$\require{mediawiki-texvc}$

연합인증

연합인증 가입 기관의 연구자들은 소속기관의 인증정보(ID와 암호)를 이용해 다른 대학, 연구기관, 서비스 공급자의 다양한 온라인 자원과 연구 데이터를 이용할 수 있습니다.

이는 여행자가 자국에서 발행 받은 여권으로 세계 각국을 자유롭게 여행할 수 있는 것과 같습니다.

연합인증으로 이용이 가능한 서비스는 NTIS, DataON, Edison, Kafe, Webinar 등이 있습니다.

한번의 인증절차만으로 연합인증 가입 서비스에 추가 로그인 없이 이용이 가능합니다.

다만, 연합인증을 위해서는 최초 1회만 인증 절차가 필요합니다. (회원이 아닐 경우 회원 가입이 필요합니다.)

연합인증 절차는 다음과 같습니다.

최초이용시에는
ScienceON에 로그인 → 연합인증 서비스 접속 → 로그인 (본인 확인 또는 회원가입) → 서비스 이용

그 이후에는
ScienceON 로그인 → 연합인증 서비스 접속 → 서비스 이용

연합인증을 활용하시면 KISTI가 제공하는 다양한 서비스를 편리하게 이용하실 수 있습니다.

[해외논문] A draft genome assembly of the solar-powered sea slug Elysia chlorotica 원문보기

Scientific data, v.6, 2019년, pp.190022 -   

Cai, Huimin (Department of Computer Science, City University of Hong Kong , Hong Kong 999077, China) ,  Li, Qiye (BGI-Shenzhen , Shenzhen 518083, China) ,  Fang, Xiaodong (BGI Genomics, BGI-Shenzhen , Shenzhen 518083, China) ,  Li, Ji (BGI-Shenzhen , Shenzhen 518083, China) ,  Curtis, Nicholas E. (Department of Biology, Ave Maria University, Ave Maria , Florida 34142, USA) ,  Altenburger, Andreas (Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen , Copenhagen 1350, Denmark) ,  Shibata, Tomoko (National Institute for Basic Biology , Okazaki 444-8585, Japan) ,  Feng, Mingji (BGI Genomics, BGI-Shenzhen , Shenzhen 518083, China) ,  Maeda, Taro (National Institute for Basic Biology , Okazaki 444-8585, Japan) ,  Schwartz, Julie A. (Department of Integrative Biology, University of South Florida, Tampa , Florida 33620, USA) ,  Shigenobu, Shuji (National Institute for Basic Biology , O) ,  Lundholm, Nina ,  Nishiyama, Tomoaki ,  Yang, Huanming ,  Hasebe, Mitsuyasu ,  Li, Shuaicheng ,  Pierce, Sidney K. ,  Wang, Jian

Abstract AI-Helper 아이콘AI-Helper

Elysia chlorotica, a sacoglossan sea slug found off the East Coast of the United States, is well-known for its ability to sequester chloroplasts from its algal prey and survive by photosynthesis for up to 12 months in the absence of food supply. Here we present a draft genome assembly of E. chloroti...

참고문헌 (97)

  1. NCBI Sequence Read Archive 2018 SRP156455 

  2. CNGB Nucleotide Sequence Archive 2019 CNP0000110 

  3. GenBank 2010 NC_011600.1 

  4. GenBank 2016 EU599581.1 

  5. GenBank 2017 KY115607.1 

  6. Figshare Cai H. et al. 2019 10.6084/m9.figshare.7057916.v2 

  7. NCBI Assembly 2019 GCA_003991915.1 

  8. NCBI Assembly 2013 GCA_000002075.2 

  9. NCBI Assembly 2017 GCA_002080005.1 

  10. NCBI Assembly 2013 GCA_000457365.1 

  11. NCBI Assembly 2012 GCA_000297895.1 

  12. GigaScience Database 2017 10.5524/100281 

  13. NCBI Assembly 2018 GCA_003130415.1 

  14. NCBI Assembly 2012 GCA_000327385.1 

  15. NCBI Assembly 2017 GCA_002080025.1 

  16. NCBI Assembly 2015 GCA_001194135.1 

  17. NCBI Assembly 2017 GCA_002113885.2 

  18. NCBI Assembly 2017 GCA_002216045.1 

  19. NCBI Assembly 2018 GCA_003073045.1 

  20. NCBI Assembly 2017 GCA_002072015.1 

  21. NCBI Assembly 2018 GCA_003671525.1 

  22. NCBI Sequence Read Archive 2018 SRR8282417 

  23. NCBI Sequence Read Archive 2018 SRP136656 

  24. Maeda T. , Kajita T. , Maruyama T. & Hirano Y. Molecular phylogeny of the sacoglossa, with a discussion of gain and loss of kleptoplasty in the evolution of the group . Biol Bull 219 , 17 – 26 ( 2010 ). 20813986 

