生信漫谈如何利用MEGA7构建系统进化树

前言

生物技术近年发展越来迅猛，掌握一门生信语言或者一个生信软件的使用，这将为我们的科研学习之路提供非常大的便利。今天我们主要来介绍如何用MEGA7进行进化树。

1、下面以MEGA7为例来进行讲解，下面是下载地址，大家根据自己的系统进行下载即可。

http://www.megasoftware.net/

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2、序列的准备，必须是fasta结尾的格式，其他像txt格式，软件不能识别，以下以拟南芥SPL15基因的蛋白序列为例，进行同源序列查找

>NP_191351.1 SPL15 [organism=Arabidopsis thaliana] [GeneID=824961]
MELLMCSGQAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSRSKNRVNTVRKSSTTARCQVEGCRMDLSN
VKAYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTALF
TSHYSRIAPSLYGNPNAAMIKSVLGDPTAWSTARSVMQRPGPWQINPVRETHPHMNVLSHGSSSFTTCPE
MINNNSTDSSCALSLLSNSYPIHQQQLQTPTNTWRPSSGFDSMISFSDKVTMAQPPPISTHQPPISTHQQ
YLSQTWEVIAGEKSNSHYMSPVSQISEPADFQISNGTTMGGFELYLHQQVLKQYMEPENTRAYDSSPQHF
NWSL

