曲小健，男，中共党员，理学博士，副教授，研究生导师。555000Jc线路检测中心（山东省逆境植物重点实验室）。

  联系地址：山东省济南市长清区大学科技园大学路1号

  邮编：250358

  邮箱：quxiaojian@sdnu.edu.cn

个人简介

主要从事植物分类、系统发生基因组学、进化生物学研究，重点关注种子植物，同时基于生物信息学开发实用的组学分析工具和平台。针对种子植物，特别是蓼科、禾本科、寄生植物和裸子植物，开展系统发生基因组学以及进化生物学研究，在系统发生关系重建、基因组结构进化、物种多样化等方面做出系统性研究成果。聚焦生命科学大数据前沿，进行生命科学和计算机科学交叉学科研究，开发的叶绿体基因组注释工具PGA（Plastid Genome Annotator）被国内外同行广泛应用，对于促进质体系统发生基因组学研究发挥了重要作用。目前共发表论文40余篇，其中以第一或通讯作者在Nature Plants、Molecular Phylogenetics and Evolution、Journal of Systematics and Evolution、Plant Methods、Genome Biology and Evolution、Frontiers in Plant Science、BMC Genomics、Plant Disease等SCI一区和二区期刊发表论文20余篇，含ESI高被引论文2篇，其中1篇同时为热点论文（Web of Science），总被引用1000余次。

工作经历

2022.1-至今，555000Jc线路检测中心，副教授

2018.9-2021.12，555000Jc线路检测中心，讲师

2017.9-2018.8，中科院昆明植物研究所，助理研究员

教育经历

2014.9-2017.7，中国科学院昆明植物研究所，生物化学与分子生物学，博士

2011.9-2014.7，中国科学院昆明植物研究所，植物学，硕士

2007.09-2011.7，555000Jc线路检测中心，生物技术，学士

研究兴趣

1、整合分类学研究

  利用形态学、组学等多种来源的数据对植物类群进行整合分类学研究，重建分类困难类群的系统发生关系，确定相关类群的分类范畴。通过整合形态学数据探究表型层面的性状创新与分子层面的系统发生冲突之间的联系。

2、基因组进化与物种多样化研究

  基于构建的系统发生框架，探讨叶绿体基因组和核基因组的进化机制，揭示基因组结构、寄生现象等关键性状的起源和多样化模式。

3、组学数据分析工具和平台开发

  针对丰富的生物学大数据所带来的分析和挖掘瓶颈，开发组学数据分析工具和平台。

承担课程

本科生：植物学实验、园林植物学、野外实习

研究生：植物系统学、生物标本制作

主持科研项目情况

1、山东省自然科学基金，结合叶绿体基因组和微条形码研究裸子植物的系统发育关系，2021.1-2023.12，在研，主持。

2、中国博士后科学基金，基于组学数据的裸子植物系统发育和进化研究，2019.7-2021.7，结题，主持。

3、中国科学院“西部青年学者”项目，裸子植物叶绿体基因组系统发育和结构演化研究，2018.1-2020.12，结题，主持。

代表性论文

2023年

Xiao-Jian Qu*, Dan Zou, Rui-Yu Zhang, Gregory W. Stull, Ting-Shuang Yi*. Progress, challenge and prospect of plant plastome annotation. Frontiers in Plant Science, 2023, 14:1166140.

Dong-Ling Cao, Xue-Jie Zhang, Xiao-Jian Qu*, Shou-Jin Fan*. Phylogenomics, divergence time estimation, and adaptive evolution in the Pologonoideae (Polygonaceae). Journal of Systematics and Evolution, 2023, https://doi.org/10.1111/jse.12946.

Lei Zhao, Ying-Ying Yang, Xiao-Jian Qu, Hong Ma, Yi Hu, Hong-Tao Li, Ting-Shuang Yi*, and De-Zhu Li*. Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae. Annals of Botany, 2023, 131:199-213.

Ying-Ying Yang#, Gregory W. Stull#, Xiao-Jian Qu, Lei Zhao, Yi Hu, Zhi-Heng Wang, Hong Ma, De-Zhu Li, Stephen A. Smith, Ting-Shuang Yi*. Genome duplications, genomic conflict, and rapid phenotypic evolution characterize the Cretaceous radiation of Fagales. bioRxiv, 2023, https://doi.org/10.1101/2023.06.11.544004.

2022年

Xiao-Jian Qu#, Xue-Jie Zhang#, Dong-Ling Cao, Xiu-Xiu Guo, Jeffrey P. Mower*, Shou-Jin Fan*. Plastid and mitochondrial phylogenomics reveal correlated substitution rate variation in Koenigia (Polygonoideae, Polygonaceae) and a reduced plastome for Koenigia delicatula including loss of all ndh genes. Molecular Phylogenetics and Evolution, 2022, https://doi.org/10.1016/j.ympev.2022.107544.

Dong-Ling Cao#, Xue-Jie Zhang#, Shao-Qiu Xie, Shou-Jin Fan*, Xiao-Jian Qu*. Application of chloroplast genome in the identification of Triditional Chinese Medicine Viola philippica. BMC Genomics, 2022, 23:540.

Dong-Ling Cao, Xue-Jie Zhang, Xiao-Jian Qu*, Shou-Jin Fan*. Plastid phylogenomics sheds light on divergence time and ecological adaptations of the tribe Persicarieae (Pologonaceae). Frontiers in Plant Science, 2022, 13:1046253.

