动植物基因组De novo三代测序

专业 准确 完整

产品介绍

动植物基因组De novo测序分析也叫从头测序分析,指不依赖于任何参考序列信息就可对某动植物进行测序分析,使用最新的生物信息学方法进行序列拼接获得某物种的基因组序列图谱,并进行基因组结构注释、功能注释、比较基因组学分析等一系列的后续分析。三代测序技术(以PacBio和Nanopore为代表)具有读长长的特点,自2015年开始在动植物基因组De novo中初露锋芒,已延用至今。该类型测序分析结果可以广泛应用于农林鱼牧医药及海洋等各个方面的研究。

1

TU1 BUTONGCEXUJISHUDUZHANG,ZHUNQUEXINGJIJIYINZULIANXUXINGPINGGU

三代测序技术原理

PacBioCEXUYUANLI

CAIYONGBIANHECHENGBIANCEXUDEFANGSHI,YIQIZHONGYITIAODNALIANWEIMOBAN,TONGGUODNAJUHEMEIHECHENGLINGWAIYITIAOLIAN,JINYIBUJIANGYINGGUANGXINHAOZHUANBIANWEIJIANJIXINHAO。TONGSHIPacBioYISHENGJILECCSCEXUMOSHIYIHUODEZHANGDUZHANGDEGAOBAOZHEN(HiFi)15 kb reads,YOUCITISHENGJIYINZUZUZHUANGDEZHUNQUEXING。

皇朝国际TU2 SANDAIPacBioCEXUYUANLI

皇朝国际NanoporeCEXUYUANLI

皇朝国际DANGDANLIANDNAFENZICHUANGUONAMIKONGSHI,XIANGDUIYUMEIGEHEGANSUAN,DOUHUIHUODEBUTONGDEDIANLIUXINHAO。JILUMEIGEKONGDELIZIDIANLIUBIANHUA,BINGJIYUMAERKEFUMOXINGHUODIGUISHENJINGWANGLUODEFANGFAJIANGQIZHUANHUANWEIJIANJIXULIE。CHUCIZHIWAI,Ultra-long reads (ULRs) SHIONTPINGTAIDELINGYIZHONGYAOTEZHENG,BINGJUYOUCUJINDAXINGJIYINZUZUZHUANGDEQIANLI。

信息分析内容

De novo研究 研究内容
基因组组装 多软件组装、组装结果评估
基因预测与注释 编码基因预测;重复序列注释和转座元件分类;非编码RNA注释;假基因注释等
Hi-C辅助基因组组装 有效数据评估;Contig聚类、排序及定向分析;挂载结果评估
 

 

 

生物学问题解析

 

 

 

比较基因组学研究

基因家族聚类;
系统发育树的构建;
基因家族扩张与收缩分析;
物种分化时间推算;
LTR形成时间估算;
全基因组复制事件;
选择压力分析
特定生物学问题剖析 结合组学研究方法,深入对某物种生物学问题进行解析

33

CAOMEIJIYINJIAZUJULEIFENXI

44

YIYIQUANJIYINZUFUZHISHIJIANFENXI

皇朝国际KAIXINGUOXITONGJINHUASHUYUJIYINJIAZUSHOUSUOKUOZHANGFENXI

皇朝国际LUDIMIANYAJIYINZUGONGXIANXINGFENXI

技术服务流程

  • 样品寄送

  • 建库测序

  • 数据分析

  • 出具报告

  • 售后答疑

产品优势

GONGSICHENGLIYU2009NIAN,SHENGENGJIYINZUCEXULINGYU11NIANZHIJIU,ZHANGJIUYILAIZHILIYUCHENGWEIJINGZHUNDEJIYINZUZUZHUANGZHUANJIA;

YONGYOUSHIJIEZAIZUIZHULIUDESANDAICEXUPINGTAI(PacBioCEXUQUANPINGTAIHENanoporeCEXUQUANPINGTAI),JUYOUFENGHOUDESHUANGPINGTAIZUZHUANGJISHANGWANZHONGWUZHONGJIYINZUZUZHUANGJINGYAN。

Hi-CRANSEZHIGOUXIANGBUHUOJISHUWENKUYOUXIAOSHUJUBILIGAO,GUAZAIXIAOLVGAODA99%,DUOBEITIWUZHONGYANJIUJINGYANFENGFU,YUSANDAIJIYINZUZUZHUANGXIANGJIEHE,HUODERANSETISHUIPINGJIYINZUDETONGSHIJINYIBUTISHENGJIYINZUZUZHUANGZHILIANG。

YONGYOUZIZHUYANFADELINGXIANDEJIYINZUCEXUHEFENXIJISHU,MUQIANYIJINGHUODE30DUOXIANGFAMINGZHUANLI,CHAOGUO150DUOXIANGHEXINRUANJIANZHUZUOQUAN。

项目经验示例

合作文章案例

案例1

以更新的亚洲棉A基因组为基础的243份二倍体棉的重要农艺性状的研究
Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits

