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次世代シーケンサーによるメタゲノム解析:桜の花びらに付着した環境DNAを解析する
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Tazro Inutano Ohta
December 26, 2018
Education
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72
次世代シーケンサーによるメタゲノム解析:桜の花びらに付着した環境DNAを解析する
JSTグローバルサイエンスキャンパス事業
「医学・医療の学際的修学、半学半教」プログラム
於 慶應義塾大学日吉キャンパス
Tazro Inutano Ohta
December 26, 2018
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Transcript
DNA (DBCLS) 2018/12/26 JST
!
"#
ࠓͷ͓ ੜֶNFBUTใՊֶ
http://docman.dbcls.jp/im/
None
ٕज़ͷਐา͕ή ϊϜՊֶͷઓུΛม͑ͨ ͝Ζ
Ή͔͠αϯΨʔ๏ʹΑΔ%/"ྻղಡ Ͱ͖Δ͜ͱ͔Βͭͭ͜͜ͱ
͜ΕΛઃܭ͠ͳ͍ͱಡΊͳ͍ ग़య: https://www.researchgate.net/figure/Principle‐of‐Sanger‐sequencing‐Incorporation‐of‐ ddNTPs‐terminates‐the‐elongation‐of‐the_fig4_265264877
͍·େنԘجྻղಡٕज़ʹΑΔཏతܭଌ ͱΓ͋͑ͣશ෦ಡΉ
ͿͭΓʹ͢Δ શ෦ʹΞμϓλʔྻΛ͚ͭΔ શͯͷྻʹରͯ͠ ૬ิͷ߹Λ͢Δ ೋ࣍ݩ্ۭؒͷܬޫΛ ΧϝϥͰࡱӨɺܦ࣌ͷ มԽΛॲཧͯ͠ྻʹ ม͢Δ ग़య: https://bitesizebio.com/13546/sequencing‐by‐synthesis‐explaining‐the‐illumina‐sequencing‐technology/
ಡΊͳ͔ͬͨͷ͕ಡΊΔΑ͏ʹ ͱΓ͋͑ͣಡΜͰΈΑʂ
ग़య: https://gold.jgi.doe.gov/statistics
͋ͷੜͷή ϊϜͬͯ͏ಡ·Ε͚ͯͨͬʁ ή ϊϜหϓϩδΣΫτ
ग़య: https://www.instagram.com/p/BcybbydAbSK/
ग़య: http://wiki.lifesciencedb.jp/mw/GenomeBentoProject
