메뉴 건너뛰기




Volumn 5, Issue 12, 2010, Pages

De novo transcriptome sequencing in anopheles funestus using illumina RNA-seq technology

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME; RNA;

EID: 78649969759     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0014202     Document Type: Article
Times cited : (130)

References (53)
  • 1
    • 78649953375 scopus 로고    scopus 로고
    • Geneva: World Health Organization
    • WHO/UNICEF World Malaria Report (2009) Geneva: World Health Organization.
    • (2009) WHO/UNICEF World Malaria Report
  • 3
    • 36849073678 scopus 로고    scopus 로고
    • Sequencing breakthroughs for genomic ecology and evolutionary biology
    • Hudson HE (2008) Sequencing breakthroughs for genomic ecology and evolutionary biology. Molecular Ecology Resources 8: 3-17.
    • (2008) Molecular Ecology Resources , vol.8 , pp. 3-17
    • Hudson, H.E.1
  • 4
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 5
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 6
    • 75349109607 scopus 로고    scopus 로고
    • ALLPATHS 2: Small genomes assembled accurately and with high continuity from short paired reads
    • Maccallum I, Przybylski D, Gnerre S, Burton J, Shlyakhter I, et al. (2009) ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biology 10: R103.
    • (2009) Genome Biology , vol.10
    • Maccallum, I.1    Przybylski, D.2    Gnerre, S.3    Burton, J.4    Shlyakhter, I.5
  • 8
    • 35348932160 scopus 로고    scopus 로고
    • Wasp gene expression supports an evolutionary link between maternal behavior and eusociality
    • Toth AL, Varala K, Newman TC, Miguez FE, Hutchison SK, et al. (2007) Wasp gene expression supports an evolutionary link between maternal behavior and eusociality. Science 318: 441: 444.
    • (2007) Science 318: , vol.441 , pp. 444
    • Toth, A.L.1    Varala, K.2    Newman, T.C.3    Miguez, F.E.4    Hutchison, S.K.5
  • 9
  • 10
    • 77951936990 scopus 로고    scopus 로고
    • Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae)
    • Renaut S, Nolte AW, Bernatchez L (2010) Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae). Molecular Ecology 19(Suppl. 1): 115-131.
    • (2010) Molecular Ecology , vol.19 , Issue.SUPPL. 1 , pp. 115-131
    • Renaut, S.1    Nolte, A.W.2    Bernatchez, L.3
  • 11
    • 64749084488 scopus 로고    scopus 로고
    • An approach to transcriptome analysis of non-model organisms using short-read sequences
    • Collins LJ, Biggs PJ, Voelckel C, Joly S (2008) An approach to transcriptome analysis of non-model organisms using short-read sequences. Genome Informatics 21: 3-14.
    • (2008) Genome Informatics , vol.21 , pp. 3-14
    • Collins, L.J.1    Biggs, P.J.2    Voelckel, C.3    Joly, S.4
  • 12
    • 77955081300 scopus 로고    scopus 로고
    • Into the unknown: Expression profiling without genome sequence information in CHO by next generation sequencing
    • doi:10.1093/nar/gkq116
    • Birzele F, Schaub J, Werner R, Clemens C, Baum P, et al. (2010) Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing. Nucleic Acids Res doi:10.1093/nar/gkq116.
    • (2010) Nucleic Acids Res
    • Birzele, F.1    Schaub, J.2    Werner, R.3    Clemens, C.4    Baum, P.5
  • 13
    • 77954450225 scopus 로고    scopus 로고
    • De novo characterization of a whitefly transcriptome and analysis of its gene expression during development
    • Wang X, Luan J, Li J, Bao Y, Zhang C, et al. (2010) De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics 11: 400.
    • (2010) BMC Genomics , vol.11 , pp. 400
    • Wang, X.1    Luan, J.2    Li, J.3    Bao, Y.4    Zhang, C.5
  • 14
    • 77449118596 scopus 로고    scopus 로고
    • Malaria management: Past, present, and future
    • Enayati A, Hemingway J (2010) Malaria management: past, present, and future. Annu Rev Entomol 55: 569-591.