皇朝国际QIKAN:Nature Genetics

YINGXIANGYINZI:27.125

皇朝国际FABIAODANWEI:ZHONGGUONONGYEKEXUEYUANMIANHUAYANJIUSUO、BEIJINGBAIMAIKESHENGWUKEJIYOUXIANGONGSIDENG

FABIAONIANFEN:2018NIAN5YUE

YANJIUBEIJING:

棉花是研究植物多倍化的有价值的资源。亚洲棉(Gossypium arboreum)和草棉(Gossypium herbaceum皇朝国际)的祖先是现代栽培异源四倍体棉花A亚基因组的供体。 本研究中,利用了三代PacBio和Hi-C技术,重新组装了高质量的亚洲棉基因组,分析了243份二倍体棉花种质的群体结构和基因组分化趋势,同时确定了一些有助于棉花皮棉产量遗传改良的候选基因位点。

YANJIUJIEGUO:

皇朝国际1、YAZHOUMIANSANDAIJIYINZUZUZHUANG:

皇朝国际LIYONGSANDAICEXUHEHi-CXIANGJIEHEDEFANGFAJINXINGYAZHOUMIANJIYINZUZUZHUANG。GONGJIHUODELE142.54 Gb ,ZUZHUANG1.71 GbYAZHOUMIANJIYINZU,Contig N50=1.1 Mb,ZUIZHANGDEContigWEI12.37 Mb。LIYONGHi-CJISHUJIANGZUZHUANGDE1573 MbDESHUJUDINGWEIDAO13TIAORANSETISHANG,YUYIJINGFABIAODEJIYINZUXIANGBI,DANGHi-CSHUJUBIDUIDAOGENGXINDEJIYINZUHOU,DUIJIAOXIANWAIDEBUYIZHIXINGMINGXIANJIANSHAO(TU1 a-b)

图1 Hi-C数据在两版亚洲棉基因组上的比对

2、ERBEITIMIANHUAQUNTIYICHUANJINHUAFENXI:

DUI230FENYAZHOUMIANHE13FENCAOMIANZHONGCEXU,JINXINGJIYINZUBIDUI、XITONGFAYUSHU、QUNTIJIEGOUFENXI、PCA、LDHEXUANZEXINGQINGCHUFENXIDECHUYAZHOUMIANHECAOMIAN(A)YULEIMENGDESHIMIANTONGSHIJINXINGLEFENHUA;YAZHOUMIANQIYUANYUZHONGGUONANBU,SUIHOUBEIYINRUZHANGJIANGHEHUANGHEDIQU,DADUOSHUJUYOUXUNHUAXIANGGUANTEXINGDEZHONGZHIDOUJINGLILEDILIGELI(TU2)。

图2 二倍体棉群体进化和群体结构分析

3、YAZHOUMIANDEQUANJIYINZUGUANLIANFENXI(GWAS):

DUILAIZIBUTONGHUANJINGXIADE11GEZHONGYAOXINGZHUANGJINXINGQUANJIYINZUGUANLIANFENXI,JIANDINGLEYAZHOUMIAN11GEZHONGYAONONGYIXINGZHUANGDE98GEXIANZHUGUANLIANWEIDIAN,GaKASIIIDEFEITONGYITIHUAN(BANGUANGANSUAN/JINGANSUANTIHUAN)SHIDEMIANZIZHONGDEZHIFANGSUANZUCHENG(C16:0HEC16:1)FASHENGLEBIANHUA;FAXIANMIANHUAKUWEIBINGKANGXINGYUGaGSTF9JIYINDEBIAODAJIHUOXIANGGUAN。XUANZELEYAZHOUMIANZHONGZHIZHONGDE158FENYOURONGMAOHE57FENWURONGMAOCAILIAOJINXINGGWASGUANLIANFENXI,FAXIANYUMAOZHUANGTIHEXIANWEIFAYUYOUGUANXINXI(TU3)。

图3 二倍体棉群体进化和群体结构分析

YANJIUJIELUN:

LIYONGSANDAICEXU+Hi-CJISHUWANCHENGLEYAZHOUMIANJIYINZUDEZHONGXINZUZHUANG,JIANGJIYINZUZUZHUANGZHIBIAOCONG72 KbTISHENGDAO1.1 Mb,WEIYAZHOUMIANHOUXUDEQUNTIYICHUANXUEDENGXIANGGUANYANJIUDIANDINGLEJICHU;TONGGUOQUNTIYICHUANJINHUADENGXIANGGUANFENXI,FAXIANYAZHOUMIANHECAOMIAN(AXING)YULEIMENGDESHIMIAN(DXING)TONGSHIJINXINGLEFENHUA,BINGZHENGMINGLEYAZHOUMIANQIYUANYUZHONGGUONANBU,SUIHOUBEIYINRUZHANGJIANGHEHUANGHEDIQU;ZHENGHEGWASYUQTLDENGFENXIFANGFA,DUIYAZHOUMIANZHIFANGSUANHANLIANG,KANGBINGXINGJIMIANRONGSHENGZHANGFAYUXIANGGUANJIYINJINXINGDINGWEI,BINGJINXINGXIANGGUANGONGNENGYANZHENG,CUJINLEYAZHOUMIANFUZANONGYIXINGZHUANGDEGAILIANG。

