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He Li, Cheng-Jiang Ruan, Li Wang, Jian Ding and Xing-Jun Tian

, transcriptome datasets have become valuable resources for SSR discovery, more and more RNA-Seq SSRs are developed to investigate the genetic relationships among species and subspecies, as well as the genetic structure of populations ( Liu et al., 2015 ; Zhang

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Xiaoxu Yang, Chang Liu, Zhishan Yan, Youjun Fan, Guojun Feng and Dajun Liu

operates under long days ( Doust et al., 2017 ). RNA-seq technology facilitates the discernment of novel perspectives in transcriptome sequence analysis by providing comprehensive coverage of transcripts. In addition, RNA-seq could be used as an alternative

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Zehuang Zhang, Qihua Lin and Qiuzhen Zhong

phenomenon was not clear. In recent years, transcriptome sequencing technology using RNA-seq, which is based on next-generation sequencing, has been widely used in a range of research fields and can provide a quick and convenient method to establish the basic

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Huihui Liu, Ke Cao, Gengrui Zhu, Weichao Fang, Changwen Chen, Xinwei Wang and Lirong Wang

transient transformation of tobacco ( Nicotiana benthamiana ) and peach ( Zhou et al., 2015 ). Recently, Cao et al. (2018) identified 66 genes were significantly correlated with anthocyanin contents through RNA-sequencing (RNA-seq), 22 of which previously

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Heidi Hargarten, Sumyya Waliullah, Lee Kalcsits and Loren A. Honaas

untargeted (e.g., RNA-Seq) techniques is accurate previous knowledge of gene sequences. As more genomes become available for important crop species, recently so for rosaceous specialty crops such as Malus ( Daccord et al., 2017 ; Velasco et al., 2010

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Yu Bai, Ying Zhou, Xiaoqing Tang, Yu Wang, Fangquan Wang and Jie Yang

., 2012 )]. RNA-seq is an important tool for obtaining transcripts from certain plant tissues under specific physiological conditions or at specific developmental stages ( Strickler et al., 2012 ; Wang et al., 2009 ). Illumina (San Diego, CA) sequencing

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Takanori Takeuchi, Miwako Cecile Matsushita, Soichiro Nishiyama, Hisayo Yamane, Kiyoshi Banno and Ryutaro Tao

out. A transcriptome analysis using the new apple reference genome may enable more accurate mapping, ultimately resulting in a more precise identification of DEGs and gene ontology (GO) analysis. However, RNA-seq studies focused on apple dormancy have

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Xue Li, Chen Zang, Hang Ge, Jing Zhang, Donald Grierson, Xue-ren Yin and Kun-song Chen

) and using an RNA-seq database, some new coding genes for these enzymes were isolated, their expression studied, and transient overexpression analysis was performed on N. tabacum to verify the role of Ej4CL1 in lignin biosynthesis. Materials and

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Kaori Ando and Rebecca Grumet

Fruit development proceeds from cell division to expansion, maturation, and ripening. Expansion is critical for size, yield, and quality; however, this period of development has received little attention. We used 454-pyrosequencing to develop a cucumber (Cucumis sativus) fruit transcriptome, identify highly expressed transcripts, and characterize key functions during exponential fruit growth. The resulting 187,406 expressed sequence tags (ESTs) were assembled into 13,878 contigs. Quantitative real-time polymerase chain reaction (qRT-PCR) verification of differentially expressed genes from fruit of different ages, and high correlation in transcript frequency between replicates, indicated that number of reads/contig reflects transcript abundance. Putative homologs were identified in Arabidopsis thaliana for 89% of the contigs represented by at least 10 ESTs; another 4% had homologs in other species. The remainder had homologs only in cucurbit species. The most highly expressed contigs were strongly enriched for growth (aquaporins, vacuolar ATPase, phloem proteins, tubulins, actins, cell wall-associated, and hormone-related), lipid, latex, and defense-related homologs. These results provide a resource for gene expression analysis in cucumber, profile gene expression in rapidly growing fruit, and shed insight into an important, but poorly characterized, developmental stage influencing fruit yield and quality.

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Paul A. Wiersma, Deniz Erogul and Shawkat Ali

each comparison scored as either “same,” with all bands or genotypes identical between the two cultivars or “diff,” with at least one different band or genotype. Single nucleotide polymorphism analysis. RNA-Seq libraries were prepared from young leaf