Data_Sheet_2_Investigation Into Different Wood Formation Mechanisms Between Angiosperm and Gymnosperm Tree Species at the Transcriptional and Post-transcriptional Level.docx

Enormous distinctions of the stem structure and cell types between gymnosperms and angiosperms tree species are expected to cause quite different wood physical and mechanical attributes, however, the molecular mechanisms underlying the differing wood morphology are still unclear. In this study, we compared the transcriptomes obtained by RNA-Seq between Populus alba × P. glandulosa clone 84K, and Larix kaempferi (Lamb.) Carr trees. Available genome resource served as reference for P. alba × P. glandulosa and the Iso-Seq results of a three-tissues mixture (xylem, phloem, and leaf) were used as the reference for L. kaempferi to compare the xylem-specifically expressed genes and their alternative splicing model. Through screening, we obtained 13,907 xylem-specifically expressed genes (5,954 up-regulated, 7,953 down-regulated) in the xylem of P. alba × P. glandulosa, and 2,596 xylem-specifically expressed genes (1,648 up-regulated, 948 down-regulated) in the xylem of L. kaempferi. From the GO and KEGG analyses, some genes associated with two wood formation-related pathways, namely those for phenylpropanoid biosynthesis, and starch and sucrose metabolism, were successfully screened. Then the distributions and gene expression models between P. alba × P. glandulosa and L. kaempferi in those pathways were compared, which suggested differential wood formation processes between the angiosperm and gymnosperm trees. Furthermore, a Weight Gene Co-expression Network Analysis (WGCNA) for total xylem-specifically expressed genes in two species was conducted, from which wood formation-related modules were selected to build a co-expression network for the two tree species. The genes within this co-expression network showed different co-expression relationships between the angiosperm and gymnosperm woody species. Comparing the alternative splicing events for wood formation-related genes suggests a different post-transcriptional regulation process exists between the angiosperm and gymnosperm trees. Our research thus provides the foundation for the in-depth investigation of different wood formation mechanisms of angiosperm and gymnosperm species.

裸子植物（gymnosperms）与被子植物（angiosperms）乔木类群的茎部结构及细胞类型存在显著差异，这会导致二者木材的物理与力学属性存在较大差异，但目前二者木材形态差异背后的分子机制仍不明确。本研究以银白杨×腺毛杨（Populus alba × P. glandulosa）84K无性系以及日本落叶松（Larix kaempferi (Lamb.) Carr）为材料，对二者通过RNA测序（RNA-Seq）获得的转录组进行比较分析。银白杨×腺毛杨可利用已公开的基因组数据作为参考序列；日本落叶松则以其3种组织（木质部、韧皮部和叶片）混合样本的全长转录组测序（Iso-Seq）结果作为参考，以此比较二者的木质部特异性表达基因及其可变剪接模式。经筛选，我们在银白杨×腺毛杨木质部中获得13907个木质部特异性表达基因（其中5954个上调表达、7953个下调表达），在日本落叶松木质部中获得2596个木质部特异性表达基因（其中1648个上调表达、948个下调表达）。通过基因本体（Gene Ontology, GO）与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）富集分析，我们成功筛选到与两条木材形成相关通路相关的基因，分别为苯丙烷生物合成通路以及淀粉与蔗糖代谢通路。随后我们比较了银白杨×腺毛杨与日本落叶松在上述通路中的基因表达分布与表达模式，结果表明被子植物与裸子植物乔木的木材形成过程存在差异。此外，我们对两个物种的全部木质部特异性表达基因开展了加权基因共表达网络分析（Weight Gene Co-expression Network Analysis, WGCNA），并筛选出与木材形成相关的模块，以此构建两个乔木物种的共表达网络。该共表达网络中的基因在被子植物与裸子植物木本物种中呈现出不同的共表达关联模式。对木材形成相关基因的可变剪接事件进行比较后发现，被子植物与裸子植物乔木存在不同的转录后调控过程。因此，本研究为深入探究被子植物与裸子植物物种不同的木材形成机制奠定了基础。