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Article(id=1210518242007838782, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1210518228766421884, articleNumber=null, orderNo=null, doi=10.16438/j.0513-4870.2022-0648, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1653494400000, receivedDateStr=2022-05-26, revisedDate=1655222400000, revisedDateStr=2022-06-15, acceptedDate=null, acceptedDateStr=null, onlineDate=1766539639236, onlineDateStr=2025-12-24, pubDate=1670774400000, pubDateStr=2022-12-12, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1766539639236, onlineIssueDateStr=2025-12-24, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1766539639236, creator=13701087609, updateTime=1766539639236, updator=13701087609, issue=Issue{id=1210518228766421884, tenantId=1146029695717560320, journalId=1189982191388893191, year='2022', volume='57', issue='12', pageStart='0', pageEnd='3698', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1766539636078, creator=13701087609, updateTime=1766539730802, updator=13701087609, preIssue=null, nextIssue=null, ext={EN=IssueExt(id=1210518626109624560, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1210518228766421884, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1210518626109624561, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1210518228766421884, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null}, startPage=3675, endPage=3685, ext={EN=ArticleExt(id=1210518243324850259, articleId=1210518242007838782, tenantId=1146029695717560320, journalId=1189982191388893191, language=EN, title=Transcriptome-wide identification and expression analysis of 2-ODD gene family in Salvia apiana Jepson, columnId=1190335348761793317, journalTitle=Acta Pharmaceutica Sinica, columnName=Original Articles, runingTitle=null, highlight=null, articleAbstract=

2-Oxoglutarate/Fe(II)-dependent dioxygenases (2-ODD) play an important role in plant primary and secondary metabolism. Based on the high-throughput sequencing platform Illumina NovaSeq 6000, the transcriptome of Salvia apiana Jepson was sequenced, and the obtained reads were de novo assembled. A total of 38 534 unigenes were obtained from the transcriptome. The assembled unigenes were annotated and 29 982 unigenes were given functional annotations. The 2-ODD genes were identified from the assembled S. apiana transcriptome database by bioinformatics methods, and the genes were analyzed, including the homology of the sequences, physicochemical characteristics, signal peptides, transmembrane domains, subcellular localization, secondary structure and tertiary structure, etc. The evolutionary relationships and the expression patterns of the identified 2-ODD genes were also analyzed. 39 full-length 2-ODD genes were identified from the transcriptome of S. apiana. The average length of these 2-ODD encoding proteins was 320 amino acids, the molecular weight was about 36.00 kDa, and most of them were hydrophilic proteins. Phylogenetic analysis divided these 2-ODD genes into several subfamilies. Gene expression analysis indicated that the 2-ODD genes were expressed in different parts of S. apiana, and the expression level of most genes was much higher in roots than that in leaves. This study can lay a foundation for further study of 2-ODD genes in S. apiana.

, correspAuthors=Qing LI, authorNote=null, correspAuthorsNote=null, copyrightStatement=Copyright ©2022 Acta Pharmaceutica Sinica. All rights reserved., copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, authorCompany=null, fund=null, authors=null, authorsList=Xiao-jing QIN, Jia-dong HU, Zhen-xi FANG, Wan-sheng CHEN, Qing LI), CN=ArticleExt(id=1210518248563536119, articleId=1210518242007838782, tenantId=1146029695717560320, journalId=1189982191388893191, language=CN, title=基于转录组测序的白鼠尾草2-ODD基因家族鉴定与表达分析, columnId=1190335348896011050, journalTitle=药学学报, columnName=研究论文, runingTitle=null, highlight=null, articleAbstract=

α-酮戊二酸(2OG)/Fe(II) 依赖双加氧酶(2-ODD) 在植物初生和次生代谢过程中发挥着重要作用。本研究基于高通量测序技术平台Illumina NovaSeq 6000进行了白鼠尾草(Salvia apiana Jepson) 转录组测序, 对测序结果进行de novo拼接后, 共获得38 534个独立基因(unigenes)。将获得的独立基因进行基因功能注释, 有29 982个独立基因获得功能注释。通过生物信息学方法在白鼠尾草转录组数据中进行2-ODD基因家族鉴定, 并对鉴定得到的基因序列进行序列特征分析, 包括序列的同源性、理化特征、信号肽、跨膜结构域、亚细胞定位、二级结构和三级结构预测等, 另对它们的进化关系及表达模式进行分析。结果显示, 从白鼠尾草转录组中共鉴定得到39个具有完整序列结构的2-ODD家族基因, 这些基因编码蛋白质的平均长度为320个氨基酸, 分子质量约为36.00 kDa, 多为亲水性蛋白。系统进化分析将白鼠尾草2-ODD基因分为多个亚家族, 这些基因在白鼠尾草不同部位均有表达, 多数基因在根中的表达量明显高于叶中的表达量。本研究可为白鼠尾草2-ODD基因的深入研究奠定基础。

