Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq.
Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq.
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DOI：
10.1186/1471-2229-14-120
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发表时间：
2014-05-05
影响因子：
5.3
通讯作者：
Jones JD
中科院分区：
文献类型：
--
作者：
Andolfo G;Jupe F;Witek K;Etherington GJ;Ercolano MR;Jones JD
农作物基因组草案的可获得性使得能够预测编码Nb-LRR抗性基因同源物的全部基因，从而能够进行更有针对性的抗病育种。最近，我们开发了RenSeq方法来重新注释马铃薯中完整的NB-LRR基因补体，并识别没有被自动基因预测软件提取的新序列。在这里，我们利用更新的茄科RenSeq诱饵文库中的260个先前发现的NB-LRR基因，在番茄(Solanum Lycopsicum)Heinz 1706的参考基因组上建立了RenSeq。在Heinz 1706的基因组DNA上使用RenSeq后的250个碱基的MiSeq读取，我们鉴定了105个新的NB-LRR序列。重新注释包括拆分基因模型，将部分基因组合成更长的序列，以及关闭组装间隙。在PimpinellifoliumLA1589基因组草案中，RenSeq实现了355个NB-LRR基因的注释。然而，其中大多数是碎片化的，5‘端和3’端位于单独的重叠群的边缘。系统发育分析表明，Heinz 1706、LA1589和马铃薯无性系DM之间的所有NB-LRR类都高度保守，表明所有亚科都已经存在于最后一个共同祖先中。与拟南芥NB-LRR补体的系统发育比较证实了更古老的CCRPW8型NB-LRR的高度保守性。在未感染和晚疫病侵染的番茄叶片中使用RenSeq可以避免对未表达的同源基因进行序列分析。RenSeq是分析植物抗病基因互补的一种很有前途的方法。本文提供的重新注释的番茄Nb-LRR互补序列、系统发育关系和染色体位置将为育种工作者和科学家鉴定新的抗病性状提供有用的工具。CDNARenSeq首次实现了针对这个非常低表达的基因家族的下一代测序方法，而不需要标准化。
The availability of draft crop plant genomes allows the prediction of the full complement of genes that encode NB-LRR resistance gene homologs, enabling a more targeted breeding for disease resistance. Recently, we developed the RenSeq method to reannotate the full NB-LRR gene complement in potato and to identify novel sequences that were not picked up by the automated gene prediction software. Here, we established RenSeq on the reference genome of tomato (Solanum lycopersicum) Heinz 1706, using 260 previously identified NB-LRR genes in an updated Solanaceae RenSeq bait library. Using 250-bp MiSeq reads after RenSeq on genomic DNA of Heinz 1706, we identified 105 novel NB-LRR sequences. Reannotation included the splitting of gene models, combination of partial genes to a longer sequence and closing of assembly gaps. Within the draft S. pimpinellifolium LA1589 genome, RenSeq enabled the annotation of 355 NB-LRR genes. The majority of these are however fragmented, with 5′- and 3′-end located on the edges of separate contigs. Phylogenetic analyses show a high conservation of all NB-LRR classes between Heinz 1706, LA1589 and the potato clone DM, suggesting that all sub-families were already present in the last common ancestor. A phylogenetic comparison to the Arabidopsis thaliana NB-LRR complement verifies the high conservation of the more ancient CCRPW8-type NB-LRRs. Use of RenSeq on cDNA from uninfected and late blight-infected tomato leaves allows the avoidance of sequence analysis of non-expressed paralogues. RenSeq is a promising method to facilitate analysis of plant resistance gene complements. The reannotated tomato NB-LRR complements, phylogenetic relationships and chromosomal locations provided in this paper will provide breeders and scientists with a useful tool to identify novel disease resistance traits. cDNA RenSeq enables for the first time next-gen sequencing approaches targeted to this very low-expressed gene family without the need for normalization.
