生信小白如何利用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/

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]MELLMCSGQAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSRSKNRVNTVRKSSTTARCQVEGCRMDLSNVKAYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTALFTSHYSRIAPSLYGNPNAAMIKSVLGDPTAWSTARSVMQRPGPWQINPVRETHPHMNVLSHGSSSFTTCPEMINNNSTDSSCALSLLSNSYPIHQQQLQTPTNTWRPSSGFDSMISFSDKVTMAQPPPISTHQPPISTHQQYLSQTWEVIAGEKSNSHYMSPVSQISEPADFQISNGTTMGGFELYLHQQVLKQYMEPENTRAYDSSPQHFNWSL

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

下载后的序列形式：

>AST51816.1 Venus [Cloning vector pSTB205]MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKLICTTGKLPVPWPTLVTTLGYGLQCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGGVQLADHYQQNTPIGDGPVLLPDNHYLSYQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYKELLMCSGQAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSRSKNRVNTVRKSSTTARCQVEGCRMDLSNVKAYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTALFTSHYSRIAPSLYGNPNAAMIKSVLGDPTAWSTARSVMQRPGPWQINPVRETHPHMNVLSHGSSSFTTCPEMINNNSTDSSCALSLLSNSYPIHQQQLQTPTNTWRPSSGFDSMISFSDKVTMAQPPPISTHQPPISTHQQYLSQTWEVIAGEKSNSHYMSPVSQISEPADFQISNGTTMGGFELYLHQQVLKQYMEPENTRAYDSSPQHFNWSL>NP_191351.1 squamosa promoter binding protein-like 15 [Arabidopsis thaliana]MELLMCSGQAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSRSKNRVNTVRKSSTTARCQVEGCRMDLSNVKAYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTALFTSHYSRIAPSLYGNPNAAMIKSVLGDPTAWSTARSVMQRPGPWQINPVRETHPHMNVLSHGSSSFTTCPEMINNNSTDSSCALSLLSNSYPIHQQQLQTPTNTWRPSSGFDSMISFSDKVTMAQPPPISTHQPPISTHQQYLSQTWEVIAGEKSNSHYMSPVSQISEPADFQISNGTTMGGFELYLHQQVLKQYMEPENTRAYDSSPQHFNWSL>KAG7634825.1 SBP domain superfamily [Arabidopsis suecica]MELLMGSGQAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSRSKNRVNTVRKSSTTARCQVEGCRMDLSNVKAYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTALFTSHYSRIAPSLYGNPNAAMIKSVLGDPTAWSTARSVMQRPGPWQINPVRETHPHMNVLSHGSSSFTTCPEMINNNSTDSSCALSLLSNSYPIHQQQLQTPTNTWRPSSGFDSMISFSDKVTMAQPPPISTHQPPISTHQQYLSQTWEVIAGEKSNSHYMSPVSQISEPADFQISNGTTMGGFELYLHQQVLKQYMEPENTRAYDSSPQHFNWSL>CAA0387110.1 unnamed protein product [Arabidopsis thaliana]MELLMGSGQAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSRSKNRVNTVRKSSTTARCQVEGCRMDLSNVKAYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTALFTSHYSRIAPSLYGNPNAAMIKSVLGDPTAWSTARSVMQRPGPWQINPVRETHPHMNVLSHGSSSFTTCPEMINNNSTDSSCALSLLSNSYPIHQQQLQTPTNTWRPSSGFDSMISFSDKVTMAQPPPISTHQPPISTHQQYLSQTWEVIAGEKSNSHYMSPVSQISEPVDFQISNGTTMGGFELYLHQQVLKQYMEPENTRAYDSSPQHFNWSL>CAD5326126.1 