Improving the genome and proteome annotations of the marine model diatom Thalassiosira pseudonana using a proteogenomics strategy  

作　　者：Xiao-Huang Chen Ming-Kun Yang Yuan-Yuan Li Zhang-Xian Xie Shu-Feng Zhang Mats Töpel Shady A.Amin Lin Lin Feng Ge Da-Zhi Wang 

机构地区：[1]State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology,Xiamen University,Xiamen,361005,China [2]Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai),Sun Yat-Sen University,Zhuhai,519082,China [3]Key Laboratory of Algal Biology,Institute of Hydrobiology,Chinese Academy of Sciences,Wuhan,430072,China [4]College of Chemistry,Chemical Engineering and Environment,Minnan Normal University,Zhangzhou,363000,China [5]Department of Marine Sciences,University of Gothenburg,Box 461,40530,Gothenburg,Sweden [6]IVL-Swedish Environmental Research Institute,Box 53021,40014,Gothenburg,Sweden [7]New York University Abu Dhabi,Saadiyat Island,129188,Abu Dhabi,United Arab Emirates

出　　处：《Marine Life Science & Technology》2023年第1期102-115,共14页海洋生命科学与技术（英文）

基　　金：This work was partially supported by research grants from the National Natural Science Foundation of China(Project No.42030404 and 41425021);the Ministry of Science and Technology of the People's Republic of China(Project No.2015CB954003);D-ZW was also supported by the Ten Thousand Talents Program for leading talents in science and technological innovation.

摘　　要：Diatoms are unicellular eukaryotic phytoplankton that account for approximately 20%of global carbon fixation and 40%of marine primary productivity;thus,they are essential for global carbon biogeochemical cycling and climate.The availability of ten diatom genome sequences has facilitated evolutionary,biological and ecological research over the past decade;however,a complimentary map of the diatom proteome with direct measurements of proteins and peptides is still lacking.Here,we present a proteome map of the model marine diatom Thalassiosira pseudonana using high-resolution mass spectrometry combined with a proteogenomic strategy.In-depth proteomic profiling of three different growth phases and three nutrient-deficient samples identified 9526 proteins,accounting for~81%of the predicted protein-coding genes.Proteogenomic analysis identified 1235 novel genes,975 revised genes,104 splice variants and 234 single amino acid variants.Furthermore,our quantitative proteomic analysis experimentally demonstrated that a considerable number of novel genes were differentially translated under different nutrient conditions.These findings substantially improve the genome annotation of T.pseudonana and provide insights into new biological functions of diatoms.This relatively comprehensive diatom proteome catalog will complement available diatom genome and transcriptome data to advance biological and ecological research of marine diatoms.

关 键 词：Marine diatoms Thalassiosira pseudonana PROTEOME PROTEOGENOMICS 

分 类 号：Q94[生物学—植物学]