Analysis of multi-organ full-length transcriptome and structural genes involved in flavonoid biosynthesis of Gymnosphaera podophylla Dalla Torre & Sarnth.
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摘要:
黑桫椤（Gymnosphaera podophylla Dalla Torre & Sarnth.）为著名的孑遗蕨类，具有很强的环境适应能力，然而其适应性机制尚不清楚。本研究采用PacBio和Illumina技术对黑桫椤的根、羽轴和羽片进行转录组测序，分别生成12 879、14 185和16 084个全长unigenes。基因表达分析结果表明，与黑桫椤抗干旱、缺水胁迫和生物胁迫相关的基因表达水平较高。根、羽轴和羽片特异性上调基因均显著富集到KEGG代谢通路中的“苯丙烷生物合成途径”，根和羽轴的器官特异性上调基因还显著富集到“类黄酮生物合成途径”。共有192个全长unigenes被注释为类黄酮生物合成途径所涉及的13个酶结构基因，其中包括112个差异表达基因（DEGs），表明黑桫椤类黄酮生物合成途径较为保守，且存在器官特异性差异表达基因。本文对黑桫椤多器官全长转录组和类黄酮生物合成途径结构基因进行了综合分析，为进一步研究其对环境的适应性提供了丰富的遗传资源。
Abstract:Gymnosphaera podophylla Dalla Torre & Sarnth. is a famous relict tree fern with strong environmental adaptability. However, the mechanisms underlying its adaptability remain unclear. In this study, the PacBio and Illumina platforms were used to sequence the root, rachis, and pinna transcriptomes of G. podophylla, resulting in the generation of 12 879, 14 185, and 16 084 full-length unigenes, respectively. Transcript quantification showed that these unigenes were related to drought resistance and biological stress and were highly expressed. KEGG enrichment analysis indicated that the up-regulated genes in the roots, rachis, and pinna were enriched in the "phenylpropane biosynthesis pathway", while the up-regulated genes in the roots and rachis were enriched in the "flavonoid biosynthetic pathway". A total of 192 full-length unigenes were annotated as structural genes involving 13 enzymes in the flavonoid biosynthesis pathway, including 112 differentially expressed genes (DEGs), suggesting that the flavonoid biosynthesis pathway was conserved in G. podophylla, with organ-specific DEGs. This research is the first to perform a comprehensive analysis of the full-length transcriptome across multiple organs in G. podophylla and to investigate the structural genes of the flavonoid biosynthetic pathway. This study provides an abundance of genetic resources for further examination of environmental adaptation in this species.
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图 1 黑桫椤3种器官的高表达和差异表达基因
A：各器官前10个高表达基因。柱状图底部的数字代表注释为同一蛋白的FL unigenes数目。柱状图上方的数字代表注释为同一蛋白的FL unigenes的总FPKM值；B：从左至右依次为根和羽轴、羽片和羽轴、羽片和根的成对比较的差异表达基因数量；C：从左至右依次是根、羽轴、羽片相对于其他两种器官上调的基因数量。
Figure 1. Highly expressed genes and DEGs in three organs of Gymnosphaera podophylla
A: The top ten highly expressed genes in three organs. Number of FL unigenes annotated as same protein is shown at the bottom of the bar. Sum of FPKM values of FL unigenes annotated for the same protein are above the bar; B: From left to right is the number of DEGs in roots versus rachis, pinna versus rachis, and pinna versus roots, respectively; C: From left to right, number of genes up-regulated in roots, rachis, and pinna relative to the other two organs, respectively.
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图 2 类黄酮生物合成通路
热图展示了3种器官中类黄酮生物合成途径的DEG表达情况。高亮表示该酶有多个FL unigenes（>10），标红字体表示未发现FNS和F3H的FL unigenes，虚线箭头表示由多个酶参与的多步反应。
Figure 2. Flavonoid biosynthesis pathway
Heatmap showing DEG expression profiles of flavonoid biosynthesis pathway in three organs. Highlighted gene contains multiple unigenes (>10) in G. podophylla. Red font indicates F3H and FNS genes were not found in transcriptome. Dotted arrows indicate multi-step reaction with multiple enzymes.
表 1 全长转录组和组装数据
Table 1 Full-length transcriptome and assembled data
器官
Organ基因类型
Unigenes type碱基量
Raw reads / Gb总数
Total numberGC含量
GC content / %N50 / bp 根 组装 8.20 35 921 50.00 1838 全长 16.26 12 879 48.00 1979 羽轴 组装 8.81 30 752 49.70 1938 全长 18.39 14 185 47.00 1898 羽片 组装 6.74 29 938 49.30 1804 全长 21.99 16 048 47.00 1875 
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