unnamed protein product [Arabidopsis thaliana]MELLMGSGQAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSRSKNRVNTVRKSSTTARCQVEGCRMDLSNVKAYYSRHKVCCIHSKSSKVIVSGLHQRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTALFTSHYSRIAPSLYGNPNAAMIKSVLGDPTAWSTARSVMQRPGPWQINPVRETHPHMNVLSHGSSSFTTCPEMINNNSTDSSCALSLLSNSYPIHQQQLQTPTNTWRPSSGFDSMISFSDKVTMAQPPPISTHQPPISTHQQYLSQTWEVIAGEKSNSHYMSPVSQISEPVDFQISNGTTMGGFELYLHQQVLKQYMEPENTRAYDSSPQHFNWSL>KAG7561265.1 SBP domain superfamily [Arabidopsis thaliana x Arabidopsis arenosa]MELLMGSGQAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSGSKNRVNTGRKSTMTARCQVEGCRMDLSNVKAYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTALFTSRYSRIAPSLYGNPNAAMIKSVLGDPMAWSTAKSVMRRSGPWQINPERESHQLLNVLSHGSSSFTTCPEIINNNSTDSSCALSLLSNSNPIQQQQLQTPTNLWRPSSGFDSLISFSDRVTMAQPPPISTHHQYLSQTWEVMAGEKSNSHYISPVSQISEPADFQISNGTTMGGFELSLHQQVLRQYMEPENTRAYDSSPQHFNWSL>XP_002878178.1 squamosa promoter-binding-like protein 15 [Arabidopsis lyrata subsp. lyrata]MELLMGSGQAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSGSKNRVNTGRKSTMTARCQVEGCRMDLSNVKAYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTALFTSRYTRIAPSLYGNPNAAMIKSVLGDPTAWSTARSVMRRSGPWQINPERESHQIMNVLSHGSSSFTTCPEITNNNSTDSSCALSLLSNSNPIQQQQLQTPTNLWRPSSGFDSMISFSDRVTMAQPPPISTHHQYLSQTWDVMAGGKSNSHYMSPVSQISEPAEFQISNGTTMGGFELSLHQQVLRQYMEPENTRAYDSSPQHFNWSL>KAG7566101.1 SBP domain [Arabidopsis suecica]MELLMGSGHAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSGSKNRVNTGRKSTMTARCQLEGCRMDLSNVKAYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTSSLFTSRYSRIAPSLYGNPNAAMIKSVLGDPMAWSTAKSVMRRSGPWQINPERESHQLLNVLSHGSSSFTTCPEIINNNSTDSSCALSLLSNSNPIQQQQLQTPTNLWRPSSGFDSLISFSDRVTMAQPPPISTHHQYLSQTWEVMAGEKSNSHYISPVSQISEPAGFQISNGTTMGGFELSLHQQVLRQYMEPENTRAYDSSPQHFNWSL>CAE6076605.1 unnamed protein product [Arabidopsis arenosa]MRRGRGKGKRQNATAREDRGSGEEEKIPAFRRRGRPQKPVKDEIEEEEVELVKKTEEEEDKDDDTNGSVTSKEDVTENGRKRKKPVESKESNITEEENGVGSKSSTEDSMKSSSSIGFRQNGSRRKNKPRRAAEAVVECNGAESGGSSSTESSSLSGGLRFGQKIYFEDGSGSGSKNRVNTGRKSTMTARCQVEGCRMDLSNVKAYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQSTTSLFTSRYSRIAPSLYGNPNAAMIKSVLGDPMAWSTAKSVMRRSGPWQINPERESHQLLNVLSHGSSSFTTCPEIINNNSTDSSCALSLLSNSNPIQQQQLQTPTNLWRPSSGFDSLISFSDRVTMAQPPPISTHHQYLSQTWEVMAGEKSNSHYISPVSQISEPADFQISNGSTMGGFELSLHQQVLRQYMEPENTRAYDSSPQHFNWSL>XP_006291402.1 