestbase Manduca Base 1 1 http / /agripestbase. org /manduca / BeetleBase 1 1 http / /beetlebase. org / DBM - DB KONAGAbase 1 1 http / /www. iae. fafu. edu. cn /DBM / 1 http / /dbm. dna. affrc. go. jp /px / MonarchBase 1 1 http / /monarchbase. umassmed. edu / APHIDBASE 1 1 http / /www. aphidbase. com / SilkDB KAIKObase 1 1 http / /www. silkdb. org /silkdb / 1 http / /sgp. dna. affrc. go. jp /KAIKObase Heliconius Genome Project 1 1 http / /butterflygenome. org / ChiloDB 1 1 http / /ento. njau. edu. cn /ChiloDB WaspAtlas 1 1 http / /waspatlas. com / InsectBase http / /www. insect - genome. com Gb Gb

16 16 Journal of Environmental Entomology 39 Res Cantarel BL Korf I Robb SM et al. J Consortium HGS. honeybee Apis mellifera J 90 and analysis platform J. Database Oxford Bombyx mori genome biology J 38 Database issue Edgar RC Myers EW. DNA RNA 4 genomic repeats J Biotechnol other organisms related with human diseases J Heather JM ChainB. sequencing DNA J References Adams MD Celniker SE Holt RA et al. The genome sequence of Drosophila melanogaster J. Science Allen JE Majoros WH Pertea M et al. JIGSAW GeneZilla and GlimmerHMM Puzzling out the features of human genes in the ENCODE regions J. Genome Biol S Bao Z Eddy SR. Automated de novo identification of repeat sequence families in sequenced genomes J. Genome Res Baxevanis AD Bateman A. The importance of biological databases in biological discovery J. Curr Protoc Bioinformatics Bellaousov S Reuter JS Seetin MG et al. RNAstructure Web servers for RNA secondary structure prediction and analysis J. Nucleic Acids Res Web Server issue W Benoit JB Adelman ZN Reinhardt K et al. Unique features of a global human ectoparasite identified through sequencing of the bed bug genome J. Nat. Commun Butler J MacCallum I Kleber M et al. ALLPATHS De novo assembly of whole - genome shotgun microreads J. Genome MAKER An easy - to - use annotation pipeline designed for emerging model organism genomes. Genome Res Chen Y Liu YS Zeng JG et al. Progresses on plant genome sequencing profile J. Life Science Research Feb Insights into social insects from the genome of the. Nature Davies NJ Tauber E. WaspAtlas A Nasonia vitripennis gene database Duan J Li R Cheng D et al. SilkDB v2. 0 A platform for silkworm. Nucleic Acids Res PILER Identification and classification of. Bioinformatics Suppl Elsik CG Mackey AJ Reese JT et al. Creating a honey bee consensus gene set J. Genome Biol R13. Friedlander MR Chen W Adamidi C et al. Discovering micrornas from deep sequencing data using mirdeep J. Nat. Giraldo - Calderon GI Emrich SJ MacCallum RM et al. VectorBase An updated bioinformatics resource for invertebrate vectors and Res Database issue Nucleic Acids The sequence of sequencers The history of. Genomics Jouraku A Yamamoto K Kuwazaki S et al. KONAGAbase A genomic and transcriptomic database for the diamondback moth Plutella xylostella J. BMC Genomics Kelley JL Peyton JT Fiston - Lavier AS et al. Compact genome of the Antarctic midge is likely an adaptation to an extreme environment J. Nat. Commun Kirkness EF Haas BJ Sun W et al. Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle J. Proceedings of the National Academy of Sciences Kozomara A Griffiths - Jones S. mirbase Annotating high confidence micrornas using deep sequencing data J. Nucleic Acids Res Database issue Legeai F Shigenobu S Gauthier JP et al. AphidBase A centralized bioinformatic resource for annotation of the pea aphid genome J. Insect Mol. Biol Suppl Liu JD Improvement of Insect Genome Annotation Method and Analysis of Two Insect Genomes D. Nanjing Agricultural University Liu Q Mackey AJ Roos DS et al. Evigan A hidden variable model

