International Journal of Genomics Plant Comparative and Functional Genomics Guest Editors: Xiaohan Yang, Jim Leebens-Mack, Feng Chen, and Yanbin Yin Plant Comparative and Functional Genomics International Journal of Genomics Plant Comparative and Functional Genomics Guest Editors: Xiaohan Yang, Jim Leebens-Mack, Feng Chen, and Yanbin Yin Copyright © 2015 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in “International Journal of Genomics.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Editorial Board Jacques Camonis, France Sylvia Hagemann, Austria Elena Pasyukova, Russia Shen Liang Chen, Taiwan Henry Heng, USA Graziano Pesole, Italy Prabhakara V. Choudary, USA Eivind Hovig, Norway Giulia Piaggio, Italy Martine A. Collart, Switzerland Peter Little, Australia Mohamed Salem, USA Ian Dunham, United Kingdom Shalima Nair, Australia Brian Wigdahl, USA Soraya E. Gutierrez, Chile Giuliana Napolitano, Italy Jinfa Zhang, USA M. Hadzopoulou-Cladaras, Greece Ferenc Olasz, Hungary Contents Plant Comparative and Functional Genomics, Xiaohan Yang, Jim Leebens-Mack, Feng Chen, and Yanbin Yin Volume 2015, Article ID 924369, 2 pages Quantification and Gene Expression Analysis of Histone Deacetylases in Common Bean during Rust Fungal Inoculation, Kalpalatha Melmaiee, Venu (Kal) Kalavacharla, Adrianne Brown, Antonette Todd, Yaqoob Thurston, and Sathya Elavarthi Volume 2015, Article ID 153243, 10 pages Divergence of the bZIP Gene Family in Strawberry, Peach, and Apple Suggests Multiple Modes of Gene Evolution after Duplication, Xiao-Long Wang, Yan Zhong, Zong-Ming Cheng, and Jin-Song Xiong Volume 2015, Article ID 536943, 11 pages Expressed Sequence Tags Analysis and Design of Simple Sequence Repeats Markers from a Full-Length cDNA Library in Perilla frutescens (L.),EunSooSeong,JiHyeYoo,JaeHooChoi,ChangHeumKim, Mi Ran Jeon, Byeong Ju Kang, Jae Geun Lee, Seon Kang Choi, Bimal Kumar Ghimire, and Chang Yeon Yu Volume 2015, Article ID 679548, 7 pages De Novo Transcriptome Sequencing of the Orange-Fleshed Sweet Potato and Analysis of Differentially Expressed Genes Related to Carotenoid Biosynthesis,RuijieLi,HongZhai,ChenKang,DegaoLiu, Shaozhen He, and Qingchang Liu Volume2015,ArticleID843802,10pages Genome-Wide Identification of Genes Probably Relevant to the Uniqueness of Tea Plant (Camellia sinensis)andItsCultivars, Yan Wei, Wang Jing, Zhou Youxiang, Zhao Mingming, Gong Yan, Ding Hua, Peng Lijun, and Hu Dingjin Volume 2015, Article ID 527054, 7 pages Analysis of Polygala tenuifolia Transcriptome and Description of Secondary Metabolite Biosynthetic Pathways by Illumina Sequencing, Hongling Tian, Xiaoshuang Xu, Fusheng Zhang, Yaoqin Wang, Shuhong Guo, Xuemei Qin, and Guanhua Du Volume 2015, Article ID 782635, 11 pages PPCM: Combing Multiple Classifiers to Improve Protein-Protein Interaction Prediction, Jianzhuang Yao, Hong Guo, and Xiaohan Yang Volume 2015, Article ID 608042, 7 pages Significant Microsynteny with New Evolutionary Highlights Is Detected through Comparative Genomic Sequence Analysis of Maize CCCH IX Gene Subfamily, Wei-Jun Chen, Yang Zhao, Xiao-Jian Peng, Qing Dong, Jing Jin, Wei Zhou, Bei-Jiu Cheng, and Qing Ma Volume 2015, Article ID 824287, 12 pages Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis), Qian Ding, Jingjuan Li, Fengde Wang, Yihui Zhang, Huayin Li, Jiannong Zhang, and Jianwei Gao Volume 2015, Article ID 473028, 11 pages Hindawi Publishing Corporation International Journal of Genomics Volume 2015, Article ID 924369, 2 pages http://dx.doi.org/10.1155/2015/924369 Editorial Plant Comparative and Functional Genomics Xiaohan Yang,1 Jim Leebens-Mack,2 Feng Chen,3 and Yanbin Yin4 1 Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA 2Department of Plant Biology, University of Georgia, Athens, GA 30602, USA 3Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA 4Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA Correspondence should be addressed to Xiaohan Yang; [email protected] Received 23 November 2015; Accepted 23 November 2015 Copyright © 2015 Xiaohan Yang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Plants form the foundation for our global ecosystem and factors associated with plant tolerance to abiotic stress. are essential for environmental and human health. With an They performed evolutionary analysis of the bZIP family in increasing number of available plant genomes and tractable three rosaceous species in multiple aspects such as selection experimental systems, comparative and functional plant pressure on protein-coding sequences and genomic synteny. genomics research is greatly expanding our knowledge of the Another transcription factor gene family relevant to abiotic molecular basis of economically and nutritionally important stress, the CCCH zinc finger family, was studied by W.