, correspAuthors=李卿, authorNote=null, correspAuthorsNote=
*李卿, Tel: 86-21-51322403, E-mail:
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Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
2. Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null), CN=AuthorExt(id=1210518251675709891, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, authorId=1210518251424051629, language=CN, stringName=陈万生, firstName=万生, middleName=null, lastName=陈, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=1, 2, address=1.上海中医药大学中药研究所, 中药资源与生物技术中心, 上海 201203
2.中国人民解放军海军军医大学第二附属医院, 药剂科, 上海 200003, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null)}, companyList=[AuthorCompany(id=1210518248798417167, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, xref=null, ext=[AuthorCompanyExt(id=1210518248806805777, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, companyId=1210518248798417167, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1. 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Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China), AuthorCompanyExt(id=1210518250073485605, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, companyId=1210518250060902689, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2.中国人民解放军海军军医大学第二附属医院, 药剂科, 上海 200003)])], figs=[ArticleFig(id=1210518253307294283, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=EN, label=null, caption=null, figureFileSmall=5a7KBsNo5VTX4p9R7uzVqQ==, figureFileBig=D6DLNOCy2bQQ1/lQMIVn0A==, tableContent=null), ArticleFig(id=1210518254502670932, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=CN, label=Figure 1, caption= Cluster of orthologous groups (COG) classification of unigenes in <i>S. apiana</i>. A: RNA processing and modification; B: Chromatin structure and dynamics; C: Energy production and conversion; D: Cell cycle control, cell division, chromosome partitioning; E: Amino acid transport and metabolism; F: Nucleotide transport and metabolism; G: Carbohydrate transport and metabolism; H: Coenzyme transport and metabolism; I: Lipid transport and metabolism; J: Translation, ribosomal structure and biogenesis; K: Transcription; L: Replication, recombination and repair; M: Cell wall/membrane/envelope biogenesis; N: Cell motility; O: Posttranslational modification, protein turnover, chaperones; P: Inorganic ion transport and metabolism; Q: Secondary metabolites biosynthesis, transport and catabolism; S: Function unknown; T: Signal transduction mechanisms; U: Intracellular trafficking, secretion, and vesicular transport; V: Defense mechanisms; Y: Nuclear structure; Z: Cytoskeleton , figureFileSmall=5a7KBsNo5VTX4p9R7uzVqQ==, figureFileBig=D6DLNOCy2bQQ1/lQMIVn0A==, tableContent=null), ArticleFig(id=1210518254737551969, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=EN, label=null, caption=null, figureFileSmall=h9aiSWYAwyJ+kaGvYkCUcg==, figureFileBig=j6RYfiYMprZA2jS/e4X4Pw==, tableContent=null), ArticleFig(id=1210518254842409578, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=CN, label=Figure 2, caption= Gene ontology (GO) classification of unigenes in <i>S. apiana</i>. 1: Biological adhesion; 2: Biological regulation; 3: Carbon utilization; 4: Cell killing; 5: Cell population proliferation; 6: Cellular component organization or biogenesis; 7: Cellular process; 8: Detoxification; 9: Developmental process; 10: Growth; 11: Immune system process; 12: Localization; 13: Locomotion; 14: Metabolic process; 15: Multicellular organismal process; 16: Multi-organism process; 17: Nitrogen utilization; 18: Pigmentation; 19: Reproduction; 20: Reproductive process; 21: Response to stimulus; 22: Rhythmic process; 23: Signaling; 24: Cell; 25: Cell junction; 26: Cell part; 27: Extracellular region; 28: Extracellular region part; 29: Membrane; 30: Membrane part; 31: Membrane-enclosed lumen; 32: Nucleoid; 33: Organelle; 34: Organelle part; 35: Other organism part; 36: Protein-containing complex; 37: Supramolecular complex; 38: Antioxidant activity; 39: Binding; 40: Cargo adaptor activity; 41: Catalytic activity; 42: Molecular carrier activity; 43: Molecular function regulator; 44: Molecular transducer activity; 45: Nutrient reservoir activity; 46: Protein folding chaperone; 47: Protein tag; 48: Small molecule sensor activity; 49: Structural molecule activity; 50: Transcription regulator activity; 51: Translation regulator activity; 52: Transporter activity , figureFileSmall=h9aiSWYAwyJ+kaGvYkCUcg==, figureFileBig=j6RYfiYMprZA2jS/e4X4Pw==, tableContent=null), ArticleFig(id=1210518254947267186, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=EN, label=null, caption=null, figureFileSmall=MD2RlqRV8Uvw8Q2u1g9cjQ==, figureFileBig=r7FTo9654t7yCRVaf+aoEg==, tableContent=null), ArticleFig(id=1210518255039541878, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=CN, label=Figure 3, caption= KEGG classification of unigenes in <i>S. apiana</i>. 1: Nucleotide metabolism; 2: Metabolism of terpenoids and polyketides; 3: Glycan biosynthesis and metabolism; 4: Lipid metabolism; 5: Energy metabolism; 6: Metabolism of other amino acids; 7: Metabolism of cofactors and vitamins; 8: Amino acid metabolism; 9: Biosynthesis of other secondary metabolites; 10: Carbohydrate metabolism; 11: Transcription; 12: Translation; 13: Replication and repair; 14: Folding, sorting and degradation; 15: Signal transduction; 16: Membrane transport; 17: Transport and catabolism; 18: Environmental adaptation; 19: Drug resistance: antimicrobial; 20: Endocrine and metabolic disease , figureFileSmall=MD2RlqRV8Uvw8Q2u1g9cjQ==, figureFileBig=r7FTo9654t7yCRVaf+aoEg==, tableContent=null), ArticleFig(id=1210518255177953917, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=EN, label=null, caption=null, figureFileSmall=CtUif4faobq4G62lpDLTLQ==, figureFileBig=zFP9mP418smOu8tl1aNzuw==, tableContent=null), ArticleFig(id=1210518255303783048, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=CN, label=Figure 4, caption= Tertiary structure of Sa2-ODDs , figureFileSmall=CtUif4faobq4G62lpDLTLQ==, figureFileBig=zFP9mP418smOu8tl1aNzuw==, tableContent=null), ArticleFig(id=1210518255412834961, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=EN, label=null, caption=null, figureFileSmall=ccqio/b4cHJkJSaadRuWYg==, figureFileBig=zDcDRIA1YvDAuUa4Mv3H8Q==, tableContent=null), ArticleFig(id=1210518255555441301, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=CN, label=Figure 5, caption= Phylogenetic tree (NJ) of Sa2-ODDs and Sm2-ODDs. A total of 171 2-ODD proteins from <i>S. apiana</i> and <i>S. miltiorrhiza</i> are clustered into 3 classes. Class DOXA (XV): The red region; Class DOXB (XIV): The yellow region; and Class DOXC (I-XIII): The blue region. Bootstrap values are presented for all branches. The red dot indicates Sm2OGD5 (SMil_00012032) mentioned in Xu's paper<sup>[<a href="javascript:;" class="mag_content_a" onclick="piaofuRef(this,'b11')" rid="b11">11</a>]</sup> and the red triangle indicates Sm2-ODD14 (SMil_00018668) mentioned in Song's paper<sup>[<a href="javascript:;" class="mag_content_a" onclick="piaofuRef(this,'b6')" rid="b6">6</a>]</sup> , figureFileSmall=ccqio/b4cHJkJSaadRuWYg==, figureFileBig=zDcDRIA1YvDAuUa4Mv3H8Q==, tableContent=null), ArticleFig(id=1210518255668687517, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=EN, label=null, caption=null, figureFileSmall=s2OlDmPCf275BWdq6zETig==, figureFileBig=rWNLqQrRX0aDBGny/u4Psg==, tableContent=null), ArticleFig(id=1210518255794516643, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=CN, label=Figure 6, caption= The expression of <i>Sa2-ODD</i>s in leaves and roots [the data in the rectangular box is the transcripts per million (TPM) value of each gene] , figureFileSmall=s2OlDmPCf275BWdq6zETig==, figureFileBig=rWNLqQrRX0aDBGny/u4Psg==, tableContent=null), ArticleFig(id=1210518255895179945, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
Sample IDRaw read/bpClean read/bpClean data rate/%Aligned read/bpAligned rate/%
SAAPI_leaf146 755 05646 218 70698.8537 886 09081.97
SAAPI_leaf248 498 06247 995 28298.9639 332 48881.95
SAAPI_leaf347 191 74446 695 85098.9538 295 08882.01
SAAPI_root151 096 84450 734 93099.2937 580 98674.07
SAAPI_root250 934 45850 484 35499.1237 257 04473.80
SAAPI_root350 185 06849 727 07899.0936 960 91274.33
), ArticleFig(id=1210518255979066028, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=CN, label=Table 1, caption=