େྔฒྻΛ༷ͬͯʑͳݱΛܭଌ͢Δ 4FRͷ࣌
ϥϘ͔Βσʔλ͕ͲΜͲΜग़ͯ͘Δ ͕ͩγʔέϯαੜମࢠΛจࣈʹม͢ΔػցͰ͋ΓࣝΛੜΉͷͰͳ͍
None
ੜֶͷࣝ ใՊֶͷٕज़Ͱ จࣈྻͷฒͼΛࣝʹม͢Δ
#JH%BUB4DJFODFͱͳͬͨੜֶܭࢉػͳ͠Ͱ͍͚ͬͯͳ͍ ੜֶNFBUTใՊֶ
Պֶతख๏ͷͭͷύϥμΠϜ ܦݧཧܭࢉσʔλ
Ծઆ͔Β࣮ݧΛσβΠϯ͢ΔPS·ͣσʔλΛऔͬͯੳ͢Δ Ծઆۦಈܕσʔλۦಈܕ
ϝλή ϊϜ Կ͕ೖͬͯΔ͔Θ͔Μͳ͍͚Ͳ%/"શ෦ಡΊΑ͘Ͷʁ
ւਫதͷ%/"͔ΒڕͷछྨΛਪఆ ͷਫશ෦ಡΉ ग़య: https://doi.org/10.1098/rsos.150088-9
ۭؾதͷ%/"͔ΒඍੜΛਪఆ ۭؾಡΉ ग़య: https://doi.org/10.1371/journal.pone.0001862
ެڞۭؒͷ%/"͔ΒඍੜΛਪఆ .FUB46#1SPKFDU ग़య: https://doi.org/10.1186/s40168‐016‐0168‐z
ഉᔔதͷ%/"͔ΒࡉەΛਪఆ ʜ͕Α͘ߦΘΕΔ͕ԼͷਤੜಈΛই͚ͭͣʹ%/"Λ࠾औ͢Δख๏ͷจ ग़య: https://doi.org/10.1038/s41598-018-20427-9
ౙɾॴ ݚڀूձʮୈ࢛ճ/(4ݱͷձʯاըձٞ
ʮ͜Ε͚ͩγʔέϯε҆͘ͳͬͨΜ͔ͩΒͳΜ͔ಡ·ͳ͍ʁʯ
None
ࡩͷछͰ͋ΔιϝΠϤγϊ͗Ͱ૿͑ΔΫϩʔϯ Ұఆͷؾ݅ͰҰ੪։Ֆ͢Δ͕Ұि͔ؒΒेͰࢄͬͯ͠·͏
॓ओͷή ϊϜಉ͡Ͱڥ͚͕݅ͩҟͳΔ ணͨ͠%/"ͷҧ͍ڥͷҧ͍Λө͢Δ͔ʁ
ͱ͍͑ҋӢʹγʔέϯε͢ΕΑ͍ͱ͍͏Θ͚Ͱͳ͍ͷͰ ݚڀσβΠϯ Λ͠·͢
༧ࢉΈ αϯϓϦϯάΩοτͱࢼༀͷௐୡ αϯϓϦϯάΛ͢Δ αϯϓϧ͔Β%/"Λநग़͢Δ 4S3/"ྖҬΛ૿෯ͯ͠γʔέϯε͢Δ ੜྨσʔλϕʔεʹ͍߹ΘͤͯಡΜͩྻ͔ΒੜछΛਪఆ͢Δ ֶձͰղੳίϯϖςΟγϣϯΛΔ จΛॻ͘
Ϋϥυιʔγϯά શࠃ͔ΒࢀՃऀΛืͬͯαϯϓϦϯάΛ͓ئ͍͢Δ
None
༧ࢉΈ αϯϓϦϯάΩοτͱࢼༀͷௐୡ ΣϒΞϓϦέʔγϣϯͷ࣮ͱެ։ એͱࢀՃऀืू ΩοτΛࢀՃऀʹૹΔ αϯϓϦϯάͯ͠Β͏ αϯϓϧΛૹͬͯΒ͏ αϯϓϧใΛॻ͍ͯొͯ͠Β͏ ૹΒΕ͖ͯͨαϯϓϧ͔Β%/"Λநग़͢Δ 4S3/"ྖҬΛ૿෯ͯ͠γʔέϯε͢Δ
ੜྨσʔλϕʔεʹ͍߹ΘͤͯಡΜͩྻ͔ΒੜछΛਪఆ͢Δ ֶձͰղੳίϯϖςΟγϣϯΛΔ จΛॻ͘
αϯϓϦϯάࢀՃऀ 149 ໊
ू·ͬͨαϯϓϧ 594
None
શࠃ੍ (ԭೄΛআ͘)
ಡΜͰΈͨ
