全长转录组和基因表达分析揭示了罗汉松种子发育过程中表达的基因和分子元件。

A full-length transcriptome and gene expression analysis reveal genes and molecular elements expressed during seed development in Gnetum luofuense.

机构信息

Hunan Academy of Forestry, Changsha, Hunan, No.658 Shaoshan Road, Tianxin District, Changsha, 410004, China.

Hunan Cili Forest Ecosystem State Research Station, Cili, Changsha, 410004, Hunan, China.

出版信息

BMC Plant Biol. 2020 Nov 23;20(1):531. doi: 10.1186/s12870-020-02729-1.

DOI:10.1186/s12870-020-02729-1

PMID:33228526

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7685604/

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.

摘要

背景

买麻藤是一种具有重要经济价值的热带和亚热带裸子植物，具有多种食用、工业和药用用途。在买麻藤种子成熟过程中会积累大量碳水化合物、蛋白质和纤维。然而，与这一过程相关的分子机制尚不清楚。

结果

因此，我们使用 PacBio 测序reads 从未成熟和成熟的买麻藤种子中组装了全长转录组。我们总共鉴定了 5726 个新基因、9061 个可变剪接事件、3551 个 lncRNA、2160 个转录因子，并且发现 8512 个基因至少具有一个 poly(A) 位点。此外，Illumina 测序生成的六个转录组的基因表达比较表明，从未成熟阶段到成熟阶段有 14323 个基因差异表达，其中 7891 个基因上调，6432 个基因下调。MADS-box、Aux/IAA 和 bHLH 家族的 14 个差异表达转录因子的表达通过 qRT-PCR 得到验证，表明它们可能在买麻藤种子成熟过程中发挥重要作用。