RNA-seq information of S. apiana

, figureFileSmall=null, figureFileBig=null, tableContent=
Sample IDRaw read/bpClean read/bpClean data rate/%Aligned read/bpAligned rate/%
SAAPI_leaf146 755 05646 218 70698.8537 886 09081.97
SAAPI_leaf248 498 06247 995 28298.9639 332 48881.95
SAAPI_leaf347 191 74446 695 85098.9538 295 08882.01
SAAPI_root151 096 84450 734 93099.2937 580 98674.07
SAAPI_root250 934 45850 484 35499.1237 257 04473.80
SAAPI_root350 185 06849 727 07899.0936 960 91274.33
), ArticleFig(id=1210518256088117940, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
Designate nameTranscript IDSm2-ODD IDIdentity/%E-valueBit scoreClassClade
Sa2-ODD1TRINITY_DN16972_c0_g1SMil_0000472691.0890583DOXBP4H
Sa2-ODD2TRINITY_DN18814_c0_g1SMil_0001899695.8480506DOXBP4H
Sa2-ODD3TRINITY_DN3023_c0_g1SMil_0001325586.2930519DOXBP4H
Sa2-ODD4TRINITY_DN3151_c0_g1SMil_0000176494.5390551DOXBP4H
Sa2-ODD5TRINITY_DN6900_c0_g1SMil_0000101595.8620550DOXBP4H
Sa2-ODD6TRINITY_DN9762_c0_g1SMil_0000686094.5210526DOXBP4H
Sa2-ODD7TRINITY_DN1005_c0_g1SMil_0001106494.2860593DOXCACO
Sa2-ODD8TRINITY_DN10817_c0_g1SMil_0000604090.6980651DOXCACO
Sa2-ODD9TRINITY_DN11493_c0_g1SMil_0002207783.2716.06E-149412DOXCACO
Sa2-ODD10TRINITY_DN12053_c0_g1SMil_0001925979.0480528DOXCAOP
Sa2-ODD11TRINITY_DN17768_c0_g1SMil_0000057433.3337.34E-0742DOXCAOP
Sa2-ODD12TRINITY_DN19158_c0_g1SMil_0000057487.0471.58E-130363DOXCAOP
Sa2-ODD13TRINITY_DN3380_c0_g1SMil_0001363691.2900558DOXCAOP
Sa2-ODD14TRINITY_DN3583_c0_g1SMil_0001676449.1389.13E-83245DOXCAOP
Sa2-ODD15TRINITY_DN5191_c0_g1SMil_0001676384.0760553DOXCAOP
Sa2-ODD16TRINITY_DN6073_c0_g1SMil_0001676487.3420572DOXCAOP
Sa2-ODD17TRINITY_DN10852_c0_g1SMil_0001308122.1791.31E-1260.5DOXCCODM/NCS
Sa2-ODD18TRINITY_DN2211_c0_g2SMil_0002428286.8132.08E-180493DOXCCODM/NCS
Sa2-ODD19TRINITY_DN22361_c0_g1SMil_0001225971.2731.54E-151422DOXCCODM/NCS
Sa2-ODD20TRINITY_DN2908_c0_g1SMil_0001611656.4751.01E-111321DOXCD4H/GSLOH/BX6
Sa2-ODD21TRINITY_DN30979_c0_g1SMil_0001866986.0960637DOXCD4H/GSLOH/BX6
Sa2-ODD22TRINITY_DN4864_c0_g1SMil_0001611681.1670620DOXCD4H/GSLOH/BX6
Sa2-ODD23TRINITY_DN9009_c0_g1SMil_0001203390.4370686DOXCD4H/GSLOH/BX6
Sa2-ODD24TRINITY_DN1201_c0_g1SMil_0002372488.0732.06E-142393DOXCDAO
Sa2-ODD25TRINITY_DN23679_c0_g1SMil_0002372454.1102.66E-115328DOXCDAO
Sa2-ODD26TRINITY_DN1185_c0_g1SMil_0001374592.7170667DOXCF3H
Sa2-ODD27TRINITY_DN1324_c0_g1SMil_0002293872.5908.89E-179491DOXCF3H
Sa2-ODD28TRINITY_DN4831_c0_g2SMil_0002813387.3306.70E-146402DOXCF3H
Sa2-ODD29TRINITY_DN8474_c0_g2SMil_0000541081.8730557DOXCF3H
Sa2-ODD30TRINITY_DN4585_c0_g1SMil_0000809086.7370672DOXCGA20ox
Sa2-ODD31TRINITY_DN13439_c0_g1SMil_0000414181.0404.08E-176484DOXCGA2ox
Sa2-ODD32TRINITY_DN8276_c0_g1SMil_0001777491.2120617DOXCGA2ox
Sa2-ODD33TRINITY_DN15665_c0_g1SMil_0002798878.4020570DOXCH6H
Sa2-ODD34TRINITY_DN17826_c0_g1SMil_0001305972.2710530DOXCS3H
Sa2-ODD35TRINITY_DN16851_c0_g1SMil_0002034291.1170638DOXCUnknown
Sa2-ODD36TRINITY_DN4633_c0_g1SMil_0000901289.7730676DOXCUnknown
Sa2-ODD37TRINITY_DN4633_c0_g2SMil_0000901382.1730587DOXCUnknown
Sa2-ODD38TRINITY_DN5898_c0_g1SMil_0001812487.8050557DOXCUnknown
Sa2-ODD39TRINITY_DN7999_c0_g1SMil_0002118587.0690619DOXCUnknown
), ArticleFig(id=1210518256192975545, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=CN, label=Table 2, caption=

The identification of homologous 2-oxoglutarate/Fe(II)-dependent dioxygenases (2-ODD) genes between S. apiana and S. miltiorrhiza