ಘΒΕͨྻͷ΄ͱΜͲ͕ ༿ମͱϛτίϯυϦΞ ίϯλϛͩ
ίϯλϛ $POUBNJOBUJPOԚછ Պֶ࣮ݧҰൠʹ͓͍ͯҙਤ͠ͳ͍࣭͕ࠞೖ͢Δ͜ͱ
ɾТɾʆ Ұൃউෛͩͱ͜͏͍͏͜ͱ͋Δ
αϯϓϦϯά࣌ʹՖͼΒͷද໘Λ ࡲΓ͗ͯ͢ࡩͷࡉ๔͕ࠞೖͨ͠ͱ ࢥΘΕΔͷਤ
࡞ઓมߋ ݟ͔ͭͬͨྻͷதʹԿ͔໘ന͍ͷͳ͍͔ʁ
΄ͱΜͲ༿ମͱϛτίϯυϦΞ·ΈΕ ΄΅ίϯλϛͱ૾͞ΕΔ͕ɺશ෦͕ͦ͏ͳͷ͔ʁ
ҧ͏২ʹ༝དྷ͢ΔͱࢥΘΕΔྻ γʔέϯεͷϛεͷՄೳੑ͋Δ͕ɺϛεϚονͷΛߟ͑Δͱʜʁ
Cryptomeria japonica Ֆ࣌ӍࡩࢄΓΏͦ͘ͷલʹ
ɾТɾʆ ͜͏ͯ͜͠ͷੈքʹ·ͨҰͭ৽ͨͳτϦϏΞ͕ੜ·Εͨʜ
None
رͳ͍ͷ͔ ͜ͷ··Ͱকདྷʹͭͳ͕Βͳ͍
ܚጯٛक़େֶઌੜ໋Պֶݚڀॴ ߥάϧʔϓ ߥ Տ ౻ݪ ٢ా ߴҪ Ѩ෦ ࠤ౻ণ͞Μ
ٕज़һ ٕज़һ ֶੜ ॿڭ ॿڭ ॿڭ ।ڭत ൿॻ 0 50
100 150 200 count abe Arakawa Fujiwara Ishii Kono sato Takai Yoshida member * * εʔύʔςΫχγϟϯҰਓউͪ ݸਓຖͷαϯϓϦϯάʹ͓͚ΔόΫςϦΞྻ ߥ͞Μ ܚጯٛक़େ
0 1000 2000 3000 count abe Arakawa Fujiwara Ishii Kono
sato Takai Yoshida member 0 50 100 150 200 count abe Arakawa Fujiwara Ishii Kono sato Takai Yoshida member ٕज़һ ٕज़һ ֶ ॿڭ ॿ ॿڭ ।ڭत ൿॻ ٕज़һ ٕज़һ ֶ ॿڭ ॿ ॿڭ ।ڭत ൿॻ ༿ମɾϛτίϯυϦΞআ֎ ༿ମɾϛτίϯυϦΞؚΉ ՖคΛଟ͘ͱͬͯ͠·͍ͬͯΔ όΫςϦΞΛ༏ઌతʹͱΕ͍ͯΔਓ͕͍Δ 10 15 20 25 30 35 40 45 50 55 4 500 1000 1500 2000 2500 17 20 40 60 80 100 4 0 500 1000 1500 2000 2500 3000 17 0 10 20 30 40 50 4 0 250 500 750 1000 1250 1500 17 0 10 20 30 40 50 4 0 250 500 750 1000 1250 1500 17 0 5 10 15 20 25 30 4 200 400 600 800 1000 1200 1400 17 0 5 10 15 20 4 0 200 400 600 800 1000 1200 17 0 50 100 150 200 4 1500 1750 2000 2250 2500 2750 3000 17 0 20 40 60 80 100 120 4 0 500 1000 1500 2000 17 ٕज़һ ٕज़һ ֶੜ ॿڭ ॿڭ ॿڭ ।ڭत ൿॻ ༿ମɾϛτίϯυϦΞͷྻͱόΫςϦΞͷྻͷ૬ؔ ߥ͞Μ ܚጯٛक़େ