Xiu-Xiu Guo#, Xiao-Jian Qu#, Xue-Jie Zhang*, Shou-Jin Fan*. Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae). Biology, 2022, 11, 63.

Rong Wang, Xue-Jie Zhang, Xiu-Xiu Guo, Yan Xing, Xiao-Jian Qu*, Shou-Jin Fan*. Plastid phylogenomics and morphological character evolution of Chloridoideae (Poaceae). Frontiers in Plant Science, 2022, 13:1002724.

2021年

Gregory W. Stull#, Xiao-Jian Qu#, Caroline Parins-Fukuchi, Ying-Ying Yang, Jun-Bo Yang, Zhi-Yun Yang, Yi Hu, Hong Ma, Pamela S. Soltis, Douglas E. Soltis, De-Zhu Li*, Stephen A. Smith*, Ting-Shuang Yi*. Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms. Nature Plants, 2021, 7, 1015–1025.

Rong Wang, Kuan Liu, Xue-Jie Zhang, Wen-Li Chen, Xiao-Jian Qu*, Shou-Jin Fan*. Comparative plastomes and phylogenetic analysis of Cleistogenes and closely related genera (Poaceae). Frontiers in Plant Science, 2021, 12:638597.

Ying-Ying Yang, Xiao-Jian Qu, Rong Zhang, Gregory W. Stull*, Ting-Shuang Yi*. Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture. Molecular Phylogenetics and Evolution, 2021, 163, 107232.

Xiao-Jian Qu*, Shou-Jin Fan*. First report of the parasitic invasive weed field dodder (Cuscuta campestris) parasitizing the confamilial invasive weed common morning-glory (Ipomoea purpurea) in Shandong, China. Plant Disease, 2021, 105:1230.

Kuan Liu, Rong Wang, Xiu-Xiu Guo, Xue-Jie Zhang, Xiao-Jian Qu*, Shou-Jin Fan*. Comparative and phylogenetic analysis of complete chloroplast genomes in Eragrostideae (Chloridoideae, Poaceae). Plants, 2021, 10(1):109.

Zhi-Fang Liu, Hui Ma, Xiu-Qin Ci, Lang Li, Yu Song, Bing Liu, His-Wen Li, Shu-Li Wang, Xiao-Jian Qu, Jian-Lin Hu, Xiao-Yan Zhang, John G. Conran, Alex D. Twyford*, Jun-Bo Yang*, Peter M. Hollingsworth*, Jie Li*. Can plastid genome sequencing be used for species identification in Lauraceae? Botanical Journal of the Linnean Society, 2021, 197, 1:1-14.

2020年

Xiao-Jian Qu*, Shou-Jin Fan*. First report of leaf wilt caused by Cuscuta japonica on generally insusceptible host plant Rhus typhina in China. Plant Disease, 2020, 104:11.

Xiao-Jian Qu, Li-Kang Liu, Luo-Yan Zhang, Xue-Jie Zhang, Shou-Jin Fan*. First report of dodder (Cuscuta japonica) parasitizing Japanese red pine (Pinus densiflora) in China. Plant Disease, 2020, 104:6.

2019年

Xiao-Jian Qu, Michael J. Moore, De-Zhu Li*, Ting-Shuang Yi*. PGA: a software package for rapid, accurate, and fexible batch annotation of plastomes. Plant Methods, 2019, 15:1.

Xiao-Jian Qu, Shou-Jin Fan, Susann Wicke*, Ting-Shuang Yi*. Plastome reduction in the only parasitic gymnosperm Parasitaxus is due to losses of photosynthesis but not housekeeping genes and apparently involves the secondary gain of a large inverted repeat. Genome Biology and Evolution, 2019, 11(10):2789-2796.

Luoyan Zhang, Xuejie Zhang, Mengfei Li, Ning Wang, Xiaojian Qu, Shoujin Fan*. Transcriptome analysis of elm (Ulmus pumila) fruit to identify phytonutrients associated genes and pathways. Forests, 2019, 10, 738.

2017年

Xiao-Jian Qu, Chung-Shien Wu, Shu-Miaw Chaw*, Ting-Shuang Yi*. Insights into the existence of isomeric plastomes in Cupressoideae (Cupressaceae). Genome Biology and Evolution, 2017, 9(4): 1110-1119.

Yin-Huan Wang, Xiao-Jian Qu, Si-Yun Chen, De-Zhu Li, Ting-Shuang Yi. Plastomes of Mimosoideae: structural and size variation, sequence divergence, and phylogenetic implication. Tree Genetics & Genomes, 2017, 13:41.

Xiao-Jian Qu, Jian-Jun Jin, Shu-Miaw Chaw, De-Zhu Li*, Ting-Shuang Yi*. Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae). Scientific Reports, 2017, 7: 41005.

代表性著作

 《555000Jc线路检测中心珍藏植物科学绘图》，副主编

 《555000Jc线路检测中心校园植物图志》，编委

获奖情况

     2022年，CULSC全国大学生生命科学竞赛（科学探究类）三等奖指导教师，全国大学生生命科学竞赛委员会

     2020年，555000Jc线路检测中心本科优秀毕业论文指导教师，555000Jc线路检测中心