, figureFileSmall=null, figureFileBig=null, tableContent=
Designate nameTranscript IDSm2-ODD IDIdentity/%E-valueBit scoreClassClade
Sa2-ODD1TRINITY_DN16972_c0_g1SMil_0000472691.0890583DOXBP4H
Sa2-ODD2TRINITY_DN18814_c0_g1SMil_0001899695.8480506DOXBP4H
Sa2-ODD3TRINITY_DN3023_c0_g1SMil_0001325586.2930519DOXBP4H
Sa2-ODD4TRINITY_DN3151_c0_g1SMil_0000176494.5390551DOXBP4H
Sa2-ODD5TRINITY_DN6900_c0_g1SMil_0000101595.8620550DOXBP4H
Sa2-ODD6TRINITY_DN9762_c0_g1SMil_0000686094.5210526DOXBP4H
Sa2-ODD7TRINITY_DN1005_c0_g1SMil_0001106494.2860593DOXCACO
Sa2-ODD8TRINITY_DN10817_c0_g1SMil_0000604090.6980651DOXCACO
Sa2-ODD9TRINITY_DN11493_c0_g1SMil_0002207783.2716.06E-149412DOXCACO
Sa2-ODD10TRINITY_DN12053_c0_g1SMil_0001925979.0480528DOXCAOP
Sa2-ODD11TRINITY_DN17768_c0_g1SMil_0000057433.3337.34E-0742DOXCAOP
Sa2-ODD12TRINITY_DN19158_c0_g1SMil_0000057487.0471.58E-130363DOXCAOP
Sa2-ODD13TRINITY_DN3380_c0_g1SMil_0001363691.2900558DOXCAOP
Sa2-ODD14TRINITY_DN3583_c0_g1SMil_0001676449.1389.13E-83245DOXCAOP
Sa2-ODD15TRINITY_DN5191_c0_g1SMil_0001676384.0760553DOXCAOP
Sa2-ODD16TRINITY_DN6073_c0_g1SMil_0001676487.3420572DOXCAOP
Sa2-ODD17TRINITY_DN10852_c0_g1SMil_0001308122.1791.31E-1260.5DOXCCODM/NCS
Sa2-ODD18TRINITY_DN2211_c0_g2SMil_0002428286.8132.08E-180493DOXCCODM/NCS
Sa2-ODD19TRINITY_DN22361_c0_g1SMil_0001225971.2731.54E-151422DOXCCODM/NCS
Sa2-ODD20TRINITY_DN2908_c0_g1SMil_0001611656.4751.01E-111321DOXCD4H/GSLOH/BX6
Sa2-ODD21TRINITY_DN30979_c0_g1SMil_0001866986.0960637DOXCD4H/GSLOH/BX6
Sa2-ODD22TRINITY_DN4864_c0_g1SMil_0001611681.1670620DOXCD4H/GSLOH/BX6
Sa2-ODD23TRINITY_DN9009_c0_g1SMil_0001203390.4370686DOXCD4H/GSLOH/BX6
Sa2-ODD24TRINITY_DN1201_c0_g1SMil_0002372488.0732.06E-142393DOXCDAO
Sa2-ODD25TRINITY_DN23679_c0_g1SMil_0002372454.1102.66E-115328DOXCDAO
Sa2-ODD26TRINITY_DN1185_c0_g1SMil_0001374592.7170667DOXCF3H
Sa2-ODD27TRINITY_DN1324_c0_g1SMil_0002293872.5908.89E-179491DOXCF3H
Sa2-ODD28TRINITY_DN4831_c0_g2SMil_0002813387.3306.70E-146402DOXCF3H
Sa2-ODD29TRINITY_DN8474_c0_g2SMil_0000541081.8730557DOXCF3H
Sa2-ODD30TRINITY_DN4585_c0_g1SMil_0000809086.7370672DOXCGA20ox
Sa2-ODD31TRINITY_DN13439_c0_g1SMil_0000414181.0404.08E-176484DOXCGA2ox
Sa2-ODD32TRINITY_DN8276_c0_g1SMil_0001777491.2120617DOXCGA2ox
Sa2-ODD33TRINITY_DN15665_c0_g1SMil_0002798878.4020570DOXCH6H
Sa2-ODD34TRINITY_DN17826_c0_g1SMil_0001305972.2710530DOXCS3H
Sa2-ODD35TRINITY_DN16851_c0_g1SMil_0002034291.1170638DOXCUnknown
Sa2-ODD36TRINITY_DN4633_c0_g1SMil_0000901289.7730676DOXCUnknown
Sa2-ODD37TRINITY_DN4633_c0_g2SMil_0000901382.1730587DOXCUnknown
Sa2-ODD38TRINITY_DN5898_c0_g1SMil_0001812487.8050557DOXCUnknown
Sa2-ODD39TRINITY_DN7999_c0_g1SMil_0002118587.0690619DOXCUnknown
), ArticleFig(id=1210518256356553408, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
IDLength/aaMolecular weight/DaTheoretical pINegatively charged residue/aaPositively charged residue/aaFormulaInstability indexAliphatic indexGrand average of hydropathicity
Sa2-ODD130233 464.885.894336C1482H2285N401O450S1736.6769.80-0.367
Sa2-ODD228932 322.249.163340C1443H2295N399O419S1245.8786.99-0.323
Sa2-ODD328932 272.658.193335C1444H2240N394O427S1040.4577.58-0.312
Sa2-ODD429232 521.716.044138C1438H2231N389O444S1445.5270.48-0.473
Sa2-ODD528932 575.867.253535C1456H2257N403O432S843.5080.97-0.424
Sa2-ODD629332 824.285.923633C1473H2281N393O438S1037.8276.25-0.398
Sa2-ODD731435 624.865.065037C1607H2496N410O474S1534.4084.81-0.291
Sa2-ODD834338 476.586.074136C1715H2659N467O515S1344.4980.35-0.429
Sa2-ODD926730 277.436.373433C1354H2105N367O402S1041.3679.59-0.456
Sa2-ODD1031235 418.395.914032C1606H2482N412O473S942.2083.97-0.402
Sa2-ODD1136240 338.286.474341C1791H2812N494O525S2155.4177.82-0.331
Sa2-ODD1231835 878.555.183925C1616H2442N414O483S1537.3777.23-0.227
Sa2-ODD1331135 470.345.914535C1605H2458N416O471S1137.7581.16-0.412
Sa2-ODD1429032 938.855.643326C1496H2279N369O433S1835.0582.59-0.050
Sa2-ODD1531335 137.795.094026C1577H2418N410O475S1341.7882.52-0.191
Sa2-ODD1631535 559.415.783931C1599H2445N417O473S1543.3575.21-0.302
Sa2-ODD1737642 871.216.434745C1935H3002N516O554S1649.0881.38-0.334
Sa2-ODD1827831 511.155.274033C1409H2221N371O421S1330.9588.38-0.364
Sa2-ODD1928231 504.655.283729C1430H2268N364O410S1248.17101.03-0.009
Sa2-ODD2029332 774.565.324031C1462H2295N399O429S1442.4090.78-0.194
Sa2-ODD2137742 030.584.885839C1849H2945N511O580S1333.7694.38-0.279
Sa2-ODD2236240 831.325.095137C1825H2847N493O549S1141.0390.99-0.246
Sa2-ODD2336541 216.315.555040C1836H2879N495O541S2151.4683.86-0.284
Sa2-ODD2422824 942.554.622818C1115H1742N288O336S1242.2292.32-0.011
Sa2-ODD2530233 354.985.413728C1483H2315N405O443S1441.2386.56-0.112
Sa2-ODD2634940 006.285.405542C1811H2775N473O536S837.1679.60-0.529
Sa2-ODD2729533 722.495.284032C1522H2340N396O445S1342.1584.27-0.324
Sa2-ODD2831034 936.575.344332C1584H2419N417O463S744.0379.64-0.396
Sa2-ODD2933237 073.205.264737C1652H2565N447O492S1631.7282.65-0.308
Sa2-ODD3037442 197.106.753937C1895H2903N515O545S1838.6775.67-0.372
Sa2-ODD3131635 724.255.384434C1587H2440N428O485S1449.8774.34-0.341
Sa2-ODD3232936 561.877.053939C1640H2568N440O481S1333.9285.35-0.233
Sa2-ODD3333738 324.806.173326C1714H2643N465O497S1955.1780.14-0.343
Sa2-ODD3433637 950.175.764437C1699H2633N453O506S1442.1682.56-0.385
Sa2-ODD3534838 962.945.314531C1733H2689N475O527S1147.6786.09-0.305
Sa2-ODD3636040 427.785.504534C1809H2778N484O540S1535.2978.33-0.280
Sa2-ODD3735339 373.905.954033C1772H2751N471O521S1235.8489.24-0.148
Sa2-ODD3834437 940.015.204532C1680H2631N463O511S1444.7384.48-0.285
Sa2-ODD3934938 728.015.813930C1721H2692N474O516S1454.8089.74-0.194
), ArticleFig(id=1210518256457216710, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518242007838782, language=CN, label=Table 3, caption=