  25. Rumpho M. E. , Pelletreau K. N. , Moustafa A. & Bhattacharya D. The making of a photosynthetic animal . J Exp Biol 214 , 303 – 311 ( 2011 ). 21177950 

  26. Pierce S. K. & Curtis N. E. Cell biology of the chloroplast symbiosis in sacoglossan sea slugs . Int Rev Cell Mol Biol 293 , 123 – 148 ( 2012 ). 22251560 

  27. Pierce S. K. , Curtis N. E. & Middlebrooks M. L. Sacoglossan sea slugs make routine use of photosynthesis by a variety of species‐specific adaptations . Invertebr Biol 134 , 103 – 115 ( 2015 ). 

  28. Pierce S. K. , Curtis N. E. , Hanten J. J. , Boerner S. L. & Schwartz J. A. Transfer, integration and expression of functional nuclear genes between multicellular species . Symbiosis 43 , 57 ( 2007 ). 

  29. Pierce S. K. , Curtis N. E. & Schwartz J. A. Chlorophyll a synthesis by an animal using transferred algal nuclear genes . Symbiosis 49 , 121 – 131 ( 2009 ). 

  30. Rumpho M. E. et al. Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica . Proc Natl Acad Sci U S A 105 , 17867 – 17871 ( 2008 ). 19004808 

  31. Rumpho M. E. et al. Molecular characterization of the Calvin cycle enzyme phosphoribulokinase in the stramenopile alga Vaucheria litorea and the plastid hosting mollusc Elysia chlorotica . Mol Plant 2 , 1384 – 1396 ( 2009 ). 19995736 

  32. Schwartz J. A. , Curtis N. E. & Pierce S. K. Using algal transcriptome sequences to identify transferred genes in the sea slug . Elysia chlorotica. Evol Biol 37 , 29 – 37 ( 2010 ). 

  33. Soule K. M. & Rumpho M. E. Light-Regulated Photosynthetic Gene Expression and Phosphoribulokinase Enzyme Activity in the Heterokont Alga Vaucheria Litorea (Xanthophyceae) and Its Symbiotic Molluskan Partner Elysia Chlorotica (Gastropoda) . J Phycol 48 , 373 – 383 ( 2012 ). 27009727 

  34. Green B. J. et al. Mollusc-algal chloroplast endosymbiosis. Photosynthesis, thylakoid protein maintenance, and chloroplast gene expression continue for many months in the absence of the algal nucleus . Plant Physiol 124 , 331 – 342 ( 2000 ). 10982447 

  35. Hanten J. J. & Pierce S. K. Synthesis of several light-harvesting complex I polypeptides is blocked by cycloheximide in symbiotic chloroplasts in the sea slug, Elysia chlorotica (Gould): A case for horizontal gene transfer between alga and animal? Biol Bull 201 , 34 – 44 ( 2001 ). 11526061 

  36. Pierce S. K. et al. Transcriptomic evidence for the expression of horizontally transferred algal nuclear genes in the photosynthetic sea slug, Elysia chlorotica . Mol Biol Evol 29 , 1545 – 1556 ( 2012 ). 22319135 

  37. Schwartz J. A. , Curtis N. E. & Pierce S. K. FISH labeling reveals a horizontally transferred algal ( Vaucheria litorea ) nuclear gene on a sea slug ( Elysia chlorotica ) chromosome . Biol Bull 227 , 300 – 312 ( 2014 ). 25572217 

  38. Chan C. X. et al. Active Host Response to Algal Symbionts in the Sea Slug Elysia chlorotica . Mol Biol Evol 35 , 1706 – 1711 ( 2018 ). 29659974 

  39. Pelletreau K. N. et al. Sea slug kleptoplasty and plastid maintenance in a metazoan . Plant Physiol 155 , 1561 – 1565 ( 2011 ). 21346171 

  40. Bhattacharya D. , Pelletreau K. N. , Price D. C. , Sarver K. E. & Rumpho M. E. Genome analysis of Elysia chlorotica Egg DNA provides no evidence for horizontal gene transfer into the germ line of this Kleptoplastic Mollusc . Mol Biol Evol 30 , 1843 – 1852 ( 2013 ). 23645554 

  41. Ponder W. F. & Lindberg D. R. Phylogeny and Evolution of the Mollusca . (Univ of California Press, 2008 ). 

  42. Sun J. et al. Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes . Nat Ecol Evol 1 , 121 ( 2017 ). 28812709 

  43. Adema C. M. et al. Whole genome analysis of a schistosomiasis-transmitting freshwater snail . Nat Commun 8 , 15451 ( 2017 ). 28508897 

  44. Zhang G. et al. The oyster genome reveals stress adaptation and complexity of shell formation . Nature 490 , 49 – 54 ( 2012 ). 22992520 

  45. Nam B. H. et al. Genome sequence of pacific abalone ( Haliotis discus hannai ): the first draft genome in family Haliotidae . Gigascience 6 , 1 – 8 ( 2017 ). 