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DOI：
10.1111/tpj.12307
发表时间：
2013-11
期刊：
The Plant journal : for cell and molecular biology
影响因子：
--
作者：
Jupe F;Witek K;Verweij W;Sliwka J;Pritchard L;Etherington GJ;Maclean D;Cock PJ;Leggett RM;Bryan GJ;Cardle L;Hein I;Jones JD
通讯作者：
Jones JD
影响因子：
5.3
作者：
OKAYAMA, H;BERG, P
通讯作者：
BERG, P
影响因子：
5.4
作者：
Zhang, Chunzhi;Liu, Lei;Li, Junming
通讯作者：
Li, Junming
影响因子：
5.4
作者：
Li, X;van Eck, HJ;Jacobsen, E
通讯作者：
Jacobsen, E
番茄基因组序列提供了对肉质果实进化的见解
影响因子：
64.8
作者：
Sato, Shusei;Tabata, Satoshi;Hirakawa, Hideki;Asamizu, Erika;Shirasawa, Kenta;Isobe, Sachiko;Kaneko, Takakazu;Nakamura, Yasukazu;Shibata, Daisuke;Aoki, Koh;Egholm, Michael;Knight, James;Bogden, Robert;Li, Changbao;Shuang, Yang;Xu, Xun;Pan, Shengkai;Cheng, Shifeng;Liu, Xin;Ren, Yuanyuan;Wang, Jun;Albiero, Alessandro;Dal Pero, Francesca;Todesco, Sara;Van Eck, Joyce;Buels, Robert M.;Bombarely, Aureliano;Gosselin, Joseph R.;Huang, Minyun;Leto, Jonathan A.;Menda, Naama;Strickler, Susan;Mao, Linyong;Gao, Shan;Tecle, Isaak Y.;York, Thomas;Zheng, Yi;Vrebalov, Julia T.;Lee, JeMin;Zhong, Silin;Mueller, Lukas A.;Stiekema, Willem J.;Ribeca, Paolo;Alioto, Tyler;Yang, Wencai;Huang, Sanwen;Du, Yongchen;Zhang, Zhonghua;Gao, Jianchang;Guo, Yanmei;Wang, Xiaoxuan;Li, Ying;He, Jun;Li, Chuanyou;Cheng, Zhukuan;Zuo, Jianru;Ren, Jianfeng;Zhao, Jiuhai;Yan, Liuhua;Jiang, Hongling;Wang, Bao;Li, Hongshuang;Li, Zhenjun;Fu, Fuyou;Chen, Bingtang;Han, Bin;Feng, Qi;Fan, Danlin;Wang, Ying;Ling, Hongqing;Xue, Yongbiao;Ware, Doreen;McCombie, W. Richard;Lippman, Zachary B.;Chia, Jer-Ming;Jiang, Ke;Pasternak, Shiran;Gelley, Laura;Kramer, Melissa;Anderson, Lorinda K.;Chang, Song-Bin;Royer, Suzanne M.;Shearer, Lindsay A.;Stack, Stephen M.;Rose, Jocelyn K. C.;Xu, Yimin;Eannetta, Nancy;Matas, Antonio J.;McQuinn, Ryan;Tanksley, Steven D.;Camara, Francisco;Guigo, Roderic;Rombauts, Stephane;Fawcett, Jeffrey;Van de Peer, Yves;Zamir, Dani;Liang, Chunbo;Spannagl, Manuel;Gundlach, Heidrun;Bruggmann, Remy;Mayer, Klaus;Jia, Zhiqi;Zhang, Junhong;Ye, Zhibiao;Bishop, Gerard J.;Butcher, Sarah;Lopez-Cobollo, Rosa;Buchan, Daniel;Filippis, Ioannis;Abbott, James;Dixit, Rekha;Singh, Manju;Singh, Archana;Pal, Jitendra Kumar;Pandit, Awadhesh;Singh, Pradeep Kumar;Mahato, Ajay Kumar;Dogra, Vivek;Gaikwad, Kishor;Sharma, Tilak Raj;Mohapatra, Trilochan;Singh, Nagendra Kumar;Causse, Mathilde;Rothan, Christophe;Schiex, Thomas;Noirot, Celine;Bellec, Arnaud;Klopp, Christophe;Delalande, Corinne;Berges, Helene;Mariette, Jerome;Frasse, Pierre;Vautrin, Sonia;Zouine, Mohamed;Latche, Alain;Rousseau, Christine;Regad, Farid;Pech, Jean-Claude;Philippot, Murielle;Bouzayen, Mondher;Pericard, Pierre;Osorio, Sonia;Fernandez del Carmen, Asuncion;Monforte, Antonio;Granell, Antonio;Fernandez-Munoz, Rafael;Conte, Mariana;Lichtenstein, Gabriel;Carrari, Fernando;De