采用转录组测序技术对茅苍术〔Atractylodes lancea （Thunb.） DC.〕二倍体和同源四倍体叶片进行无参转录组测序，并在前期研究基础上筛选叶片中的高可信度差异表达unigenes。结果显示：共获得495 797个unigenes，GC含量为46.54%，平均长度为402.8 bp，N50和N90分别为413和225 bp。与GO、NR、String、SwissProt、KEGG和Pfam数据库的比对结果表明：共注释到259 841个unigenes，占unigenes总数的52.41%。NR数据库比对结果显示：茅苍术与同科植物Cynara cardunculus var. scolymus （Linn.） Fiori和向日葵（Helianthus annuus Linn.）的unigenes序列同源性明显高于其他种类。通过表达量比较，共筛选出923个差异表达unigenes。GO功能分类结果表明：这些差异表达unigenes的功能被分成3个大类61个小类。KEGG富集分析结果表明：这些差异表达unigenes被注释到5个大类中，其中，注释到代谢中的差异表达unigenes最多（75），且富集在次生代谢物生物合成、淀粉和蔗糖代谢及脂肪酸延伸等8条代谢通路中。茅苍术二倍体和同源四倍体叶片和全株的共有高可信度差异表达unigenes有298个，其中，热激蛋白基因（DnaK/Hsp70）、ACC氧化酶基因（ACO）、脂肪酸脱氢酶基因（FAD2）和长链-3-羟酰基-CoA脱水酶基因（PHS1/PAS2）的表达量在同源四倍体中上调，而乙烯受体基因（ETR/ERS）、丙二烯氧化物合酶基因（AOS）、脂氧合酶基因（LOX）和14-3-3结构域蛋白基因（YWHAE）的表达量在同源四倍体中下调。研究结果显示：茅苍术二倍体和同源四倍体叶片在细胞发育、代谢、能量转化、物质积累及信号转导上存在差异，筛选的差异表达unigenes可能参与茅苍术叶片发育调控，筛选的高可信度差异表达基因可作为茅苍术倍性育种的关键候选基因。

 De novo transcriptome sequencing and analysis were conducted for leaves of diploid and autotetraploid of Atractylodes lancea （Thunb.） DC. by using transcriptome sequencing technology， and high confidence differentially expressed unigenes in leaves were screened on the basis of preliminary research. The results show that 495 797 unigenes are obtained in total， the GC content is 46.54%， the average length is 402.8 bp， and the N50 and N90 are 413 and 225 bp， respectively. The comparison results with GO， NR， String， SwissProt， KEGG， and Pfam databases show that there are 259 841 unigenes annotated in total， accounting for 52.41% of total unigenes. The comparison result in NR database shows that the unigene sequence homology of A. lancea with the same family species Cynara cardunculus var. scolymus （Linn.） Fiori and Helianthus annuus Linn. are evidently higher than that with other species. 923 differentially expressed unigenes are obtained through expression level comparison. GO functional classification result shows that these differentially expressed unigenes are classified into 3 categories and 61 subcategories. KEGG enrichment analysis result shows that these differentially expressed unigenes are annotated to 5 categories， in which， the differentially expressed unigenes annotated to metabolism is the most （75） and enriched in 8 pathways， including biosynthesis of secondary metabolites， starch and sucrose metabolism， and fatty acid elongation， etc. There are 298 common high confidence differentially expressed genes in leaves and whole plants of diploid and autotetraploid of A. lancea， in which， the expression levels of heat shock protein gene （DnaK/Hsp70）， ACC oxidase gene （ACO）， fatty acid dehydrogenase gene （FAD2）， and long chain-3-hydroxyacyl-CoA dehydratase gene （PHS1/PAS2） are up-regulated in autotetraploid， while those of ethylene receptor gene （ETR/ERS）， allene oxide synthase gene （AOS）， lipoxygenase gene （LOX）， and 14-3-3 domain-containing protein gene （YWHAE） are downregulated in autotetraploid. It is suggested that there are differences in cellular development， metabolism， energy conversion， material accumulation， and signal transduction of diploid and autotetraploid leaves of A. lancea， the obtained differentially expressed unigenes may be involved in leaf development regulation of A. lancea， and the obtained high confidence differentially expressed genes can be served as key candidate genes for polyploid breeding of A. lancea.