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选择其中同源序列高的前19条蛋白序列进行下载进行示范

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下载后的序列形式：

>AST51816.1 Venus [Cloning vector pSTB205]
MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKLICTTGKLPVPWPTLVTTLGYGLQCFARYPDHMK
QHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKN
GIKANFKIRHNIEDGGVQLADHYQQNTPIGDGPVLLPDNHYLSYQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYKE
LLMCSGQAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSRSKNRVNTVRKSSTTARCQVEGCRMDLSNVKAYYSRHKVCC
IHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTALFTSHYSRIAPSLYGNPNAAMIKS
VLGDPTAWSTARSVMQRPGPWQINPVRETHPHMNVLSHGSSSFTTCPEMINNNSTDSSCALSLLSNSYPIHQQQLQTPTN
TWRPSSGFDSMISFSDKVTMAQPPPISTHQPPISTHQQYLSQTWEVIAGEKSNSHYMSPVSQISEPADFQISNGTTMGGF
ELYLHQQVLKQYMEPENTRAYDSSPQHFNWSL
>NP_191351.1 squamosa promoter binding protein-like 15 [Arabidopsis thaliana]
MELLMCSGQAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSRSKNRVNTVRKSSTTARCQVEGCRMDLSNVKAYYSRHKV
CCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTALFTSHYSRIAPSLYGNPNAAMI
KSVLGDPTAWSTARSVMQRPGPWQINPVRETHPHMNVLSHGSSSFTTCPEMINNNSTDSSCALSLLSNSYPIHQQQLQTP
TNTWRPSSGFDSMISFSDKVTMAQPPPISTHQPPISTHQQYLSQTWEVIAGEKSNSHYMSPVSQISEPADFQISNGTTMG
GFELYLHQQVLKQYMEPENTRAYDSSPQHFNWSL
>KAG7634825.1 SBP domain superfamily [Arabidopsis suecica]
MELLMGSGQAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSRSKNRVNTVRKSSTTARCQVEGCRMDLSNVKAYYSRHKV
CCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTALFTSHYSRIAPSLYGNPNAAMI
KSVLGDPTAWSTARSVMQRPGPWQINPVRETHPHMNVLSHGSSSFTTCPEMINNNSTDSSCALSLLSNSYPIHQQQLQTP
TNTWRPSSGFDSMISFSDKVTMAQPPPISTHQPPISTHQQYLSQTWEVIAGEKSNSHYMSPVSQISEPADFQISNGTTMG
GFELYLHQQVLKQYMEPENTRAYDSSPQHFNWSL
>CAA0387110.1 unnamed protein product [Arabidopsis thaliana]
MELLMGSGQAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSRSKNRVNTVRKSSTTARCQVEGCRMDLSNVKAYYSRHKV
CCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTALFTSHYSRIAPSLYGNPNAAMI
KSVLGDPTAWSTARSVMQRPGPWQINPVRETHPHMNVLSHGSSSFTTCPEMINNNSTDSSCALSLLSNSYPIHQQQLQTP
TNTWRPSSGFDSMISFSDKVTMAQPPPISTHQPPISTHQQYLSQTWEVIAGEKSNSHYMSPVSQISEPVDFQISNGTTMG
GFELYLHQQVLKQYMEPENTRAYDSSPQHFNWSL
>CAD5326126.1 unnamed protein product [Arabidopsis thaliana]
MELLMGSGQAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSRSKNRVNTVRKSSTTARCQVEGCRMDLSNVKAYYSRHKV
CCIHSKSSKVIVSGLHQRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTALFTSHYSRIAPSLYGNPNAAMIKSVLGDP
TAWSTARSVMQRPGPWQINPVRETHPHMNVLSHGSSSFTTCPEMINNNSTDSSCALSLLSNSYPIHQQQLQTPTNTWRPS
SGFDSMISFSDKVTMAQPPPISTHQPPISTHQQYLSQTWEVIAGEKSNSHYMSPVSQISEPVDFQISNGTTMGGFELYLH
QQVLKQYMEPENTRAYDSSPQHFNWSL
>KAG7561265.1 SBP domain superfamily [Arabidopsis thaliana x Arabidopsis arenosa]
MELLMGSGQAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSGSKNRVNTGRKSTMTARCQVEGCRMDLSNVKAYYSRHKV
CCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTALFTSRYSRIAPSLYGNPNAAMI
KSVLGDPMAWSTAKSVMRRSGPWQINPERESHQLLNVLSHGSSSFTTCPEIINNNSTDSSCALSLLSNSNPIQQQQLQTP
TNLWRPSSGFDSLISFSDRVTMAQPPPISTHHQYLSQTWEVMAGEKSNSHYISPVSQISEPADFQISNGTTMGGFELSLH
QQVLRQYMEPENTRAYDSSPQHFNWSL
>XP_002878178.1 squamosa promoter-binding-like protein 15 [Arabidopsis lyrata subsp. lyrata]
MELLMGSGQAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSGSKNRVNTGRKSTMTARCQVEGCRMDLSNVKAYYSRHKV
CCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTALFTSRYTRIAPSLYGNPNAAMI
KSVLGDPTAWSTARSVMRRSGPWQINPERESHQIMNVLSHGSSSFTTCPEITNNNSTDSSCALSLLSNSNPIQQQQLQTP
TNLWRPSSGFDSMISFSDRVTMAQPPPISTHHQYLSQTWDVMAGGKSNSHYMSPVSQISEPAEFQISNGTTMGGFELSLH
QQVLRQYMEPENTRAYDSSPQHFNWSL
>KAG7566101.1 SBP domain [Arabidopsis suecica]
MELLMGSGHAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSGSKNRVNTGRKSTMTARCQLEGCRMDLSNVKAYYSRHKV
CCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTSSLFTSRYSRIAPSLYGNPNAAMI
KSVLGDPMAWSTAKSVMRRSGPWQINPERESHQLLNVLSHGSSSFTTCPEIINNNSTDSSCALSLLSNSNPIQQQQLQTP
TNLWRPSSGFDSLISFSDRVTMAQPPPISTHHQYLSQTWEVMAGEKSNSHYISPVSQISEPAGFQISNGTTMGGFELSLH
QQVLRQYMEPENTRAYDSSPQHFNWSL
>CAE6076605.1 unnamed protein product [Arabidopsis arenosa]
MRRGRGKGKRQNATAREDRGSGEEEKIPAFRRRGRPQKPVKDEIEEEEVELVKKTEEEEDKDDDTNGSVTSKEDVTENGR
KRKKPVESKESNITEEENGVGSKSSTEDSMKSSSSIGFRQNGSRRKNKPRRAAEAVVECNGAESGGSSSTESSSLSGGLR
FGQKIYFEDGSGSGSKNRVNTGRKSTMTARCQVEGCRMDLSNVKAYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQ
LSEFDLEKRSCRRRLACHNERRRKPQSTTSLFTSRYSRIAPSLYGNPNAAMIKSVLGDPMAWSTAKSVMRRSGPWQINPE
RESHQLLNVLSHGSSSFTTCPEIINNNSTDSSCALSLLSNSNPIQQQQLQTPTNLWRPSSGFDSLISFSDRVTMAQPPPI
STHHQYLSQTWEVMAGEKSNSHYISPVSQISEPADFQISNGSTMGGFELSLHQQVLRQYMEPENTRAYDSSPQHFNWSL
>XP_006291402.1 squamosa promoter-binding-like protein 15 [Capsella rubella]
MELLMGSGQAESGGSSSTESSLLSGGLRFGQKIYFEDGSGSGSKNRVSTGHKSSMTTVARCQVEGCKMDLSNAKAYYSRH
KVCCIHSKSSKVIVSGLHQRFCQQCSRFHHLSEFDLEKRSCRRRLACHNERRRKPQPATLFTSHYTRIAPSLYGNANAAM
IKSVLGDPTAWSTSRSVMRSSGPWQINPVKESNQLMNVYSQESSSFTITCPEMMNNNSTDSGCALSLLSNSNPIQQQQQQ
PQTQTNIWRSSSGFDSMILDRVTMAQPPPISGHHQYLNQTLAFMAGEKSNSHYMSPVLGPSQISEPDEFQISNGTTMDGF
ELSLHQQVLRQYMEPENTRAYDSSPHYFNWSL
>CAH2063751.1 unnamed protein product [Thlaspi arvense]
MELLMGSGQNRTESYGSSSTESSSLSGGLRFGQKIYFEDGSGSGGGSNKNRVNTGRKSRTARCQVEGCRMDLSNVKTYYS
RHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQATTSLLTSRYSRIAPSLYGNAN
TAMIRSVLGDPTAWSTARSVMRRSAPWQINPERESHQLMNVFSHDSSSFTTTCPEMMNSNGTDSSCALSLLSNSNTNQQQ
QLLQTSTNIWRPSSGFDSANADRATMAQPPPVSNQHQYLNQTWEFMAGEKSNSHYLSPVLGLSQISEPVDFQISNGTTMG
GFELSIHQQVLRHYMEPENTRAYDSSAQHFNWSL
>XP_010516431.1 PREDICTED: squamosa promoter-binding-like protein 15 [Camelina sativa]
MELLIGGSGQTESGGASSTKSSSLSGGLRFGQKIYFEDGSGSGSKNRVGTGHKSSTTTTTARCQVEGCKMDLSNAKAYYS
RHKVCCIHSKSSKVIVSGLRQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTLYTSQYTRIAPSLYGDANA
AMMKSVLGDPTVWSTARSVMRRSGPWQISPVKESHHQLMNVFSQESSSFTITCPEMMNNNSTDSSCALSLLSNSNSNSNP
IQQQQQQLQTQTHIWRPSLGFDSMTVDRVTMAQPPPISSHHQYLNQTLEFMAGEKSSSHYMSPVLGPSQISEPDEFQISN
GTTMDGFELSLHQQVLRQYMEPENTRAYDSSPHHFNWSL
>AKC05620.1 squamosa promoter-binding-like protein 15 [Cardamine hirsuta]
MELLMGSGQSESGASSSNESSSLSGGLRFGQKIYFEDGSGSGSKNRVSSTGRKSSTTTARCQVEGCRMDLSNAKTYYSRH
KVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPATTLFTSRFTRTAPSHYGNANAA
MIKSVLGDPTAWTAERSVMRRSAPWQSNPSHQVMIDFSHGSSSLTTTCPEMMNNTSTDSSCALSLLSNSNQTQQLQQQLQ
TPANIWRASSGFDSMIADRVTMAQPPPISTHHQYLNQSWEFMPGEKNDSHYMSPMSQISEPADLHMRNRTTMGGFEVSLH
QQVMRQYMAPENTRAYDSSPQHFNWSL
>XP_010504729.1 PREDICTED: squamosa promoter-binding-like protein 15 [Camelina sativa]