    • (2010) Annu Rev Entomol , vol.55 , pp. 569-591
    • Enayati, A.1    Hemingway, J.2
  • 15
    • 77049109244 scopus 로고    scopus 로고
    • Evolutionary forces on Anopheles: What makes a malaria vector?
    • Cohuet A, Harris C, Robert V, Fontenille D (2010) Evolutionary forces on Anopheles: what makes a malaria vector? Trends Parasitol 26: 130-136.
    • (2010) Trends Parasitol , vol.26 , pp. 130-136
    • Cohuet, A.1    Harris, C.2    Robert, V.3    Fontenille, D.4
  • 18
    • 33646067726 scopus 로고    scopus 로고
    • Analysis of the complete mitochondrial DNA from Anopheles funestus: An improved dipteran mitochondrial genome annotation and a temporal dimension of mosquito evolution
    • Krzywinski J, Grushko OG, Besansky NJ (2006) Analysis of the complete mitochondrial DNA from Anopheles funestus: an improved dipteran mitochondrial genome annotation and a temporal dimension of mosquito evolution. Mol Phylogenet Evol 39: 417-423.
    • (2006) Mol Phylogenet Evol , vol.39 , pp. 417-423
    • Krzywinski, J.1    Grushko, O.G.2    Besansky, N.J.3
  • 19
    • 0037020116 scopus 로고    scopus 로고
    • Inversions and gene order shuffling in Anopheles gambiae and A. funestus
    • Sharakhov IV, Serazin AC, Grushko OG, Dana A, Lobo N, et al. (2002) Inversions and gene order shuffling in Anopheles gambiae and A. funestus. Science 298: 182-185.
    • (2002) Science , vol.298 , pp. 182-185
    • Sharakhov, I.V.1    Serazin, A.C.2    Grushko, O.G.3    Dana, A.4    Lobo, N.5
  • 21
    • 3142516480 scopus 로고    scopus 로고
    • Advances in the study of Anopheles funestus, a major vector of malaria in Africa
    • Coetzee M, Fontenille D (2004) Advances in the study of Anopheles funestus, a major vector of malaria in Africa. Insect Biochem Mol Biol 34: 599-605.
    • (2004) Insect Biochem Mol Biol , vol.34 , pp. 599-605
    • Coetzee, M.1    Fontenille, D.2
  • 22
    • 33846351583 scopus 로고    scopus 로고
    • An insight into the sialome of Anopheles funestus reveals an emerging pattern in anopheline salivary protein families
    • Calvo E, Dao A, Pham VM, Ribeiro JM (2007) An insight into the sialome of Anopheles funestus reveals an emerging pattern in anopheline salivary protein families. Insect Biochem Mol Biol 37: 164-175.
    • (2007) Insect Biochem Mol Biol , vol.37 , pp. 164-175
    • Calvo, E.1    Dao, A.2    Pham, V.M.3    Ribeiro, J.M.4
  • 23
    • 70949099252 scopus 로고    scopus 로고
    • Comparative analysis of the global transcriptome of Anopheles funestus from Mali, West Africa
    • Serazin AC, Dana AN, Hillenmeyer ME, Lobo NF, Coulibaly MB, et al. (2009) Comparative analysis of the global transcriptome of Anopheles funestus from Mali, West Africa. PLoS One 4: e7976.
    • (2009) PLoS One , vol.4
    • Serazin, A.C.1    Dana, A.N.2    Hillenmeyer, M.E.3    Lobo, N.F.4    Coulibaly, M.B.5
  • 24
    • 25444468365 scopus 로고    scopus 로고
    • Laboratory selection for and characteristics of pyrethroid resistance in the malaria vector Anopheles funestus
    • Hunt RH, Brooke BD, Pillay C, Koekemoer LL, Coetzee M (2005) Laboratory selection for and characteristics of pyrethroid resistance in the malaria vector Anopheles funestus. Med and Vet Entom 19: 271-275.