squamosa promoter-binding-like protein 15 [Capsella rubella]MELLMGSGQAESGGSSSTESSLLSGGLRFGQKIYFEDGSGSGSKNRVSTGHKSSMTTVARCQVEGCKMDLSNAKAYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHHLSEFDLEKRSCRRRLACHNERRRKPQPATLFTSHYTRIAPSLYGNANAAMIKSVLGDPTAWSTSRSVMRSSGPWQINPVKESNQLMNVYSQESSSFTITCPEMMNNNSTDSGCALSLLSNSNPIQQQQQQPQTQTNIWRSSSGFDSMILDRVTMAQPPPISGHHQYLNQTLAFMAGEKSNSHYMSPVLGPSQISEPDEFQISNGTTMDGFELSLHQQVLRQYMEPENTRAYDSSPHYFNWSL>CAH2063751.1 unnamed protein product [Thlaspi arvense]MELLMGSGQNRTESYGSSSTESSSLSGGLRFGQKIYFEDGSGSGGGSNKNRVNTGRKSRTARCQVEGCRMDLSNVKTYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQATTSLLTSRYSRIAPSLYGNANTAMIRSVLGDPTAWSTARSVMRRSAPWQINPERESHQLMNVFSHDSSSFTTTCPEMMNSNGTDSSCALSLLSNSNTNQQQQLLQTSTNIWRPSSGFDSANADRATMAQPPPVSNQHQYLNQTWEFMAGEKSNSHYLSPVLGLSQISEPVDFQISNGTTMGGFELSIHQQVLRHYMEPENTRAYDSSAQHFNWSL>XP_010516431.1 PREDICTED: squamosa promoter-binding-like protein 15 [Camelina sativa]MELLIGGSGQTESGGASSTKSSSLSGGLRFGQKIYFEDGSGSGSKNRVGTGHKSSTTTTTARCQVEGCKMDLSNAKAYYSRHKVCCIHSKSSKVIVSGLRQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTLYTSQYTRIAPSLYGDANAAMMKSVLGDPTVWSTARSVMRRSGPWQISPVKESHHQLMNVFSQESSSFTITCPEMMNNNSTDSSCALSLLSNSNSNSNPIQQQQQQLQTQTHIWRPSLGFDSMTVDRVTMAQPPPISSHHQYLNQTLEFMAGEKSSSHYMSPVLGPSQISEPDEFQISNGTTMDGFELSLHQQVLRQYMEPENTRAYDSSPHHFNWSL>AKC05620.1 squamosa promoter-binding-like protein 15 [Cardamine hirsuta]MELLMGSGQSESGASSSNESSSLSGGLRFGQKIYFEDGSGSGSKNRVSSTGRKSSTTTARCQVEGCRMDLSNAKTYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPATTLFTSRFTRTAPSHYGNANAAMIKSVLGDPTAWTAERSVMRRSAPWQSNPSHQVMIDFSHGSSSLTTTCPEMMNNTSTDSSCALSLLSNSNQTQQLQQQLQTPANIWRASSGFDSMIADRVTMAQPPPISTHHQYLNQSWEFMPGEKNDSHYMSPMSQISEPADLHMRNRTTMGGFEVSLHQQVMRQYMAPENTRAYDSSPQHFNWSL>XP_010504729.1 PREDICTED: squamosa promoter-binding-like protein 15 [Camelina sativa]MELLMGGSGQTESGGASSTESSSLSGGLRFGQKIYFEDGSGSGSKNRVGAGHKSSTTARCQVEGCKMDLSNAKAYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTLYTRIAASLYGNANAAMIKSVLGDPTVWSTARSVMRRSGPWQINPVKESHHQHMNVFSQESSSFTITCPEMMNNNSTDSSCALSLLSNSNSNPIQQQQQQLQTQTNIWRPSSGFDYMTVDRVTLAQPPPIPSHHQYLNQTLEFMTGEKNSSHYMSPALGPSQISAPDEFQISNGTTMDGFELSLHQQVLRQYMAPENTRAYDSSPHHFNWSL>CAA7060637.1 unnamed