메뉴 건너뛰기




Volumn 15, Issue 1, 2017, Pages

Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus)

(20)  Larsen, Peter A a   Harris, R Alan b   Liu, Yue b   Murali, Shwetha C b,g   Campbell, C Ryan a   Brown, Adam D c,h   Sullivan, Beth A c   Shelton, Jennifer d,i   Brown, Susan J d   Raveendran, Muthuswamy b   Dudchenko, Olga b,e,f   Machol, Ido b,e,f   Durand, Neva C b,e,f   Shamim, Muhammad S b,e,f   Aiden, Erez Lieberman b,e,f   Muzny, Donna M b   Gibbs, Richard A b   Yoder, Anne D a   Rogers, Jeffrey b   Worley, Kim C b  


Author keywords

Centromeres; De novo assembly; Hi C; Optical maps; Physical maps; Strepsirrhine primate; Super scaffolding

Indexed keywords

ANIMAL; BIOLOGY; CENTROMERE; CHEIROGALEIDAE; DNA SEQUENCE; FEMALE; GENETICS; GENOME; HIGH THROUGHPUT SEQUENCING;

EID: 85034103051     PISSN: None     EISSN: 17417007     Source Type: Journal    
DOI: 10.1186/s12915-017-0439-6     Document Type: Article
Times cited : (44)

