A full-length transcriptome and gene expression analysis reveal genes and molecular elements expressed during seed devel
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RESEARCH ARTICLE
Open Access
A full-length transcriptome and gene expression analysis reveal genes and molecular elements expressed during seed development in Gnetum luofuense Nan Deng1,2†, Chen Hou3,4†, Boxiang He3,4, Fengfeng Ma1,2, Qingan Song1,2, Shengqing Shi5, Caixia Liu1* and Yuxin Tian1,2*
Abstract Background: Gnetum is an economically important tropical and subtropical gymnosperm genus with various dietary, industrial and medicinal uses. Many carbohydrates, proteins and fibers accumulate during the ripening of Gnetum seeds. However, the molecular mechanisms related to this process remain unknown. Results: We therefore assembled a full-length transcriptome from immature and mature G. luofuense seeds using PacBio sequencing reads. We identified a total of 5726 novel genes, 9061 alternative splicing events, 3551 lncRNAs, 2160 transcription factors, and we found that 8512 genes possessed at least one poly(A) site. In addition, gene expression comparisons of six transcriptomes generated by Illumina sequencing showed that 14,323 genes were differentially expressed from an immature stage to a mature stage with 7891 genes upregulated and 6432 genes downregulated. The expression of 14 differentially expressed transcription factors from the MADS-box, Aux/IAA and bHLH families was validated by qRT-PCR, suggesting that they may have important roles in seed ripening of G. luofuense. Conclusions: These findings provide a valuable molecular resource for understanding seed development of gymnosperms. Keywords: Gnetales, Full-length transcriptome, Functional genes, Seed, lncRNA
Background Gnetum is a genus of tropical and subtropical gymnosperm trees and shrubs distributed in South America, eastern Africa, and Asia [1]. Gnetum possesses remarkable economic potential for dietary and industrial use: its leaves are used as a vegetable, its stems and bark are made into string, nets and paper, and its seeds are used in oil and drinks. A Gnetum seed originates from a * Correspondence: [email protected]; [email protected] † Nan Deng and Chen Hou contributed equally to this work. 1 Hunan Academy of Forestry, Changsha, Hunan, No.658 Shaoshan Road, Tianxin District, Changsha 410004, China Full list of author information is available at the end of the article
female reproductive unit that is produced on the collar involucre of a female strobilus [1, 2]. A Gnetum seed is composed of three layers of envelopes, the outermost of which gives rise to a seed coat—aril [3, 4]. Gnetum seeds are rich in a variety of chemicals, such as carbohydrates, proteins and fibers [5, 6]. The primary metabolism (e.g. carbohydrate metabolism) is probably associated with seed ripening process (during which the aril color changes from green to red, Fig. 1) in Gnetum, but the molecular mechanisms that underlie the process have not been carefully investigated.
© The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction
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