protein product [Microthlaspi erraticum]MELLMDSSQTESGGSSSIESSSLTGGLRFGQKIYFEDGSGSGAKSSKNRVNTARKSSTSTARCQVEGCRMDLSNAKTYYSRHKVCCIHSKSSNVIVSGLHQRFHLLSEFDLEKRSCRRRLACHNERRRKPHATTNLLTSRYSRIAPSLYENANTAIFRSVLGDTTAWSAARPVMRRSGPWQINPERESNLNVFSHGSSSFTTCPAMMNNNSTDSSCALSLLSNSNTNTNQQQQQPLQTSTDTWRPSSGFDSMIADRVTMAQPPPVSIHNQYLNQSWDFMEGEKSNSHHMSPVLGLSQISEPADFQLSNGMGGGFELSLHQQVLKQYMEPENTRAYDSSPQHFNWSL>KAG2324838.1 hypothetical protein Bca52824_007566 [Brassica carinata]MELLMGSGQDHPQSAGSSSTLSGGLRFGQKIYFEDGSGAGLSRNRVNNTGRKSMTARCQVEGCRMDLSNAKTYYSRHKVCCVHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQTTTTLLTSHYSSIAPSLYGNAIRSVLGDPTLWSTARGSSAPWQINPERESHHQLMNIISFGSSSFTNSTDSSCALSLLSNSNRNQQEQQPLQTPTNAWRPSLDFDSIVADRVTMAQPPPVSIQNQYLNQTWEFMSGEKSNAHCISPVLGLSQISEPVDFQTSNGATMSGVELSLHQQVLRQYLEPENTRAYDSSHQHFNWSL>CAH8384605.1 unnamed protein product [Eruca vesicaria subsp. sativa]MELEMGSGQKKPESAGSSSTLSGGLRFGQKIYFEDGSGAGLSKNRVSSTGRKSMTARCQVEGCRTDLSNAKTYYSRHKVCCVHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQATTTLLTSRYSSLYGNAIRSVLGDPTTWSTARGSAPWKINQESDRHQLMNVISFGSSSFTTCPEMMNNNSTDSSCALSLLSNSNPNQQEQQPLQTSNTIWRPSLDFDSTVADRVTMAQPPPVSMQNQYLNQTWEFMSGEKSNAQCISPVLGQSQISEPVDFQIGTTMGGGFELSLHQQVLRQYMEPENTRAYDTSPQYFNWSL>KAF8114775.1 hypothetical protein N665_0034s0114 [Sinapis alba]MELLMGSGQNQPESAGSSSSTLSGGLRFGQKIYFEDGSGAGLSKNRVNTGRKSTTARCQVEGCRMDLSSAKTYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQATTTFLTSHYSSIAPSLYGNAIRGVLGDSTTWSTARGSAPLQINPERESHRLMNVFSFGSSSFTNNSTDSSCALSLLSNSNPNQQEQQPLQTPTNTWRPSLDFDSIVADRVTMAQPPPVSVQNQYLNQTWEFMSGEKSNGQHYISPVLGLSQISEPVDFQISNGATMSGVELSLHQQVLRQYLEPENTRAYDSSPQHFNWSL>XP_010427684.1 PREDICTED: squamosa promoter-binding-like protein 15 [Camelina sativa]MELLMGGTESGGASSTESSSLSGGLRFGQKIYFEDGSGSGSKNRVVTGHKSSTTTTTARCQVEGCKMDLSNAKAYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQPTTLFTSHYTRIAPSLYGNANAAMIKSVLGDPTVWSTARSVMRRSGPWQINPVKESHHQLMNVFSQESSSFTITCPEMMNNNNSTDSSCALSLLSNSNSNPIQQQQQQLQTQTNIWRPSLGFDSMTVDRVTLAQPPPILSHHQYMSPVLGPSQISAPDEFQISNVTTMDGFELSLHQQVLRQYMEPQNTRAYDSSPHHFNWSL

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

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。

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

比对后的结果如下图：

5、系统进化树构建，选择NJ法进行构建系统进化树

6、结果展示

第一种，步长树

第二种步长对齐树

其他形状的树，点击以上按钮进行展示

7、保存nwk树文件，导入树图片进行美化

生信漫谈，小知识，大智慧！

欢迎大家一起讨论学习