  46. Uliano-Silva M. et al. A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel . Limnoperna fortunei. Gigascience 7 , 1 – 10 ( 2018 ). 

  47. Simakov O. et al. Insights into bilaterian evolution from three spiralian genomes . Nature 493 , 526 – 531 ( 2013 ). 23254933 

  48. Albertin C. B. et al. The octopus genome and the evolution of cephalopod neural and morphological novelties . Nature 524 , 220 – 224 ( 2015 ). 26268193 

  49. Wang S. et al. Scallop genome provides insights into evolution of bilaterian karyotype and development . Nat Ecol Evol 1 , 120 ( 2017 ). 28812685 

  50. Du X. et al. The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization . Gigascience 6 , 1 – 12 ( 2017 ). 

  51. Schell T. et al. An annotated draft genome for Radix auricularia (Gastropoda, Mollusca) . Genome Biol Evol ( 2017 ). 

  52. Mun S. et al. The Whole-Genome and Transcriptome of the Manila Clam ( Ruditapes philippinarum ) . Genome Biol Evol 9 , 1487 – 1498 ( 2017 ). 28505302 

  53. Liu C. et al. The genome of the golden apple snail Pomacea canaliculata provides insight into stress tolerance and invasive adaptation . Gigascience 7 , 1 – 13 ( 2018 ). 

  54. Powell D. et al. The genome of the oyster Saccostrea offers insight into the environmental resilience of bivalves . DNA Res 25 , 655 – 665 ( 2018 ). 30295708 

  55. Winnepenninckx B. , Backeljau T. & De Wachter R. Extraction of high molecular weight DNA from molluscs . Trends in genetics : TIG 9 , 407 ( 1993 ). 8122306 

  56. Chen Y. et al. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data . Gigascience 7 , 1 – 6 ( 2018 ). 

  57. Pierce S. K. , Mahadevan P. , Massey S. E. & Middlebrooks M. L. A Preliminary Molecular and Phylogenetic Analysis of the Genome of a Novel Endogenous Retrovirus in the Sea Slug Elysia chlorotica . Biol Bull 231 , 236 – 244 ( 2016 ). 28048954 

  58. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997 ( 2013 ). 

  59. Marcais G. & Kingsford C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers . Bioinformatics 27 , 764 – 770 ( 2011 ). 21217122 

  60. Ross M. G. et al. Characterizing and measuring bias in sequence data . Genome Biol 14 , R51 ( 2013 ). 23718773 

  61. Vurture G. W. et al. GenomeScope: fast reference-free genome profiling from short reads . Bioinformatics 33 , 2202 – 2204 ( 2017 ). 28369201 

  62. Jiao W. et al. High-resolution linkage and quantitative trait locus mapping aided by genome survey sequencing: building up an integrative genomic framework for a bivalve mollusc . DNA Res 21 , 85 – 101 ( 2014 ). 24107803 

  63. Gnerre S. et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data . Proc Natl Acad Sci U S A 108 , 1513 – 1518 ( 2011 ). 21187386 

  64. Huang S. , Kang M. & Xu A. HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly . Bioinformatics 33 , 2577 – 2579 ( 2017 ). 28407147 

  65. Koren S. et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads . Nat Biotechnol 30 , 693 – 700 ( 2012 ). 22750884 

  66. Koren S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation . Genome Res 27 , 722 – 736 ( 2017 ). 28298431 

  67. Wences A. H. & Schatz M. C. Metassembler: merging and optimizing de novo genome assemblies . Genome Biol 16 , 207 ( 2015 ). 26403281 

  68. Boetzer M. , Henkel C. V. , Jansen H. J. , Butler D. & Pirovano W. Scaffolding pre-assembled contigs using SSPACE . Bioinformatics 27 , 578 – 579 ( 2011 ). 21149342 

  69. English A. C. et al. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology . PloS One 7 , e47768 ( 2012 ). 23185243 

  70. English A. C. , Salerno W. J. & Reid J. G. PBHoney: identifying genomic variants via long-read discordance and interrupted mapping . BMC bioinformatics 15 , 180 ( 2014 ). 24915764 