References (56)
  • 1
    • 83855165105 scopus 로고    scopus 로고
    • Repetitive DNA and next-generation sequencing: computational challenges and solutions
    • Treangen TJ, Salzberg SL. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Gen. 2012;13:36-46.
    • (2012) Nat Rev Gen , vol.13 , pp. 36-46
    • Treangen, T.J.1    Salzberg, S.L.2
  • 2
    • 84892698555 scopus 로고    scopus 로고
    • Next-generation sequence assembly: four stages of data processing and computational challenges
    • El-Metwally S, Hamza T, Zakaria M, Helmy M. Next-generation sequence assembly: four stages of data processing and computational challenges. PLoS Comput Biol. 2013;9:e1003345.
    • (2013) PLoS Comput Biol , vol.9
    • El-Metwally, S.1    Hamza, T.2    Zakaria, M.3    Helmy, M.4
  • 3
    • 78650909427 scopus 로고    scopus 로고
    • Limitations of next-generation genome sequence assembly
    • Alkan C, Sajjadian S, Eichler EE. Limitations of next-generation genome sequence assembly. Nat Methods. 2011;8:61-5.
    • (2011) Nat Methods , vol.8 , pp. 61-65
    • Alkan, C.1    Sajjadian, S.2    Eichler, E.E.3
  • 5
    • 79951794116 scopus 로고    scopus 로고
    • Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses
    • Vilella AJ, Birney E, Flicek P, Herrero J. Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses. Genome Biol. 2011;12(2):401.
    • (2011) Genome Biol , vol.12 , Issue.2 , pp. 401
    • Vilella, A.J.1    Birney, E.2    Flicek, P.3    Herrero, J.4
  • 7
    • 84898808163 scopus 로고    scopus 로고
    • Comparative primate genomics: emerging patterns of genome content and dynamics
    • Rogers J, Gibbs RA. Comparative primate genomics: emerging patterns of genome content and dynamics. Nat Rev Gen. 2014;15:347-59.
    • (2014) Nat Rev Gen , vol.15 , pp. 347-359
    • Rogers, J.1    Gibbs, R.A.2
  • 8
    • 28944439470 scopus 로고    scopus 로고
    • Beware of mis-assembled genomes
    • Salzberg SL, Yorke JA. Beware of mis-assembled genomes. Bioinformatics. 2005;21:4320-1.
    • (2005) Bioinformatics , vol.21 , pp. 4320-4321
    • Salzberg, S.L.1    Yorke, J.A.2
  • 14
    • 84893040699 scopus 로고    scopus 로고
    • The past, present, and future of human centromere genomics
    • Aldrup-MacDonald ME, Sullivan BA. The past, present, and future of human centromere genomics. Genes. 2014;5:33-50.
    • (2014) Genes , vol.5 , pp. 33-50
    • Aldrup-MacDonald, M.E.1    Sullivan, B.A.2
  • 15
    • 84929498966 scopus 로고    scopus 로고
    • A unique chromatin complex occupies young α-satellite arrays of human centromeres
    • Henikoff JG, Thakur J, Kasinathan S, Henikoff S. A unique chromatin complex occupies young α-satellite arrays of human centromeres. Sci Adv. 2015;1:e1400234.
    • (2015) Sci Adv , vol.1
    • Henikoff, J.G.1    Thakur, J.2    Kasinathan, S.3    Henikoff, S.4
  • 19
    • 33644761191 scopus 로고    scopus 로고
    • Microcebus murinus. a useful primate model for human cerebral aging and Alzheimer's disease?
    • Bons N, Rieger F, Prudhomme D, Fisher A, Krause KH. Microcebus murinus. a useful primate model for human cerebral aging and Alzheimer's disease? Genes Brain Behav. 2006;5:120-30.
    • (2006) Genes Brain Behav , vol.5 , pp. 120-130
    • Bons, N.1    Rieger, F.2    Prudhomme, D.3    Fisher, A.4    Krause, K.H.5
  • 20
    • 77958559464 scopus 로고    scopus 로고
    • Distinct transcriptome expression of the temporal cortex of the primate Microcebus murinus during brain aging versus Alzheimer's disease-like pathology
    • Rassoul RA, Alves S, Pantesco V, De Vos J, Michel B, Perret M, Mestre-Francés N, Verdier J-M, Devau G. Distinct transcriptome expression of the temporal cortex of the primate Microcebus murinus during brain aging versus Alzheimer's disease-like pathology. PLoS One. 2010;5:e12770.
    • (2010) PLoS One , vol.5
    • Rassoul, R.A.1    Alves, S.2    Pantesco, V.3    Vos, J.4    Michel, B.5    Perret, M.6    Mestre-Francés, N.7    Verdier, J.-M.8    Devau, G.9
  • 23
    • 84890034912 scopus 로고    scopus 로고
    • Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
    • Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol. 2013;31:1119-25.
    • (2013) Nat Biotechnol , vol.31 , pp. 1119-1125
    • Burton, J.N.1    Adey, A.2    Patwardhan, R.P.3    Qiu, R.4    Kitzman, J.O.5    Shendure, J.6
  • 26
    • 84897108483 scopus 로고    scopus 로고
    • Exploring genome characteristics and sequence quality without a reference
    • Simpson JT. Exploring genome characteristics and sequence quality without a reference. Bioinformatics. 2014;30:1228-35.
    • (2014) Bioinformatics , vol.30 , pp. 1228-1235
    • Simpson, J.T.1
  • 27
    • 79952592810 scopus 로고    scopus 로고
    • A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
    • Marcais G, Kingsford C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics. 2011;27:764-70.
    • (2011) Bioinformatics , vol.27 , pp. 764-770
    • Marcais, G.1    Kingsford, C.2
  • 29
    • 9244228574 scopus 로고    scopus 로고
    • Application of molecular cytogenetics for chromosomal evolution of the Lemuriformes (Prosimians)
    • Warter S, Hauwy M, Dutrillaux B, Rumpler Y. Application of molecular cytogenetics for chromosomal evolution of the Lemuriformes (Prosimians). Cytogenet Genome Res. 2005;108:197-203.
    • (2005) Cytogenet Genome Res , vol.108 , pp. 197-203
    • Warter, S.1    Hauwy, M.2    Dutrillaux, B.3    Rumpler, Y.4
  • 31
    • 84873077979 scopus 로고    scopus 로고
    • The lemur revolution starts now: the genomic coming of age for a non-model organism
    • Yoder AD. The lemur revolution starts now: the genomic coming of age for a non-model organism. Mol Phylogenet Evol. 2013;66:442-52.
    • (2013) Mol Phylogenet Evol , vol.66 , pp. 442-452
    • Yoder, A.D.1
  • 32
    • 85014697376 scopus 로고    scopus 로고
    • The Alu neurodegeneration hypothesis: a primate-specific mechanism for neuronal transcription noise, mitochondrial dysfunction, and manifestation of neurodegenerative disease
    • Larsen PA, Lutz MW, Hunnicutt KE, Mihovilovic M, Saunders AM, Yoder AD, Roses AD. The Alu neurodegeneration hypothesis: a primate-specific mechanism for neuronal transcription noise, mitochondrial dysfunction, and manifestation of neurodegenerative disease. Alzheimers Dement. 2017;13:828-38.
    • (2017) Alzheimers Dement , vol.13 , pp. 828-838
    • Larsen, P.A.1    Lutz, M.W.2    Hunnicutt, K.E.3    Mihovilovic, M.4    Saunders, A.M.5    Yoder, A.D.6    Roses, A.D.7
  • 36
    • 77949428750 scopus 로고    scopus 로고
    • Detection and correction of false segmental duplications caused by genome mis-assembly
    • Kelley DR, Salzberg SL. Detection and correction of false segmental duplications caused by genome mis-assembly. Genome Biol. 2010;11:R28.
    • (2010) Genome Biol , vol.11 , pp. R28
    • Kelley, D.R.1    Salzberg, S.L.2
  • 37
    • 0033168288 scopus 로고    scopus 로고
    • Optical mapping and its potential for large-scale sequencing projects
    • Aston C, Mishra B, Schwartz DC. Optical mapping and its potential for large-scale sequencing projects. Trends Biotechnol. 1999;17:297-302.
    • (1999) Trends Biotechnol , vol.17 , pp. 297-302
    • Aston, C.1    Mishra, B.2    Schwartz, D.C.3
  • 42
    • 85007240180 scopus 로고    scopus 로고
    • Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing
    • Sevim V, Bashir A, Chin C-S, Miga KH. Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing. Bioinformatics. 2016;32:1921-4.
    • (2016) Bioinformatics , vol.32 , pp. 1921-1924
    • Sevim, V.1    Bashir, A.2    Chin, C.-S.3    Miga, K.H.4
  • 49
    • 84925373900 scopus 로고    scopus 로고
    • Aligning sequence reads, clone sequences, and assembly contigs with BWA-MEM
    • Li H. Aligning sequence reads, clone sequences, and assembly contigs with BWA-MEM. arXiv Prepr arXiv. 2013;0:3.
    • (2013) arXiv Prepr arXiv. , pp. 3
    • Li, H.1
  • 50
    • 0036226603 scopus 로고    scopus 로고
    • BLAT--the BLAST-like alignment tool
    • Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002;12:656-64.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 55
    • 0028789523 scopus 로고
    • Identification of centromeric antigens in dicentric Robertsonian translocations. CENP-C and CENP-E are necessary components of functional centromeres
    • Sullivan BA, Schwartz S. Identification of centromeric antigens in dicentric Robertsonian translocations. CENP-C and CENP-E are necessary components of functional centromeres. Hum Mol Genet. 1995;4:2189-97.
    • (1995) Hum Mol Genet , vol.4 , pp. 2189-2197
    • Sullivan, B.A.1    Schwartz, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.