DataSheet2_Integrated mRNA and Small RNA Sequencing Reveals microRNAs Associated With Xylem Development in Dalbergia odorifera.pdf

Dalbergia odorifera is a rare and precious rosewood specie, whose wood is a very high-quality material for valuable furniture and carving crafts. However, limited information is available about the process of wood formation in D. odorifera. To determine genes that might be closely associated with the xylem differentiation process, we analyzed the differentially expressed genes (DEGs) and microRNAs (miRNAs) from specific xylem tissues of D. odorifera by RNA sequencing (RNA-seq) and small RNA sequencing (small RNA-seq). In total, we obtained 134,221,955 clean reads from RNA-seq and 90,940,761 clean reads from small RNA-seq. By comparing the transition zone (Dotz) and sapwood (Dosw) samples, a total of 395 DEGs were identified. Further analysis revealed that DEGs encoded for WRKY transcription factors (eight genes), lignin synthesis (PER47, COMT, CCR2), cell wall composition (UXS2), gibberellin synthesis (KAO2, GA20OX1), jasmonic acid synthesis (OPR2, CYP74A), and synthesis of flavonoids (PAL2) and terpenoids (CYP71A1). Subsequently, a preliminary analysis by small RNA-seq showed that the expressions of 14 miRNAs (such as miR168a-5p, miR167f-5p, miR167h-5p, miR167e, miR390a, miR156g, novel_52, and novel_9) were significantly different between Dotz and Dosw. Further analysis revealed that the target genes of these differentially expressed miRNAs were enriched in the GO terms “amino acid binding,” “cellulase activity,” and “DNA beta-glucosyltransferase activity”. Further, KEGG pathway annotation showed significant enrichment in “fatty acid elongation” and “biosynthesis of unsaturated fatty acids”. These processes might be participating in the xylem differentiation of D. odorifera. Next, expression correlation analysis showed that nine differentially expressed miRNAs were significantly negatively associated with 21 target genes, which encoded for proteins such as pyrH, SPL6, SPL12, GCS1, and ARF8. Overall, this is the first study on miRNAs and their potential functions in the xylem development of D. odorifera, which provides a stepping stone for a detailed functional investigation of D. odorifera miRNAs.

降香黄檀（Dalbergia odorifera）是一种珍稀名贵的红木树种，其木材是打造高档家具与雕刻工艺品的优质原料。目前关于降香黄檀木材形成过程的相关研究报道较为有限。为筛选与降香黄檀木质部分化过程密切相关的功能基因，本研究通过RNA测序（RNA-seq）与小RNA测序（small RNA-seq）技术，对降香黄檀特定木质部组织的差异表达基因（differentially expressed genes, DEGs）及微小RNA（microRNAs, miRNAs）进行了分析。本次测序共获得RNA-seq纯净读段（clean reads）134,221,955条、小RNA-seq纯净读段（clean reads）90,940,761条。通过对比过渡区（Dotz）与边材（Dosw）样本，共鉴定出395个DEGs。进一步分析显示，上述DEGs所编码的蛋白涵盖WRKY转录因子（共8个基因）、木质素合成相关酶（PER47、COMT、CCR2）、细胞壁组成相关蛋白（UXS2）、赤霉素合成相关酶（KAO2、GA20OX1）、茉莉酸合成相关酶（OPR2、CYP74A）、黄酮类化合物合成酶（PAL2）以及萜类化合物合成酶（CYP71A1）。随后通过小RNA-seq开展的初步分析显示，14个miRNAs（如miR168a-5p、miR167f-5p、miR167h-5p、miR167e、miR390a、miR156g、novel_52及novel_9）在过渡区与边材样本中的表达量存在显著差异。进一步分析发现，这些差异表达miRNAs的靶基因显著富集于基因本体论（GO）术语"amino acid binding"、"cellulase activity"以及"DNA beta-glucosyltransferase activity"。此外，京都基因与基因组百科全书（KEGG）通路注释结果显示，靶基因显著富集于"fatty acid elongation"与"biosynthesis of unsaturated fatty acids"通路。上述生物学过程可能参与降香黄檀的木质部分化过程。表达相关性分析结果显示，9个差异表达miRNAs与21个靶基因呈显著负相关关系，这些靶基因编码的蛋白包括pyrH、SPL6、SPL12、GCS1及ARF8等。综上，本研究是首个针对降香黄檀miRNAs及其在木质部发育中潜在功能的相关研究，为后续深入解析降香黄檀miRNAs的功能提供了重要基础。