17 1 17 for integrating gene evidence for eukaryotic gene prediction J. Bioinformatics Luo R Liu B Xie Y et al. SOAPdenovo2 An empirically improved memory - efficient short - read de novo assembler J. Gigascience Maxam AM Gilbert W. A new method for sequencing DNA J. Proc. Natl. Acad Sci. USA Miller JR Delcher AL Koren S et al. Aggressive assembly of pyrosequencing reads with mates J. Bioinformatics Munoz - Torres MC Reese JT Childers CP et al. Hymenoptera Genome Database Integrated community resources for insect species of the order Hymenoptera J. Nucleic Acids Res Database issue Ouzounis C A Valencia A. Early bioinformatics The birth of a discipline a personal view J. Bioinformatics Pang KC Stephen S Dinger ME et al. RNAdb 2. 0 An expanded database of mammalian non - coding RNAs J. Nucleic Acids Res Database issue Papanicolaou A Schetelig MF Arensburger P et al. The whole genome sequence of the Mediterranean fruit fly Ceratitis capitata Wiedemann reveals insights into the biology and adaptive evolution of a highly invasive pest species J. Genome Biol Parra G Bradnam K Korf I. CEGMA A pipeline to accurately annotate core genes in eukaryotic genomes J. Bioinformatics Poelchau M Childers C Moore G et al. The i5k Workspace@ NAL enabling genomic data access visualization and curation of arthropod genomes J. Nucleic Acids Res Database issue Price AL JonesNC Pevzner PA. De novo identification of repeat families in large genomes J. Bioinformatics Suppl Richards S Murali SC. Best Practices in Insect Genome Sequencing What Works and What Doesn't J. Curr. Opin. Insect. Sci Robinson GE Hackett KJ Purcell - Miramontes M et al. Creating a buzz about insect genomes J. Science Sanger F Coulson AR. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase J. J. Mol. Biol Sanger F Air GM Barrell BG et al. Nucleotide sequence of bacteriophage phi X174 DNA J. Nature Scott JG Warren WC Beukeboom LW et al. Genome of the house fly Musca domestica L. a global vector of diseases with adaptations to a septic environment J. Genome Biol Shimomura M Minami H Suetsugu Y et al. KAIKObase An integrated silkworm genome database and data mining tool J. BMC Genomics Simao FA Waterhouse RM Ioannidis P et al. BUSCO Assessing genome assembly and annotation completeness with single - copy orthologs J. Bioinformatics Simpson JT Wong K Jackman SD et al. ABySS A parallel assembler for short read sequence data J. Genome Res Stephens ZD Lee SY Faghri F et al. Big Data Astronomical or Genomical J. PLoS Biol e Tang W Yu L He W et al. DBM - DB The diamondback moth genome database J. Database Oxford Tarailo - Graovac M Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences J. Curr. Protoc. Bioinformatics 2009 Chapter 4Unit Venter JC Adams MD Myers EW et al. The sequence of the human genome J. Science Wajid B Serpedin E. Review of general algorithmic features for genome assemblers for next generation sequencers J. Genomics Proteomics Bioinformatics Wang J Xia Q He X et al. SilkDB A knowledgebase for silkworm biology and genomics J. Nucleic Acids Res Database issue Wang X Fang X Yang P et al. The locust genome provides insight into swarm formation and long - distance flight J. Nat. Commun Werren JH Richards S Desjardins CA et al. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species J. Science Xia Q Zhou Z Lu C et al. A draft sequence for the genome of the domesticated silkworm Bombyx mori J. Science Xiao JH Yue Z Jia LY et al. Obligate mutualism within a host drives the extreme specialization of a fig wasp genome J. Genome Biol R141. Xu Y Wang X Yang J et al. PASA a program for automated protein NMR backbone signal assignment by pattern - filtering approach J. J. Biomol. NMR Xu Z Wang H. LTR_ FINDER An efficient tool for the prediction of full - length LTR retrotransposons J. Nucleic Acids Res Web Server issue Xue C Li F He T et al. Classification of real and pseudo microrna precursors using local structure - sequence features and support vector machine J. BMC Bioinformatics Xue J Zhou X Zhang CX et al. Genomes of the rice pest brown planthopper and its endosymbionts reveal complex complementary contributions for host adaptation J. Genome Biol Yin C Liu Y Liu J et al. ChiloDB A genomic and transcriptome database for an important rice insect pest Chilo suppressalis J. Database Oxford Yin C Shen G Guo D et al. InsectBase A resource for insect genomes and transcriptomes J. Nucleic Acids Res. 2016

18 18 Journal of Environmental Entomology D You M Yue Z He W et al. A heterozygous moth genome provides insights into herbivory and detoxification J. Nature Genetics Zhan S Merlin C Boore J L et al. The monarch butterfly genome yields insights into long - distance migration J. Cell Zhan S Reppert S M. MonarchBase The monarch butterfly genome database J. Nucleic Acids Res Database issue Zhang CX Current research status and prospects of genomes of insects important to agriculture in China J. Scientia Agricultura Sinica Zhao Y Li H Fang S et al. NONCODE 2016 An informative and valuable data source of long non - coding RNAs J. Nucleic Acids Res D Chen Y Liu YS Zeng JG. Progresses on plant genome Sequencing profile J. Life Science Research J Liu JD. Improlement of insect genome annotation method and analysis of two insect geomes D. Nanjing Agriculture University D Zhang CX. Current research status and prospects of genomes of insect important to agriculture in China J. Scientia Agricuttura Sinica J

为实斲这项收贩行劢, 雅培将支付 21.2 亿美元癿预付款, 而后在仍 2011 年开始癿 4 年里, 每年再支付 4 亿美元该仺制药部门主要在印度斯里兮卡和尼泊尔销售零售便利药品 4

为实斲这项收贩行劢, 雅培将支付 21.2 亿美元癿预付款, 而后在仍 2011 年开始癿 4 年里, 每年再支付 4 亿美元该仺制药部门主要在印度斯里兮卡和尼泊尔销售零售便利药品 4 2010 年国际医药并购事件 2010 生物医药产业盘点 2010 年癿国际医药市场风于发幻诺华雅培强生梯瓦百旪美斲贵宝赛诺菲安万特等全球知名药企癿一系列收贩行为丌断搅劢着全球医药市场, 诺华 516 亿美元买断爱尔康, 赛诺菲收贩