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.

沉香木（Dalbergia odorifera）是一种罕见且珍贵的花梨木种，其木质是制作高档家具和雕刻工艺的优质材料。然而，关于沉香木木质形成过程的资料极为有限。为了确定可能与木质部分化过程密切相关的基因，本研究通过对沉香木特定木质部组织的差异表达基因（DEGs）和微小RNA（miRNAs）进行RNA测序（RNA-seq）和微小RNA测序（small RNA-seq）分析。总计，我们从RNA-seq获得了1,342,219,555个清洁读段，从小RNA-seq中获得了90,940,761个清洁读段。通过比较过渡带（Dotz）和边材（Dosw）样本，共鉴定出395个DEGs。进一步分析显示，DEGs编码的蛋白质包括WRKY转录因子（八个基因）、木质素合成（PER47、COMT、CCR2）、细胞壁组成（UXS2）、赤霉素合成（KAO2、GA20OX1）、茉莉酸合成（OPR2、CYP74A）、黄酮类（PAL2）和萜类化合物（CYP71A1）的合成。随后，通过small RNA-seq的初步分析显示，14个miRNAs（如miR168a-5p、miR167f-5p、miR167h-5p、miR167e、miR390a、miR156g、novel_52和novel_9）在Dotz和Dosw之间的表达存在显著差异。进一步分析表明，这些差异表达miRNAs的目标基因在GO术语“氨基酸结合”、“纤维素酶活性”和“DNA β-葡萄糖苷转移酶活性”中富集。此外，KEGG通路注释显示在“脂肪酸延长”和“不饱和脂肪酸生物合成”中存在显著富集。这些过程可能参与了沉香木木质部的分化。进一步地，表达相关性分析显示，九个差异表达的miRNAs与21个目标基因显著负相关，这些基因编码的蛋白质包括pyrH、SPL6、SPL12、GCS1和ARF8。总体而言，这是首次关于miRNAs及其在沉香木木质部发育中潜在功能的研究，为深入探究沉香木miRNAs的功能提供了基础。