Genome Annotation of a Model Diatom Phaeodactylum tricornutum Using an Integrated Proteogenomic Pipeline.
Genome Annotation of a Model Diatom Phaeodactylum tricornutum Using an Integrated Proteogenomic Pipeline.
复制标题
使用集成蛋白质组管道对模型硅藻三角褐指藻进行基因组注释。
DOI：
10.1016/j.molp.2018.08.005
复制
发表时间：
2018-10
期刊：
影响因子：
27.5
通讯作者：
Ge Feng
中科院分区：
文献类型：
--
作者：
Yang Mingkun;Lin Xiaohuang;Liu Xin;Zhang Jia;Ge Feng
硅藻是一类具有重要生态意义的真核浮游植物，对海洋初级生产力和全球碳循环有重要贡献。三角褐指藻是研究硅藻生物学的常用模式生物。虽然它的基因组已经在2008年测序，但高质量的基因组注释仍然无法为这种硅藻提供。在这里，我们报告了一个完整的蛋白质组流水线的开发及其应用，以改进基于质谱仪(MS)的蛋白质组学数据对三角星菌基因组的注释。我们的蛋白质组分析明确地识别了大约8300个基因，揭示了606个新的蛋白质，506个修订的基因，94个剪接变异体，58个单一氨基酸变异体，以及对三角弯角侧耳的翻译后修饰的整体看法。我们通过实验证实了一个新事件的子集，并获得了三角原甲藻中200多个微肽的MS证据。这些发现拓展了三角藻的基因组图谱，为硅藻生物学的研究提供了丰富的资源。我们在本研究中开发的蛋白质组流水线适用于任何已测序的真核生物，因此对真核生物蛋白质基因组分析的工具集做出了重大贡献。流水线及其源代码可在https://sourceforge.net/projects/gapeproteogenomic.免费获得
Diatoms comprise a diverse and ecologically important group of eukaryotic phytoplankton that significantly contributes to marine primary production and global carbon cycling.Phaeodactylum tricornutumis commonly used as a model organism for studying diatom biology. Although its genome was sequenced in 2008, a high-quality genome annotation is still not available for this diatom. Here we report the development of an integrated proteogenomic pipeline and its application for improved annotation ofP.tricornutumgenome using mass spectrometry (MS)-based proteomics data. Our proteogenomic analysis unambiguously identified approximately 8300 genes and revealed 606 novel proteins, 506 revised genes, 94 splice variants, 58 single amino acid variants, and a holistic view of post-translational modifications inP.tricornutum. We experimentally confirmed a subset of novel events and obtained MS evidence for more than 200 micropeptides inP.tricornutum. These findings expand the genomic landscape ofP.tricornutumand provide a rich resource for the study of diatom biology. The proteogenomic pipeline we developed in this study is applicable to any sequenced eukaryote and thus represents a significant contribution to the toolset for eukaryotic proteogenomic analysis. The pipeline and its source code are freely available at https://sourceforge.net/projects/gapeproteogenomic.
登录
查看更多内容
影响因子：
64.8
作者：
Kim, Min-Sik;Pinto, Sneha M.;Getnet, Derese;Nirujogi, Raja Sekhar;Manda, Srikanth S.;Chaerkady, Raghothama;Madugundu, Anil K.;Kelkar, Dhanashree S.;Isserlin, Ruth;Jain, Shobhit;Thomas, Joji K.;Muthusamy, Babylakshmi;Leal-Rojas, Pamela;Kumar, Praveen;Sahasrabuddhe, Nandini A.;Balakrishnan, Lavanya;Advani, Jayshree;George, Bijesh;Renuse, Santosh;Selvan, Lakshmi Dhevi N.;Patil, Arun H.;Nanjappa, Vishalakshi;Radhakrishnan, Aneesha;Prasad, Samarjeet;Subbannayya, Tejaswini;Raju, Rajesh;Kumar, Manish;Sreenivasamurthy, Sreelakshmi K.;Marimuthu, Arivusudar;Sathe, Gajanan J.;Chavan, Sandip;Datta, Keshava K.;Subbannayya, Yashwanth;Sahu, Apeksha;Yelamanchi, Soujanya D.;Jayaram, Savita;Rajagopalan, Pavithra;Sharma, Jyoti;Murthy, Krishna R.;Syed, Nazia;Goel, Renu;Khan, Aafaque A.;Ahmad, Sartaj;Dey, Gourav;Mudgal, Keshav;Chatterjee, Aditi;Huang, Tai-Chung;Zhong, Jun;Wu, Xinyan;Shaw, Patrick G.;Freed, Donald;Zahari, Muhammad S.;Mukherjee, Kanchan K.;Shankar, Subramanian;Mahadevan, Anita;Lam, Henry;Mitchell, Christopher J.;Shankar, Susarla Krishna;Satishchandra, Parthasarathy;Schroeder, John T.;Sirdeshmukh, Ravi;Maitra, Anirban;Leach, Steven D.;Drake, Charles G.;Halushka, Marc K.;Prasad, T. S. Keshava;Hruban, Ralph H.;Kerr, Candace L.;Bader, Gary D.;Iacobuzio-Donahue, Christine A.;Gowda, Harsha;Pandey, Akhilesh
通讯作者：
Pandey, Akhilesh
影响因子：
12.3
作者：
Maheswari U;Jabbari K;Petit JL;Porcel BM;Allen AE;Cadoret JP;De Martino A;Heijde M;Kaas R;La Roche J;Lopez PJ;Martin-Jézéquel V;Meichenin A;Mock T;Schnitzler Parker M;Vardi A;Armbrust EV;Weissenbach J;Katinka M;Bowler C
通讯作者：
Bowler C
影响因子：
14.8
作者：
Saghatelian A;Couso JP
通讯作者：
Couso JP
影响因子：
16.6
作者：
Wright JC;Mudge J;Weisser H;Barzine MP;Gonzalez JM;Brazma A;Choudhary JS;Harrow J
通讯作者：
Harrow J
影响因子：
14.9
作者：
Olexiouk V;Van Criekinge W;Menschaert G
通讯作者：
Menschaert G