Bellis, Gianluca;Fuligni, Fabio;Peano, Clelia;Grandillo, Silvana;Termolino, Pasquale;Pietrella, Marco;Fantini, Elio;Falcone, Giulia;Fiore, Alessia;Giuliano, Giovanni;Lopez, Loredana;Facella, Paolo;Perrotta, Gaetano;Daddiego, Loretta;Bryan, Glenn;Orozco, Modesto;Pastor, Xavier;Torrents, David;van Schriek, Keygene N. V. Marco G. M.;Feron, Richard M. C.;van Oeveren, Jan;de Heer, Peter;daPonte, Lorena;Jacobs-Oomen, Saskia;Cariaso, Mike;Prins, Marcel;van Eijk, Michiel J. T.;Janssen, Antoine;van Haaren, Mark J. J.;Jo, Sung-Hwan;Kim, Jungeun;Kwon, Suk-Yoon;Kim, Sangmi;Koo, Dal-Hoe;Lee, Sanghyeob;Hur, Cheol-Goo;Clouser, Christopher;Rico, Alain;Hallab, Asis;Gebhardt, Christiane;Klee, Kathrin;Joecker, Anika;Warfsmann, Jens;Goebel, Ulrike;Kawamura, Shingo;Yano, Kentaro;Sherman, Jamie D.;Fukuoka, Hiroyuki;Negoro, Satomi;Bhutty, Sarita;Chowdhury, Parul;Chattopadhyay, Debasis;Datema, Erwin;Smit, Sandra;Schijlen, Eliog. W. M.;van de Belt, Jose;van Haarst, Jan C.;Peters, Sander A.;van Staveren, Marjo J.;Henkens, Marleen H. C.;Mooyman, Paul J. W.;Hesselink, Thamara;van Ham, Roeland C. H. J.;Jiang, Guoyong;Droege, Marcus;Choi, Doil;Kang, Byung-Cheol;Kim, Byung Dong;Park, Minkyu;Kim, Seungill;Yeom, Seon-In;Lee, Yong-Hwan;Choi, Yang-Do;Li, Guangcun;Gao, Jianwei;Liu, Yongsheng;Huang, Shengxiong;Fernandez-Pedrosa, Victoria;Collado, Carmen;Zuniga, Sheila;Wang, Guoping;Cade, Rebecca;Dietrich, Robert A.;Rogers, Jane;Knapp, Sandra;Fei, Zhangjun;White, Ruth A.;Thannhauser, Theodore W.;Giovannoni, James J.;Angel Botella, Miguel;Gilbert, Louise;Gonzalez, Ramon;Goicoechea, Jose Luis;Yu, Yeisoo;Kudrna, David;Collura, Kristi;Wissotski, Marina;Wing, Rod;Schoof, Heiko;Meyers, Blake C.;Gurazada, Aishwarya Bala;Green, Pamela J.;Mathur, Saloni;Vyas, Shailendra;Solanke, Amolkumar U.;Kumar, Rahul;Gupta, Vikrant;Sharma, Arun K.;Khurana, Paramjit;Khurana, Jitendra P.;Tyagi, Akhilesh K.;Dalmay, Tamas;Mohorianu, Irina;Walts, Brandon;Chamala, Srikar;Barbazuk, W. Brad;Li, Jingping;Guo, Hui;Lee, Tae-Ho;Wang, Yupeng;Zhang, Dong;Paterson, Andrew H.;Wang, Xiyin;Tang, Haibao;Barone, Amalia;Chiusano, Maria Luisa;Ercolano, Maria Raffaella;D'Agostino, Nunzio;Di Filippo, Miriam;Traini, Alessandra;Sanseverino, Walter;Frusciante, Luigi;Seymour, Graham B.;Elharam, Mounir;Fu, Ying;Hua, Axin;Kenton, Steven;Lewis, Jennifer;Lin, Shaoping;Najar, Fares;Lai, Hongshing;Qin, Baifang;Qu, Chunmei;Shi, Ruihua;White, Douglas;White, James;Xing, Yanbo;Yang, Keqin;Yi, Jing;Yao, Ziyun;Zhou, Liping;Roe, Bruce A.;Vezzi, Alessandro;D'Angelo, Michela;Zimbello, Rosanna;Schiavon, Riccardo;Caniato, Elisa;Rigobello, Chiara;Campagna, Davide;Vitulo, Nicola;Valle, Giorgio;Nelson, David R.;De Paoli, Emanuele;Szinay, Dora;de Jong, Hans H.;Bai, Yuling;Visser, Richard G. F.;Lankhorst, Rene M. Klein;Beasley, Helen;McLaren, Karen;Nicholson, Christine;Riddle, Claire;Gianese, Giulio
通讯作者：
Gianese, Giulio