    • (2005) Med and Vet Entom , vol.19 , pp. 271-275
    • Hunt, R.H.1    Brooke, B.D.2    Pillay, C.3    Koekemoer, L.L.4    Coetzee, M.5
  • 25
    • 0033291921 scopus 로고    scopus 로고
    • Chromosomal and bionomic heterogeneities suggest incipient speciation in Anopheles funestus from Burkina Faso
    • Costantini C, Sagnon NF, Ilboudo-Sanogo E, Coluzzi M, Boccolini D (1999) Chromosomal and bionomic heterogeneities suggest incipient speciation in Anopheles funestus from Burkina Faso. Parassitologia 41: 595-611.
    • (1999) Parassitologia , vol.41 , pp. 595-611
    • Costantini, C.1    Sagnon, N.F.2    Ilboudo-Sanogo, E.3    Coluzzi, M.4    Boccolini, D.5
  • 26
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 27
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
    • (1994) Nucleic Acids Research , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 29
    • 0036094818 scopus 로고    scopus 로고
    • An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks
    • Gaunt MW, Miles MA (2002) An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks. Mol. Biol. Evol 19: 748-761.
    • (2002) Mol. Biol. Evol , vol.19 , pp. 748-761
    • Gaunt, M.W.1    Miles, M.A.2
  • 30
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5
  • 31
    • 24644503098 scopus 로고    scopus 로고
    • Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research
    • Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
    • (2005) Bioinformatics , vol.21 , pp. 3674-3676
    • Conesa, A.1    Gotz, S.2    Garcia-Gomez, J.M.3    Terol, J.4    Talon, M.5
  • 32
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European Molecular Biology Open Software Suite
    • Rice P, Longden I, Bleasby A (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics 16: 276-277.
    • (2000) Trends in Genetics , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 37
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows- Wheeler transform
    • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 25: 1754-60.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 39
    • 61549106577 scopus 로고    scopus 로고
    • Population genetic inference from resequencing data
    • Jiang R, Tavare S, Marjoram P (2009) Population genetic inference from resequencing data. Genetics 181: 187-197.
    • (2009) Genetics , vol.181 , pp. 187-197
    • Jiang, R.1    Tavare, S.2    Marjoram, P.3
  • 41
    • 41149089793 scopus 로고    scopus 로고
    • Seqin{R} 1.0-2: A contributed package to the R project for statistical computing devoted to biological sciences retrieval and analysis
    • In: Bastolla U, Porto M, Roman HE, Vendruscolo M, eds, New York: Springer Verlag
    • Charif D, Lobry JR (2007) Seqin{R} 1.0-2: a contributed package to the R project for statistical computing devoted to biological sciences retrieval and analysis. In: Bastolla U, Porto M, Roman HE, Vendruscolo M, eds. Structural approaches to sequence evolution: Molecules, networks, populations. New York: Springer Verlag. pp 207-232.
    • (2007) Structural approaches to sequence evolution: Molecules, networks, populations , pp. 207-232
    • Charif, D.1    Lobry, J.R.2
  • 42
    • 78649294100 scopus 로고    scopus 로고
    • Optimization of de novo transcriptome assembly from next-generation sequencing data
    • Surget-Groba Y, Montoya-Burgos J (2010) Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Research 20: 1432-1440.
    • (2010) Genome Research , vol.20 , pp. 1432-1440
    • Surget-Groba, Y.1    Montoya-Burgos, J.2
  • 43
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 28: 511-515.
    • (2010) Nature Biotechnology , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5
  • 44
    • 77950447605 scopus 로고    scopus 로고
    • Transcriptome response to pollutants and insecticides in the dengue vector Aedes aegypti using next-generation sequencing technology
    • David J, Coissac E, Melodelima C, Poupardin R, Riaz MA, et al. (2010) Transcriptome response to pollutants and insecticides in the dengue vector Aedes aegypti using next-generation sequencing technology. BMC Genomics 11: 216.