ྻσʔλɺϝλσʔλɺจͦͷଞશ෦͜͜ʹ͋Γ·͢ EBUBECDMTKQdJOVUBOPPNHTFR
αϯϓϦϯάͷख๏Λ͢ΕΑΓΑ͍σʔλ͕ಘΒΕΔ ͔ SF͓ՖݟϓϩδΣΫτ ٻΉϓϩδΣΫτϦʔμʔ
Պֶݚڀͱཱͯͤ͠͞Δ͜ͱ͚ͩͰͳ͍ ͓ՖݟϓϩδΣΫτਅͷత
༧ࢉΈ αϯϓϦϯάΩοτͱࢼༀͷௐୡ ΣϒΞϓϦέʔγϣϯͷ࣮ͱެ։ એͱࢀՃऀืू ΩοτΛࢀՃऀʹૹΔ αϯϓϦϯάͯ͠Β͏ αϯϓϧΛૹͬͯΒ͏ αϯϓϧใΛॻ͍ͯొͯ͠Β͏ ૹΒΕ͖ͯͨαϯϓϧ͔Β%/"Λநग़͢Δ 4S3/"ྖҬΛ૿෯ͯ͠γʔέϯε͢Δ
ੜྨσʔλϕʔεʹ͍߹ΘͤͯಡΜͩྻ͔ΒੜछΛਪఆ͢Δ ֶձͰղੳίϯϖςΟγϣϯΛΔ จΛॻ͘
$
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None
࣌ΣϒΞϓϦέʔγϣϯ͕ࣗಈೖྗ αϯϓϦϯάͷॴ Ңܦߴ (14Ͱࣗಈೖྗ ఱީ࣌ͱ(14ใΛݩʹؾி%#͔Βநग़ͯࣗ͠ಈิ ։Ֆޙͷ࣌ͱ(14ใ͔Βಉ͘͡ࡩ։ՖใΑΓࣗಈิ ͦͷଞͷใࣗ༝هड़
ϓϩͷݚڀैࣄऀ͕ಉ͡ରʹ͍ͭͯௐΔ ؍ͱهड़ͷ࣭ͱྔ
ඈௗࢁଆ ࢪઃೖΓޱ ࢪઃෑ JRԦࢠӺଆ ύʔΫαΠυ λϫʔαΠυ ιϝΠϤγϊ ಓ࿏Ԋ͍ೖΓޱ ߴ80.5m αΫϥͷՖ1ݸ
ιϝΠϤγϊݩ $BTFT4JNQMFUFSNTPOMZ ղऍ͍͕͠ɺػց͕ಡΊΔ
000353(ը૾000353_1)ʹ͍ͭͯɻ000361ͱͷ૬ҧ:ڳߴܘ56cmɻथߴ10.02m(ը૾000353_2தஈ)ɻथྸ͓Α ͼ২ޙͷ͕ߴ͍ͱਪఆ͞Ε·͢ɻը૾ڳߴ෦ҎԼͷथൽ্ͷணੜ২ͷඃ෴80%ɻணੜ২ϋ ϦΨωΰέՊͳͲ᥌ଽྨ,ϊΩγϊϒͳͲ༽ࣃྨ,ϝϊΩΰέϨϓϥΰέͳͲҥମ͕ओͰɺΩϊίྨݟͨ Γ·ͤΜͰͨ͠(ը૾000353_3)ɻৗ༿थΛओͱ͢Δೋ࣍ྛ·ͨεεΩ͔Βͷڑ21mɻ000353ͱ 000361ͷڞ௨:ՖͷܗଶͷΈ͔ΒιϝΠϤγϊͱஅ͠·͕ͨ͠,ͰެԂͳͲʹ͍ΘΏΔατβΫϥͷෳ छΛࠞ২͢Δ͜ͱ͕͋ΔͷͰ,ՄೳͰ͋Εը૾(000353_4)͔Βछͷ֬ೝΛ͓ئ͍͠·͢ɻࢼྉ࠾औࣛࣇ ౡࢢɻḈຎౡ౦ଆͷࣛࣇౡʹ໘͠ɺՐࡅྲྀग़͕ଯੵͯ͠Ͱ্͖ͨϊݪ্ɻඪߴ90mɻ1978ʹ ͞Εͨॅ֎ԑͷެԂʹ২͞Εͨݸମɻ২ͷެԂͷ౦ଆͱଆʹंಓΛִͯͯ,֓Ͷೋ֊ՈҰށݐ ͯͷॅ͕͋Γ·͢ɻ૬ରর100%ɻंಓ͓ΑͼंಓԊ͍ͷ֗౮͔Βͷڑ΄΅ಉ͡ɻࣛࣇౡํؾ ۙͷԹྔࢦ140લޙɻௐࠪඪߴ͕80mఔߴ͍ͷͰͦΕΑΓΘ͔ͣʹ͍ͱߟ͑ΒΕ·͢ɻஆԹଳͷর༿
