Plant Growth Regul (2017) 83:141–156
Noncoding and coding transcriptome analysis reveals
the regulation roles of long noncoding RNAs in fruit development
of hot pepper (Capsicum annuum L.)
· Zhoubin Liu
· Zhuqing Zhang
· Ge Wei
· Yuping Zhang
· Linyu Kang
· Bozhi Yang
· Sha Yang
· Yuhua Liu
· Wenchao Chen
· Xiongze Dai
· Xuefeng Li
· Shudong Zhou
· Yanqing Ma
Received: 28 October 2016 / Accepted: 7 June 2017 / Published online: 7 July 2017
© Springer Science+Business Media B.V. 2017
Many potential protein-coding (PC) genes targeted by
lncRNAs with cis or trans-acting were also identiﬁed.
Six of them and their target genes were further validated
by quantitative RT-PCR. Some of these target genes were
involved in plant hormone signal transduction, cell wall
formation and carotenoid biosynthesis, indicating the roles
of lncRNAs in the regulation of fruit development and
quality. This study identiﬁed a large number of lncRNAs
in hot pepper, thereby providing some insights into the fruit
development of hot pepper.
Keywords Long non-coding RNAs (lncRNAs) · Fruit
development · Fruit quality · RNA-seq · Capsicum annuum
Abstract Long non-coding RNAs (lncRNAs) have been
shown to play critical regulatory roles in diverse biological
processes in plants. However, the presence of lncRNAs and
their potential functions in hot pepper are still unknown.
Using strand-speciﬁc RNA-sequencing, a total of 2505
putative lncRNAs were identiﬁed in the fruits of hot pep-
per. The lncRNAs were transcribed from all pepper chro-
mosomes and 95.37% of them originated from intergenic
regions. And 1066 lncRNAs were diﬀerentially expressed
among the four samples during pepper fruit development.
Lijun Ou, Zhoubin Liu, Zhuqing Zhang, Ge Wei, Yuping Zhang
have contributed equally.
Electronic supplementary material The online version of this
article (doi:10.1007/s10725-017-0290-3) contains supplementary
material, which is available to authorized users.
* Yanqing Ma
* Xuexiao Zou
Hunan Vegetable Research Institute, Changsha 410125,