Composition and physicochemical character analysis of Sa2-ODDs

, figureFileSmall=null, figureFileBig=null, tableContent=
IDLength/aaMolecular weight/DaTheoretical pINegatively charged residue/aaPositively charged residue/aaFormulaInstability indexAliphatic indexGrand average of hydropathicity
Sa2-ODD130233 464.885.894336C1482H2285N401O450S1736.6769.80-0.367
Sa2-ODD228932 322.249.163340C1443H2295N399O419S1245.8786.99-0.323
Sa2-ODD328932 272.658.193335C1444H2240N394O427S1040.4577.58-0.312
Sa2-ODD429232 521.716.044138C1438H2231N389O444S1445.5270.48-0.473
Sa2-ODD528932 575.867.253535C1456H2257N403O432S843.5080.97-0.424
Sa2-ODD629332 824.285.923633C1473H2281N393O438S1037.8276.25-0.398
Sa2-ODD731435 624.865.065037C1607H2496N410O474S1534.4084.81-0.291
Sa2-ODD834338 476.586.074136C1715H2659N467O515S1344.4980.35-0.429
Sa2-ODD926730 277.436.373433C1354H2105N367O402S1041.3679.59-0.456
Sa2-ODD1031235 418.395.914032C1606H2482N412O473S942.2083.97-0.402
Sa2-ODD1136240 338.286.474341C1791H2812N494O525S2155.4177.82-0.331
Sa2-ODD1231835 878.555.183925C1616H2442N414O483S1537.3777.23-0.227
Sa2-ODD1331135 470.345.914535C1605H2458N416O471S1137.7581.16-0.412
Sa2-ODD1429032 938.855.643326C1496H2279N369O433S1835.0582.59-0.050
Sa2-ODD1531335 137.795.094026C1577H2418N410O475S1341.7882.52-0.191
Sa2-ODD1631535 559.415.783931C1599H2445N417O473S1543.3575.21-0.302
Sa2-ODD1737642 871.216.434745C1935H3002N516O554S1649.0881.38-0.334
Sa2-ODD1827831 511.155.274033C1409H2221N371O421S1330.9588.38-0.364
Sa2-ODD1928231 504.655.283729C1430H2268N364O410S1248.17101.03-0.009
Sa2-ODD2029332 774.565.324031C1462H2295N399O429S1442.4090.78-0.194
Sa2-ODD2137742 030.584.885839C1849H2945N511O580S1333.7694.38-0.279
Sa2-ODD2236240 831.325.095137C1825H2847N493O549S1141.0390.99-0.246
Sa2-ODD2336541 216.315.555040C1836H2879N495O541S2151.4683.86-0.284
Sa2-ODD2422824 942.554.622818C1115H1742N288O336S1242.2292.32-0.011
Sa2-ODD2530233 354.985.413728C1483H2315N405O443S1441.2386.56-0.112
Sa2-ODD2634940 006.285.405542C1811H2775N473O536S837.1679.60-0.529
Sa2-ODD2729533 722.495.284032C1522H2340N396O445S1342.1584.27-0.324
Sa2-ODD2831034 936.575.344332C1584H2419N417O463S744.0379.64-0.396
Sa2-ODD2933237 073.205.264737C1652H2565N447O492S1631.7282.65-0.308
Sa2-ODD3037442 197.106.753937C1895H2903N515O545S1838.6775.67-0.372
Sa2-ODD3131635 724.255.384434C1587H2440N428O485S1449.8774.34-0.341
Sa2-ODD3232936 561.877.053939C1640H2568N440O481S1333.9285.35-0.233
Sa2-ODD3333738 324.806.173326C1714H2643N465O497S1955.1780.14-0.343
Sa2-ODD3433637 950.175.764437C1699H2633N453O506S1442.1682.56-0.385
Sa2-ODD3534838 962.945.314531C1733H2689N475O527S1147.6786.09-0.305
Sa2-ODD3636040 427.785.504534C1809H2778N484O540S1535.2978.33-0.280
Sa2-ODD3735339 373.905.954033C1772H2751N471O521S1235.8489.24-0.148
Sa2-ODD3834437 940.015.204532C1680H2631N463O511S1444.7384.48-0.285
Sa2-ODD3934938 728.015.813930C1721H2692N474O516S1454.8089.74-0.194
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IDRandom coil/%Alpha helix/%Extended strand/%Beta turn/%
Sa2-ODD154.6421.5218.874.97
Sa2-ODD249.1322.8421.806.23
Sa2-ODD351.2122.1520.426.23
Sa2-ODD452.4023.9718.495.14
Sa2-ODD550.1724.2219.036.57
Sa2-ODD649.1521.8422.536.48
Sa2-ODD731.5343.9517.836.69
Sa2-ODD841.4034.6918.375.54
Sa2-ODD940.4531.4620.607.49
Sa2-ODD1042.3137.1815.714.81
Sa2-ODD1142.2734.8114.928.01
Sa2-ODD1239.9436.1617.925.97
Sa2-ODD1340.5137.6217.044.82
Sa2-ODD1440.0037.2416.905.86
Sa2-ODD1541.2134.8217.576.39
Sa2-ODD1643.1735.5615.875.40
Sa2-ODD1742.0238.5615.433.99
Sa2-ODD1836.6938.8519.425.04
Sa2-ODD1935.4640.4317.736.38
Sa2-ODD2038.5738.9118.094.44
Sa2-ODD2135.2841.1117.775.84
Sa2-ODD2238.1237.8517.406.63
Sa2-ODD2338.9038.0817.815.21
Sa2-ODD2443.4235.5315.795.26
Sa2-ODD2542.0535.4316.895.63
Sa2-ODD2640.9736.1018.344.58
Sa2-ODD2741.6934.9218.315.08
Sa2-ODD2842.9030.9719.356.77
Sa2-ODD2945.4835.5415.963.01
Sa2-ODD3041.7134.2217.656.42
Sa2-ODD3141.1432.2820.256.33
Sa2-ODD3242.8634.3517.025.78
Sa2-ODD3341.2535.9117.515.34
Sa2-ODD3440.4835.7117.566.25
Sa2-ODD3540.5237.3615.236.90
Sa2-ODD3641.1135.5618.065.28
Sa2-ODD3737.9636.5418.986.52
Sa2-ODD3843.0234.5917.444.94
Sa2-ODD3940.1136.3917.486.02
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Sa2-ODD154.6421.5218.874.97
Sa2-ODD249.1322.8421.806.23
Sa2-ODD351.2122.1520.426.23
Sa2-ODD452.4023.9718.495.14
Sa2-ODD550.1724.2219.036.57
Sa2-ODD649.1521.8422.536.48
Sa2-ODD731.5343.9517.836.69
Sa2-ODD841.4034.6918.375.54
Sa2-ODD940.4531.4620.607.49
Sa2-ODD1042.3137.1815.714.81
Sa2-ODD1142.2734.8114.928.01
Sa2-ODD1239.9436.1617.925.97
Sa2-ODD1340.5137.6217.044.82
Sa2-ODD1440.0037.2416.905.86
Sa2-ODD1541.2134.8217.576.39
Sa2-ODD1643.1735.5615.875.40
Sa2-ODD1742.0238.5615.433.99
Sa2-ODD1836.6938.8519.425.04
Sa2-ODD1935.4640.4317.736.38
Sa2-ODD2038.5738.9118.094.44
Sa2-ODD2135.2841.1117.775.84
Sa2-ODD2238.1237.8517.406.63
Sa2-ODD2338.9038.0817.815.21
Sa2-ODD2443.4235.5315.795.26
Sa2-ODD2542.0535.4316.895.63
Sa2-ODD2640.9736.1018.344.58
Sa2-ODD2741.6934.9218.315.08
Sa2-ODD2842.9030.9719.356.77
Sa2-ODD2945.4835.5415.963.01
Sa2-ODD3041.7134.2217.656.42
Sa2-ODD3141.1432.2820.256.33
Sa2-ODD3242.8634.3517.025.78
Sa2-ODD3341.2535.9117.515.34
Sa2-ODD3440.4835.7117.566.25
Sa2-ODD3540.5237.3615.236.90
Sa2-ODD3641.1135.5618.065.28
Sa2-ODD3737.9636.5418.986.52
Sa2-ODD3843.0234.5917.444.94
Sa2-ODD3940.1136.3917.486.02
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基于转录组测序的白鼠尾草2-ODD基因家族鉴定与表达分析
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秦晓静 1 , 胡佳栋 1 , 房振西 1 , 陈万生 1, 2 , 李卿 2, *
药学学报 | 研究论文 2022,57(12): 3675-3685
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药学学报 | 研究论文 2022, 57(12): 3675-3685
基于转录组测序的白鼠尾草2-ODD基因家族鉴定与表达分析
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秦晓静1, 胡佳栋1, 房振西1, 陈万生1, 2, 李卿2, *
作者信息
  • 1.上海中医药大学中药研究所, 中药资源与生物技术中心, 上海 201203
  • 2.中国人民解放军海军军医大学第二附属医院, 药剂科, 上海 200003