案例2、

二倍体、野生和栽培四倍体花生比较基因组分析揭示亚基因组不对称进化和改良
Comparison of Arachis monticola with diploid and cultivated tetraploid genomes reveals asymmetric subgenome evolution and improvement of peanut

QIKAN:Advanced Science

YINGXIANGYINZI:15.804

皇朝国际FABIAODANWEI:HENANNONGYEDAXUE、BEIJINGBAIMAIKESHENGWUKEJIYOUXIANGONGSIDENG

皇朝国际FABIAONIANFEN:2019NIAN11YUE

YANJIUBEIJING:

花生作为我国重要的经济作物,是提供重要的蛋白和油料的基础。花生属一共包括30个二倍体品种,1个异源四倍体野生花生(A. monticola)和1个栽培花生(A. hypogaea)。作为栽培花生农艺性状改良的重要野生资源供体,野生四倍体花生一直是国内外学者的研究热点。研究中对花生属唯一的野生异源四倍体花生Arachis monticola基因组进行了研究,同时对17个野生二倍体花生(AA;BB;EE;KK和CC)与30个野生和栽培四倍体花生进行了重测序分析。

YANJIUJIEGUO:

皇朝国际1、野生四倍体花生基因组denovo及与栽培四倍体花生的比较分析:

基于 Illumina、PacBio 、Hi-C和光学图谱数据,组装Arachis monticola(2n = 4x = 40)基因组大小为2.62 Gb ,contigs N50=106.66 Kb,scaffolds N50=124.92 Mb;与栽培四倍体花生A. hypogaea皇朝国际基因组结构变异高度保守,且比野生祖先二倍体更加保守;

2、A、B亚基因组的单系起源和多样性:

DUI17GEERBEITIYESHENGZHONG(AA、BB、EE、KKHECC)HE30GEYESHENGHEZAIPEISIBEITIHUASHENGJINXINGLEJINHUASHUHEPCAFENXI。JIEGUOBIAOMING,ZAIPEISIBEITIHUASHENGYUYESHENGSIBEITIHUASHENGZUIJIEJIN, AHEBYAJIYINZUDEDANXIQIYUAN(TU1);

图1 野生和栽培花生的系统进化模型

3、四倍体花生不对称亚基因组进化及表达差异

ZAIPEIHUASHENGHEYESHENGHUASHENGDEYAJIYINZUJIANDETONGYUANXULIEJIAOHUANLV(HSE)FENBIEWEI2.46%HE2.54%。YESHENGHUASHENGZHONGADAOBDEHSEFUJIDEJIYINWEILEIHUANGTONGSHENGWUHECHENGHEZHOUYEJIELVTUJINGDEJIYIN,ANSHIBUDUICHENGHSEsZAISHENGWUXUEGONGNENGZHONGDEZUOYONG;

4、SV对荚发育和驯化相关基因表达的影响及抗病基因鉴定

DUIYESHENGSIBEITIHUASHENGHEZAIPEISIBEITIHUASHENGBUTONGFAYUJIEDUANJIAGUODESVFENXIFAXIANSVZAIJIAGUOFAYUGUOCHENGZHONGJIYINBIAODADEBIANHUASHANGKENENGQIZHEZHONGYAOZUOYONG;TONGSHIZAIZAIPEISIBEITIHUASHENGZHONGJIANDINGDAO190GESVKANGBINGJIYIN(SV-RGAs),QIZHONG32GEJIYINZAIJIEZHONGHOUYIGANZUHUOKANGXINGZUZHONGBIAOXIANCHUXIANZHUDEBIAODABIANHUA(TU2)。

图2 野生花生到栽培品系的豆荚性状驯化

 

YANJIUJIELUN:

CHONGFENZHUSHILEGAOZHILIANGYESHENGSIBEITIHUASHENGJIYINZU,JIESHILEHUASHENGYAJIYINZUDANXIQIYUANHEYICHUANJINHUAMOXING,BIAOMINGLEYESHENGHEZAIPEISIBEITIHUASHENGYAJIYINZUFASHENGLEBUDUICHENGJINHUA;CIWAI,YESHENGHUASHENGZHONGCUNZAIDEDUTEDENGWEIJIYINKEYIGAISHANZAIPEIHUASHENGDEKANGXINGHEJIAGUODAXIAODENGXINGZHUANG,WEIYANJIUDUOBEITIJIYINZUJINHUA、ZUOWUXUNHUAHEJIYINZUFUZHUHUASHENGSHENGCHANGAILIANGTIGONGDUTEDEJIAZHI。

 

var _hmt = _hmt || []; (function() { var hm = document.createElement("script"); hm.src = "https://hm.baidu.com/hm.js?06a9f91b3627ff69f489962891893811"; var s = document.getElementsByTagName("script")[0]; s.parentNode.insertBefore(hm, s); })();