  71. Luo R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler . Gigascience 1 , 18 ( 2012 ). 23587118 

  72. Walker B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement . PloS One 9 , e112963 ( 2014 ). 25409509 

  73. Smit A. F. , Hubley R. & Green P. RepeatMasker http://www.repeatmasker.org ( 2017 ). 

  74. Smit A. & Hubley R. RepeatModeler http://www.repeatmasker.org/RepeatModeler/ ( 2017 ). 

  75. Benson G. Tandem repeats finder: a program to analyze DNA sequences . Nucleic Acids Res 27 , 573 – 580 ( 1999 ). 9862982 

  76. Altschul S. F. , Gish W. , Miller W. , Myers E. W. & Lipman D. J. Basic local alignment search tool . J Mol Biol 215 , 403 – 410 ( 1990 ). 2231712 

  77. Birney E. , Clamp M. & Durbin R. GeneWise and Genomewise . Genome Res 14 , 988 – 995 ( 2004 ). 15123596 

  78. Kim D. , Langmead B. & Salzberg S. L. HISAT: a fast spliced aligner with low memory requirements . Nat Methods 12 , 357 – 360 ( 2015 ). 25751142 

  79. Pertea M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads . Nat Biotechnol 33 , 290 – 295 ( 2015 ). 25690850 

  80. UniProt Consortium, T. UniProt: the universal protein knowledgebase . Nucleic Acids Res 46 , 2699 ( 2018 ). 29425356 

  81. Stanke M. , Diekhans M. , Baertsch R. & Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding . Bioinformatics 24 , 637 – 644 ( 2008 ). 18218656 

  82. Xiong Z. et al. Draft genome of the leopard gecko . Eublepharis macularius. Gigascience 5 , 47 ( 2016 ). 27784328 

  83. Jones P. et al. InterProScan 5: genome-scale protein function classification . Bioinformatics 30 , 1236 – 1240 ( 2014 ). 24451626 

  84. Corpet F. , Servant F. , Gouzy J. & Kahn D. ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons . Nucleic Acids Res 28 , 267 – 269 ( 2000 ). 10592243 

  85. Attwood T. K. et al. PRINTS and its automatic supplement, prePRINTS . Nucleic Acids Res 31 , 400 – 402 ( 2003 ). 12520033 

  86. Finn R. D. et al. Pfam: the protein families database . Nucleic Acids Res 42 , D222 – D230 ( 2014 ). 24288371 

  87. Letunic I. , Doerks T. & Bork P. SMART: recent updates, new developments and status in 2015 . Nucleic Acids Res 43 , D257 – D260 ( 2015 ). 25300481 

  88. Mi H. , Poudel S. , Muruganujan A. , Casagrande J. T. & Thomas P. D. PANTHER version 10: expanded protein families and functions, and analysis tools . Nucleic Acids Res 44 , D336 – D342 ( 2016 ). 26578592 

  89. Sigrist C. J et al. PROSITE, a protein domain database for functional characterization and annotation . Nucleic Acids Res 38 , D161 – D166 ( 2010 ). 19858104 

  90. Kanehisa M. & Goto S. KEGG: kyoto encyclopedia of genes and genomes . Nucleic Acids Res 28 , 27 – 30 ( 2000 ). 10592173 

  91. Li H. et al. The Sequence Alignment/Map format and SAMtools . Bioinformatics 25 , 2078 – 2079 ( 2009 ). 19505943 

  92. Okonechnikov K. , Conesa A. & Garcia-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data . Bioinformatics 32 , 292 – 294 ( 2016 ). 26428292 

  93. Broad Institute. Picard https://github.com/broadinstitute/picard ( 2017 ). 

  94. Hunt M. et al. REAPR: a universal tool for genome assembly evaluation . Genome Biol 14 , R47 ( 2013 ). 23710727 

  95. Torresen O. K. et al. An improved genome assembly uncovers prolific tandem repeats in Atlantic cod . BMC Genomics 18 , 95 ( 2017 ). 28100185 

  96. Simao F. A. , Waterhouse R. M. , Ioannidis P. , Kriventseva E. V. & Zdobnov E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs . Bioinformatics 31 , 3210 – 3212 ( 2015 ). 26059717 

  97. Dohmen E. , Kremer L. P. , Bornberg-Bauer E. & Kemena C. DOGMA: domain-based transcriptome and proteome quality assessment . Bioinformatics 32 , 2577 – 2581 ( 2016 ). 27153665 

섹션별 컨텐츠 바로가기

AI-Helper ※ AI-Helper는 오픈소스 모델을 사용합니다.

AI-Helper 아이콘
AI-Helper
안녕하세요, AI-Helper입니다. 좌측 "선택된 텍스트"에서 텍스트를 선택하여 요약, 번역, 용어설명을 실행하세요.
※ AI-Helper는 부적절한 답변을 할 수 있습니다.

선택된 텍스트

맨위로