通讯作者:

*李卿, Tel: 86-21-51322403, E-mail:
Transcriptome-wide identification and expression analysis of 2-ODD gene family in Salvia apiana Jepson
Xiao-jing QIN1, Jia-dong HU1, Zhen-xi FANG1, Wan-sheng CHEN1, 2, Qing LI2, *
Affiliations
  • 1. Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
  • 2. Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
出版时间: 2022-12-12 doi: 10.16438/j.0513-4870.2022-0648
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α-酮戊二酸(2OG)/Fe(II) 依赖双加氧酶(2-ODD) 在植物初生和次生代谢过程中发挥着重要作用。本研究基于高通量测序技术平台Illumina NovaSeq 6000进行了白鼠尾草(Salvia apiana Jepson) 转录组测序, 对测序结果进行de novo拼接后, 共获得38 534个独立基因(unigenes)。将获得的独立基因进行基因功能注释, 有29 982个独立基因获得功能注释。通过生物信息学方法在白鼠尾草转录组数据中进行2-ODD基因家族鉴定, 并对鉴定得到的基因序列进行序列特征分析, 包括序列的同源性、理化特征、信号肽、跨膜结构域、亚细胞定位、二级结构和三级结构预测等, 另对它们的进化关系及表达模式进行分析。结果显示, 从白鼠尾草转录组中共鉴定得到39个具有完整序列结构的2-ODD家族基因, 这些基因编码蛋白质的平均长度为320个氨基酸, 分子质量约为36.00 kDa, 多为亲水性蛋白。系统进化分析将白鼠尾草2-ODD基因分为多个亚家族, 这些基因在白鼠尾草不同部位均有表达, 多数基因在根中的表达量明显高于叶中的表达量。本研究可为白鼠尾草2-ODD基因的深入研究奠定基础。

白鼠尾草  /  转录组  /  α-酮戊二酸/Fe(II) 依赖双加氧酶  /  生物信息学  /  表达分析

2-Oxoglutarate/Fe(II)-dependent dioxygenases (2-ODD) play an important role in plant primary and secondary metabolism. Based on the high-throughput sequencing platform Illumina NovaSeq 6000, the transcriptome of Salvia apiana Jepson was sequenced, and the obtained reads were de novo assembled. A total of 38 534 unigenes were obtained from the transcriptome. The assembled unigenes were annotated and 29 982 unigenes were given functional annotations. The 2-ODD genes were identified from the assembled S. apiana transcriptome database by bioinformatics methods, and the genes were analyzed, including the homology of the sequences, physicochemical characteristics, signal peptides, transmembrane domains, subcellular localization, secondary structure and tertiary structure, etc. The evolutionary relationships and the expression patterns of the identified 2-ODD genes were also analyzed. 39 full-length 2-ODD genes were identified from the transcriptome of S. apiana. The average length of these 2-ODD encoding proteins was 320 amino acids, the molecular weight was about 36.00 kDa, and most of them were hydrophilic proteins. Phylogenetic analysis divided these 2-ODD genes into several subfamilies. Gene expression analysis indicated that the 2-ODD genes were expressed in different parts of S. apiana, and the expression level of most genes was much higher in roots than that in leaves. This study can lay a foundation for further study of 2-ODD genes in S. apiana.