MELLMGGSGQTESGGASSTESSSLSGGLRFGQKIYFEDGSGSGSKNRVGAGHKSSTTARCQVEGCKMDLSNAKAYYSRHK
VCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTLYTRIAASLYGNANAAMIKSVL
GDPTVWSTARSVMRRSGPWQINPVKESHHQHMNVFSQESSSFTITCPEMMNNNSTDSSCALSLLSNSNSNPIQQQQQQLQ
TQTNIWRPSSGFDYMTVDRVTLAQPPPIPSHHQYLNQTLEFMTGEKNSSHYMSPALGPSQISAPDEFQISNGTTMDGFEL
SLHQQVLRQYMAPENTRAYDSSPHHFNWSL
>CAA7060637.1 unnamed protein product [Microthlaspi erraticum]
MELLMDSSQTESGGSSSIESSSLTGGLRFGQKIYFEDGSGSGAKSSKNRVNTARKSSTSTARCQVEGCRMDLSNAKTYYS
RHKVCCIHSKSSNVIVSGLHQRFHLLSEFDLEKRSCRRRLACHNERRRKPHATTNLLTSRYSRIAPSLYENANTAIFRSV
LGDTTAWSAARPVMRRSGPWQINPERESNLNVFSHGSSSFTTCPAMMNNNSTDSSCALSLLSNSNTNTNQQQQQPLQTST
DTWRPSSGFDSMIADRVTMAQPPPVSIHNQYLNQSWDFMEGEKSNSHHMSPVLGLSQISEPADFQLSNGMGGGFELSLHQ
QVLKQYMEPENTRAYDSSPQHFNWSL
>KAG2324838.1 hypothetical protein Bca52824_007566 [Brassica carinata]
MELLMGSGQDHPQSAGSSSTLSGGLRFGQKIYFEDGSGAGLSRNRVNNTGRKSMTARCQVEGCRMDLSNAKTYYSRHKVC
CVHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQTTTTLLTSHYSSIAPSLYGNAIRSVLG
DPTLWSTARGSSAPWQINPERESHHQLMNIISFGSSSFTNSTDSSCALSLLSNSNRNQQEQQPLQTPTNAWRPSLDFDSI
VADRVTMAQPPPVSIQNQYLNQTWEFMSGEKSNAHCISPVLGLSQISEPVDFQTSNGATMSGVELSLHQQVLRQYLEPEN
TRAYDSSHQHFNWSL
>CAH8384605.1 unnamed protein product [Eruca vesicaria subsp. sativa]
MELEMGSGQKKPESAGSSSTLSGGLRFGQKIYFEDGSGAGLSKNRVSSTGRKSMTARCQVEGCRTDLSNAKTYYSRHKVC
CVHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQATTTLLTSRYSSLYGNAIRSVLGDPTT
WSTARGSAPWKINQESDRHQLMNVISFGSSSFTTCPEMMNNNSTDSSCALSLLSNSNPNQQEQQPLQTSNTIWRPSLDFD
STVADRVTMAQPPPVSMQNQYLNQTWEFMSGEKSNAQCISPVLGQSQISEPVDFQIGTTMGGGFELSLHQQVLRQYMEPE
NTRAYDTSPQYFNWSL
>KAF8114775.1 hypothetical protein N665_0034s0114 [Sinapis alba]
MELLMGSGQNQPESAGSSSSTLSGGLRFGQKIYFEDGSGAGLSKNRVNTGRKSTTARCQVEGCRMDLSSAKTYYSRHKVC
CIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQATTTFLTSHYSSIAPSLYGNAIRGVLG
DSTTWSTARGSAPLQINPERESHRLMNVFSFGSSSFTNNSTDSSCALSLLSNSNPNQQEQQPLQTPTNTWRPSLDFDSIV
ADRVTMAQPPPVSVQNQYLNQTWEFMSGEKSNGQHYISPVLGLSQISEPVDFQISNGATMSGVELSLHQQVLRQYLEPEN
TRAYDSSPQHFNWSL
>XP_010427684.1 PREDICTED: squamosa promoter-binding-like protein 15 [Camelina sativa]
MELLMGGTESGGASSTESSSLSGGLRFGQKIYFEDGSGSGSKNRVVTGHKSSTTTTTARCQVEGCKMDLSNAKAYYSRHK
VCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTLFTSHYTRIAPSLYGNANAAMI
KSVLGDPTVWSTARSVMRRSGPWQINPVKESHHQLMNVFSQESSSFTITCPEMMNNNNSTDSSCALSLLSNSNSNPIQQQ
QQQLQTQTNIWRPSLGFDSMTVDRVTLAQPPPILSHHQYMSPVLGPSQISAPDEFQISNVTTMDGFELSLHQQVLRQYME
PQNTRAYDSSPHHFNWSL

3、导入蛋白序列，点击File菜单栏导入或者直接拖进MEGA7软件都可以

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以上任一种形式都可以。

4、多序列比对，导入成功后如下图所示。

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选择Alignment > Align by ClustalW > OK > 默认参数

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比对后的结果如下图：

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5、系统进化树构建，选择NJ法进行构建系统进化树

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6、结果展示

第一种，步长树

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第二种步长对齐树

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其他形状的树，点击以上按钮进行展示

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7、保存nwk树文件，导入树图片进行美化

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生信漫谈

生信漫谈，认识生信，学习生信，跨越生信入门路上的障碍，从而利用生信技术解决科研学习路上的绊脚石！