-J. traits in crop plants. Inferences drawn from comparative Chen et al. in “Significant Microsynteny with New Evolution- genomics are motivating experimental investigations of gene ary Highlights Is Detected through Comparative Genomic functionandgeneinteractions.Thisspecialissueaimsto Sequence Analysis of Maize CCCH IX Gene Subfamily.” They highlight recent advances made in comparative and func- performed comparative analysis of the CCCH IX subfamily tional genomics research in plants. Nine original research in three cereal grain species (i.e., Zea mays, Oryza sativa,and articles in this special issue cover five important topics: (1) Sorghum bicolor) and found that segmental duplication has transcription factor gene families relevant to abiotic stress tol- played an important role in the expansion of this gene family. erance; (2) plant secondary metabolism; (3) transcriptome- Their analysis also indicates that deletions, multiplications, based markers for quantitative trait locus; (4) epigenetic inversions, and purifying selection have contributed to the modifications in plant-microbe interactions; and (5) compu- evolution of the CCCH IX subfamily. tational prediction of protein-protein interactions. The plant species studied in these articles include model species as well Plant Secondary Metabolism.Plantsproduceawiderange as nonmodel plant species of economic importance (e.g., food of secondary metabolites that underpin functional diversity crops and medicinal plants). in plants. Gene expression profiling through transcriptome sequencing is a powerful approach for understanding the Evolution of Transcription Factor Gene Families Relevant to molecular basis of plant secondary metabolism. H. Tian Abiotic Stress Tolerance. The extant flowering plants have et al. in “Analysis of Polygala tenuifolia Transcriptome and experienced multiple rounds of genome duplication and gene Description of Secondary Metabolite Biosynthetic Pathways duplication is the primary source of gene family evolution. by Illumina Sequencing” analyzed expression of secondary X.-L. Wang et al. in “Divergence of the bZIP Gene Family metabolite biosynthetic genes in P. te nuifoli a , a well-known in Strawberry, Peach, and Apple Suggests Multiple Modes of medicinal plant, using RNA-seq approach. Their analysis Gene Evolution after Duplication” explored the evolutionary revealed candidate genes that are potentially involved in dynamics of the bZIP family, which contains transcription biosynthesis of several important secondary metabolites such 2 International Journal of Genomics as triterpene saponins and phenylpropanoid. Similarly, R. Li Rust Fungal Inoculation” revealed that epigenetic modifica- et al. in “De Novo Transcriptome Sequencing of the Orange- tion via histone deacetylases is involved in the response of Fleshed Sweet Potato and Analysis of Differentially Expressed common bean to rust fungal inoculation. The results from Genes Related to Carotenoid Biosynthesis” performed RNA- this paper provide new insight into the molecular mechanism seqanalysisofsecondarymetabolisminIpomoea batatas, underlying plant-microbe interactions. an important food crop. Through comparing the global gene expression profile in relation to the differences in the Computational Prediction of Protein-Protein Interactions. carotenoid content of two I. batatas cultivars, they identi- Protein-protein interaction (PPI) is an important molecular fied more than 50 genes potentially involved in carotenoid mechanism underlying various biological processes. Compu- biosynthesis. Also, Y. Wei et al. in “Genome-Wide Identi- tational prediction of protein-protein interactions based on fication of Genes Probably Relevant to the Uniqueness of protein sequences is a straightforward approach to the utiliza- Tea Plant (Camellia sinensis)andItsCultivars”performed tion of whole-genome gene annotation for the global view of comparative analysis of RNA-seq data in several species of protein-protein interaction network in an organism. Various the genus Camellia, an important source for tea production. algorithms have been developed for protein sequence-based They identified differentially expressed genes relevant tothe PPI prediction, though with limited success.