Salvia apiana Jepson  /  transcriptome  /  2-oxoglutarate/Fe(II)-dependent dioxygenase  /  bioinformatics  /  expression analysis
秦晓静, 胡佳栋, 房振西, 陈万生, 李卿. 基于转录组测序的白鼠尾草2-ODD基因家族鉴定与表达分析. 药学学报, 2022 , 57 (12) : 3675 -3685 . DOI: 10.16438/j.0513-4870.2022-0648
Xiao-jing QIN, Jia-dong HU, Zhen-xi FANG, Wan-sheng CHEN, Qing LI. Transcriptome-wide identification and expression analysis of 2-ODD gene family in Salvia apiana Jepson[J]. Acta Pharmaceutica Sinica, 2022 , 57 (12) : 3675 -3685 . DOI: 10.16438/j.0513-4870.2022-0648
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白鼠尾草(Salvia apiana Jepson) 是唇形科鼠尾草属多年生草本植物, 原产于墨西哥北部和美国南部地区, 我国有小部分人工种植区域。在原产地, 白鼠尾草作为丘马什人(Chumash) 的食物添加剂和传统药物, 具有悠久的药用历史[1], 我国尚无白鼠尾草的药用记录。白鼠尾草的种子具有清洁眼睛的作用; 其叶能用于治疗感冒, 具有清洁头发、防止头发变白和消除体味等作用; 其烟雾具有净化居所、驱虫灭菌的功效, 能用于治疗鼻炎、鼻窦炎, 可缓解鼻塞、多涕等症状, 还能用于热灸治疗, 缓解经期痉挛和一些更年期症状[2]。现代药理学研究表明, 白鼠尾草具有抗菌、抗炎、抗氧化、抗肿瘤和镇痛等药理学活性[3]。天然产物化学研究发现白鼠尾草主要含有酚酸类和大量二萜类化合物[3, 4]。本课题组前期研究显示, 白鼠尾草具有与同属植物——我国传统中药丹参(Salvia miltiorrhiza Bge.) 类似的化合物及生物合成途径, 特别是以丹参酮IIA为代表的松香烷类二萜化合物的生物合成[5]。探究白鼠尾草中丹参酮IIA的分子调控机制, 可将白鼠尾草培育成丹参酮IIA提取的替代植物, 达到丹参药用资源保护的目的。Song等[6]发现丹参中的Sm2-ODD14基因在丹参酮IIA生物合成过程中发挥了重要作用, 能将隐丹参酮直接转化为丹参酮IIA。
α-酮戊二酸(2OG)/Fe(II) 依赖双加氧酶[2-oxoglutarate/Fe(II)-dependent dioxygenases, 2-ODD] 广泛存在于自然界, 在微生物、植物和动物中均有报道[7]。植物中的2-ODD基因家族成员数量庞大, 不仅广泛参与植物的生长发育过程, 还在次生代谢产物的生物合成过程中发挥着重要作用[8]。根据序列相似性, 2-ODD基因家族中的成员可分为三大类: DOXA、DOXB和DOXC。DOXA亚家族成员由大肠杆菌中的DNA修复蛋白Alkb进化而来[9], 主要参与初生代谢过程; DOXB亚家族成员相对保守, 编码脯氨酰4-羟化酶(prolyl 4-hydroxylase, P4Hs), 主要参与多肽链的翻译后修饰, 对植物信号肽类激素和细胞壁形成意义重大[10]。DOXC亚家族成员复杂, 该亚家族成员在不同植物体内的功能和数量差异悬殊, 具有明显的物种间特异性; 该亚家族成员主要参与植物的次生代谢过程, 包括萜类、生物碱类、植物激素、黄酮类和酚酸类等物质的生物合成, 绝大多数参与植物次生代谢的2-ODD基因都可以归为这一亚家族[9]。
2-ODD基因广泛存在, 且作用重要, 目前对白鼠尾草2-ODD基因的相关研究尚未见报道。由于白鼠尾草缺少基因组信息, 因此本研究基于转录组测序, 对白鼠尾草2-ODD基因家族进行了鉴定, 并对其表达模式进行了分析, 以期为白鼠尾草2-ODD基因的功能研究及其在白鼠尾草次生代谢途径中的作用提供参考。
材料与方法
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植物材料  植物材料种植于上海中医药大学药圃, 经中国科学院昆明植物研究所向春雷研究员鉴定为白鼠尾草(Salvia apiana Jepson)。为了获得白鼠尾草de novo拼接的转录组序列, 采集6月龄(2020年5~11月) 白鼠尾草全株, 提取总RNA后, 用于转录组测序。为了获得白鼠尾草地上与地下部分的差异表达基因, 分别采集根和叶(3个生物学重复), -80 ℃保存, 用于表达谱测序。
总RNA提取、cDNA文库构建与转录组测序  用TRIzol®试剂(美国Invitrogen公司) 提取白鼠尾草不同部位的总RNA, 并用DNase I试剂[宝日医生物技术(北京) 有限公司] 处理总RNA。用Agilent 2100 Bioanalyzer生物分析仪(美国安捷伦公司) 进行样品RNA完整性测定, RNA纯度和含量通过NanoDrop ND-2000紫外分光光度计(美国赛默飞公司) 测定。选取A260/A280 = 1.8~2.2、A260/A230 ≥ 2.0、RIN ≥ 8.0、28S∶18S ≥ 1.0, 且RNA含量 > 1 μg的样品进行后续分析。
使用Illumina TruSeq RNA Sample Prep Kit (美国Illumina公司) 试剂盒制备cDNA文库, 由上海美吉生物医药科技有限公司完成转录组和表达谱测序, 测序平台为Illumina NovaSeq 6000, 采用2×150 bp双端测序。
白鼠尾草转录组拼接、注释与表达量计算  使用fastp软件及默认参数对测序所得的原始数据(raw reads) 进行过滤和质控, 通过Trinity软件对去掉低质量数据后的待分析数据(clean reads) 进行de novo拼接得到转录组数据。表达量数据以转录组数据为模板进行拼接。拼接得到的独立基因(unigenes) 通过BLASTX算法分别与NCBI非冗余蛋白数据库(non-redundant protein sequence database, Nr)、蛋白质数据库(uniProt)、京都基因与基因组数据库(Kyoto encyclopedia of genes and genomes, KEGG) 和蛋白质直系同源数据库(cluster of orthologous groups, COG) 进行比对, 得到白鼠尾草独立基因的蛋白功能注释结果, 并对独立基因进行基因本体数据库(gene ontology, GO) 功能分类统计。通过HMMER v3.1b2进行独立基因蛋白结构域搜索。基因表达量通过TopHat2和Cufflinks软件计算, 用TPM值(transcripts per million) 表示。
白鼠尾草2-ODD基因的寻找与确认  根据文献[11]报道, 从拟南芥数据库(TAIR, https://www.arabidopsis.org/) 中下载拟南芥的130个2-ODD基因作为参考序列, 通过TBLASTN算法, 在白鼠尾草转录组中进行同源基因比对(E-value = 1.0×10-5)。比对得到的候选序列, 用TBtools软件[12]预测开放阅读框(open reading frame, ORF), 将ORF翻译成氨基酸序列后, 通过隐马尔可夫模型(hidden Markov model, HMM) 搜索是否具有2-ODD基因的特征结构域2OG-FeII_Oxy motif (PF03171)。筛除不具有2OG-FeII_Oxy结构域的片段序列后, 将余下的候选序列分别在NCBI数据库中进行BLASTP比对, 进一步删除非2-ODD基因序列或片段序列。