    • (2010) BMC Genomics , vol.11 , pp. 216
    • David, J.1    Coissac, E.2    Melodelima, C.3    Poupardin, R.4    Riaz, M.A.5
  • 45
    • 34250860637 scopus 로고    scopus 로고
    • Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes
    • Waterhouse RM, Kriventseva EV, Meister S, Xi Z, Kanwal S, et al. (2007) Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes. Science 316: 1738-1743.
    • (2007) Science , vol.316 , pp. 1738-1743
    • Waterhouse, R.M.1    Kriventseva, E.V.2    Meister, S.3    Xi, Z.4    Kanwal, S.5
  • 46
    • 56649115780 scopus 로고    scopus 로고
    • Anopheles gambiae APL1 is a family of variable LRR proteins required for Rel1- mediated protection from the malaria parasite, Plasmodium berghei
    • Riehle MM, Xu J, Lazzaro BP, Rottschaefer SM, Coulibaly B, et al. (2008) Anopheles gambiae APL1 is a family of variable LRR proteins required for Rel1- mediated protection from the malaria parasite, Plasmodium berghei. PLoS One 3: e3672.
    • (2008) PLoS One , vol.3
    • Riehle, M.M.1    Xu, J.2    Lazzaro, B.P.3    Rottschaefer, S.M.4    Coulibaly, B.5
  • 47
    • 61849177493 scopus 로고    scopus 로고
    • Two mosquito LRR proteins function as complement control factors in the TEP1- mediated killing in Plasmodium
    • Fraiture M, Baxter RHG, Steinert S, Chelliah Y, Frolet C, et al. (2009) Two mosquito LRR proteins function as complement control factors in the TEP1- mediated killing in Plasmodium. Cell Host & Microbe 5: 273-284.
    • (2009) Cell Host & Microbe , vol.5 , pp. 273-284
    • Fraiture, M.1    Baxter, R.H.G.2    Steinert, S.3    Chelliah, Y.4    Frolet, C.5
  • 49
    • 33846840758 scopus 로고    scopus 로고
    • Identification and analysis of single nucleotide polymorphisms (SNPs) in the mosquito Anopheles funestus, malaria vector
    • Wondji CS, Hemingway J, Ranson H (2007) Identification and analysis of single nucleotide polymorphisms (SNPs) in the mosquito Anopheles funestus, malaria vector. BMC Genomics 8: 5.
    • (2007) BMC Genomics , vol.8 , pp. 5
    • Wondji, C.S.1    Hemingway, J.2    Ranson, H.3
  • 50
    • 67650721450 scopus 로고    scopus 로고
    • Inferring selection in the Anopheles gambiae species complex: An example from immune-related serine protease inhibitors
    • Obbard DJ, Welch JJ, Little TJ (2009) Inferring selection in the Anopheles gambiae species complex: an example from immune-related serine protease inhibitors. Malaria Journal 8: 117.
    • (2009) Malaria Journal , vol.8 , pp. 117
    • Obbard, D.J.1    Welch, J.J.2    Little, T.J.3
  • 51
    • 44449105687 scopus 로고    scopus 로고
    • SNP discovery and molecular evolution in Anopheles gambiae, with special emphasis on innate immune system
    • Cohuet A, Krishnakumar S, Simard F, Morlais I, Koutsos A, et al. (2008) SNP discovery and molecular evolution in Anopheles gambiae, with special emphasis on innate immune system. BMC genomics 9: 227.
    • (2008) BMC genomics , vol.9 , pp. 227
    • Cohuet, A.1    Krishnakumar, S.2    Simard, F.3    Morlais, I.4    Koutsos, A.5
  • 52
    • 47149117454 scopus 로고    scopus 로고
    • Evolution of genes and genomes on the Drosophila phylogeny
    • Drosophila 12 Genomes Consortium
    • Drosophila 12 Genomes Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Science 450: 203-218.
    • (2007) Science , vol.450 , pp. 203-218


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.