थྛଳʹ૬͠·͕͢,ஆԹଳͷর༿थྛଳʹ૬͠·͕͢,২ͷެԂͷೆଆͷࣼ30°ͷ֑ͷࣼ໘ʹৗ ༿थΛओͱ͢Δೋ࣍ྛ·͕ͨଘ͍ͯ͠Δ͚ͩͰ͢ɻ࿈׆ൃʹՐ͍ͯ͠ΔࡩౡতՐޱ͔Βͷڑ ͓Αͦ15kmɻ෩͖ʹΑͬͯ߱փ͕͋Γ·͢ɻҰൠʹࣛࣇౡपลͰۭத࣪ͷߴ͞ͱՐࢁփͷணʹΑΓ थͷװʹணੜ২͕ੜҭ͍͕͋͢͠Γ·͢ɻαϯϓϧͷՖห্ʹՐࢁփ͋Δ͍ԫ࠭ͱࢥΘΕΔԚΕ͕ ΈΒΕ·͢ɻҰൠతʹ,Ұ੪ʹ࡙͍ͯҰ੪ʹࢄΔؔ౦ͱൺΔͱ,Ͱ1ຊͷथͷ։Ֆظ͕͍ؒ(ݸʑͷՖ͕ॱ ࡙͍࣍ͯ,ॱ࣍ࢄΔ)͕͋ΔΑ͏Ͱ͢ɻ্هͷ։ՖޙͷαϯϓϦϯάͨ͠ʮՖʯͷ։ՖͰ͢ɻҢܦ ʹ͍ͭͯGPSઐ༻ػͷใ(ը૾000353_2Լஈ)Λೖྗ͠·ͨ͠ɻ $BTFJOEFUBJM ྔଟ͍͕ɺػցՄಡੑ͍
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هड़ͷίετWTղੳ࣌ͷॊೈੑ ϝλσʔλͷ࣭ͷ্͕EBUBESJWFOTDJFODFͷ伴ΛѲ͍ͬͯΔ
• ܭଌٕज़ͷਐา͕Պֶͷख๏Λม͑Δ • σʔλۦಈܕՊֶͱͳͬͨੜֶܭࢉػՊֶͱ༥߹͢Δ • ੵͨ͠σʔλ͕ҖྗΛൃش͢Δ࣌ͦ͜σʔλͷهड़͕ॏཁ • ͍͔ʹ࣭ͷߴ͍σʔλΛऩू͢Δ͔ %
Պֶͱهड़͢Δ͜ͱ ॻ͖ͱͲΊΑɻٞͨ͜͠ͱ෩ͷதʹਧ͖ඈ͍͚ͯ͠ͳ͍
& ୈ࢛ճNGSݱͷձ اըνʔϜ ͓ՖݟϓϩδΣΫτࢀՃऀͷΈͳ͞· ຊͷσʔλϕʔεΛࢧ͑Δ DBCLS/NBDC/DDBJ ͷΈͳ͞· Bio OSSίϛϡχςΟ BioHackathon/SPARQLthon/PitagoraNetwork
ͷΈͳ͞·
' • ྻղੳͷڭՊॻతͳॻ੶ • Dr. Bonoͷੜ໋Պֶσʔλղੳ (ϝσΟΧϧαΠΤϯε Πϯλʔφγϣφϧ) • NGSͷ࣮ݧख๏ղੳͷํ๏ʹ͍ͭͯΔͨΊͷॻ੶
• ࣍ੈγʔΫΤϯεղੳελϯμʔυʙNGSͷϙςϯ γϟϧΛ׆͔͖͠ΔWET&DRY (༽ࣾ) • ౷ܭػցֶशͷଆ໘͔ΒόΠΦΠϯϑΥϚςΟΫεΛ Γ͍ͨਓ͚ • ੜ໋ใॲཧʹ͓͚Δػցֶश ଟॏݕఆͱਪఆྔઃܭ (ػցֶशϓϩϑΣογϣφϧγϦʔζ) (ߨஊࣾ) • ࠷৽ͷݚڀൃදߨԋΛYouTubeͰݟΔ • ౷߹TV http://togotv.dbcls.jp/ja/lecture.html • εϥΠυ • speakerdeck.com/inutano