白鼠尾草2-ODD基因的生物信息学分析  利用各种生物信息学分析软件和在线网站对白鼠尾草2-ODD基因编码蛋白序列进行分析。白鼠尾草2-ODD基因的分类通过与已知的同属植物丹参序列进行同源比对获得[11]; 白鼠尾草2-ODD基因编码蛋白的理化性质通过ProtParam (http://web.expasy.org/protparam/) 网站进行预测; 信号肽预测在SignalP-5.0 (https://services.healthtech.dtu.dk/service.php?SignalP-5.0) 网站上进行; 使用TMHMM-2.0 (https://services.healthtech.dtu.dk/service.php?TMHMM-2.0) 网站进行跨膜结构预测; 亚细胞定位在subCELlular LOcalization predictor (http://cello.life.nctu.edu.tw) 网站上完成; 通过SOPMA (https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html) 网站进行2-ODD蛋白的二级结构预测; 2-ODD蛋白的高级结构同源建模在Phyre2 (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index)[13]网站上进行。
白鼠尾草2-ODD基因家族系统进化分析  为了获得白鼠尾草2-ODD基因家族中各成员的系统进化关系, 结合132个丹参2-ODD基因, 利用MEGA 11内置的ClustalW软件对以上基因的蛋白序列进行多序列比对, 通过MEGA 11软件中的邻位连接法(neighbor-joining, NJ) 构建系统进化树, 用bootstrap值检验进化树的拓扑结构, 设置参数为: 重复抽样次数设为1 000, Gaps/Missing Data Treatment选择pairwise deletion。
白鼠尾草2-ODD基因的特异性表达  根据白鼠尾草表达谱数据, 找到每个2-ODD基因的表达量, 用TBtools软件[12]绘制热图, 使用0~1 (也称min-max) 标准化方式, 使基因在不同样品中的表达量最高值为1, 最低值为0, 比较2-ODD基因在白鼠尾草根与叶中的表达差异。
结果
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1 白鼠尾草转录组和表达谱的测序拼接结果
白鼠尾草经过Illumina测序平台的高通量测序和拼接后, 共获得29 895 709 bp碱基, 38 534个独立基因。独立基因的长度范围居于201~6 392 bp之间, 平均长度为775.83 bp, 中位长度为539 bp, N50 = 1 203 bp, 独立基因的GC含量为44%。
白鼠尾草根和叶两个部位3个生物学重复共6个样本表达谱的测序数据如表 1所示, 每个样本测序得到的待分析数据(去除原始测序数据中的接头污染数据、重复冗余数据和低质量数据后) 占原始数据的比例均在98.85%以上, 表明此次RNA-seq高通量测序获得的数据质量较优。
2 白鼠尾草转录组注释结果
利用BLASTX将拼接得到的38 534个独立基因分别与Nr、UniProt、Pfam、KO (KEGG ontology)、COG和GO数据库(E-value < 1.0×10-5) 进行比对, 结果显示, 分别有29 592、21 369、20 224、13 420、25 895和25 833个独立基因比对上Nr、UniProt、Pfam、KO、COG和GO数据库, 共有29 982个独立基因获得功能注释, 占总独立基因的77.81%。其中有9 646个独立基因在所有数据库中都有注释结果。
在Nr注释结果中, 与一串红(Salvia splendens) 比对上的基因最多, 共有21 934条注释, 占Nr注释结果的74.12%; 其次为芝麻(Sesamum indicum), 有1 930条注释, 占注释结果的6.52%。此注释结果提示, 在已知基因组信息的物种中, 白鼠尾草与同属植物一串红的序列相似性最大。
3 白鼠尾草转录组独立基因的COG注释及分类
白鼠尾草独立基因与COG数据库比对结果显示: 共有25 895个独立基因被归纳到23个不同功能的分类当中。其中, 有13 922个独立基因的功能未知, 占总功能序列的53.76%, 在所有功能基因中占比最高; 然后依次为蛋白质翻译后修饰-蛋白质周转-分子伴侣(1 819个独立基因, 7.02%)、转录(1 700个独立基因, 6.57%) 和信号转导机制(1 276个独立基因, 4.93%)。只有极少数序列归纳到细胞能动性(11个独立基因, 0.04%) 和核结构(1个独立基因) 中(图 1)。
4 白鼠尾草转录组独立基因的GO注释及分类
分析白鼠尾草转录组独立基因的GO功能注释结果显示: 共有25 833个独立基因(总独立基因的67.04%) 获得功能注释, 分布在52个亚类中。其中有15 433、18 936和21 129个独立基因分别注释到生物过程、细胞组成和分子功能中(图 2)。在生物过程的23个功能亚类中, 细胞过程和代谢过程占比较多, 分别为40.44%和35.21%。在细胞组成的14个功能亚类中, 以细胞组分占比最多, 为50.63%, 其次为膜部件和细胞器, 分别占38.41%和29.18%。在分子功能所包括的15个亚类中, 捆绑和催化活性占比最多, 分别为53.02%和50.06%。负荷衔接子活性占比最少, 只注释上3个独立基因, 占比仅为0.01%。
5 白鼠尾草转录组KEGG代谢通路分析
白鼠尾草转录组测序结果通过比对KEGG数据库显示: 共有13 420个独立基因获得了注释, 占总独立基因的34.83%, 分布在20条代谢通路上(图 3)。按照获得注释的独立基因数目进行排序, 翻译(1 390个独立基因, 10.36%) 通路所获注释最多, 然后依次是糖代谢(953个独立基因, 7.10%), 折叠、分类和降解(804个独立基因, 5.99%), 运输和分解代谢(613个独立基因, 4.57%), 以及信号传导(592个独立基因, 4.41%) 等通路。另外, 注释到萜类和聚酮类代谢以及其他次生代谢产物生物合成通路的独立基因各有291个, 分别占KEGG代谢通路注释结果的2.17%。此次获得注释的代谢通路几乎代表了白鼠尾草发育的所有代谢过程, 为进一步开展白鼠尾草功能基因组学的研究提供了丰富的数据支撑。
6 白鼠尾草2-ODD基因的确认及序列组成分析
通过拟南芥2-ODD基因与白鼠尾草转录组的同源比对, 以及2-ODD基因特征结构域(PF03171) 寻找, 共找到39条具有完整序列结构的白鼠尾草2-ODD基因(Sa2-ODD), 它们与同属植物丹参已知2-ODD基因(Sm2-ODD) 的对应及分组关系, 如表 2所示。
对这39条完整的白鼠尾草2-ODD基因的编码蛋白进行序列组成成分和理化性质分析(表 3), 发现它们编码氨基酸的数量从228aa (Sa2-ODD24) 到377aa (Sa2-ODD21) 不等, 分子质量约为36.00 kDa, 最大为42.87 kDa (Sa2-ODD17), 最小为24.94 kDa (Sa2-ODD24)。这些2-ODD基因编码蛋白的理论等电点除Sa2-ODD32 (pI = 7.05)、Sa2-ODD5 (pI = 7.25)、Sa2-ODD3 (pI = 8.19) 和Sa2-ODD2 (pI = 8.19) 外, 均小于7, 提示Sa2-ODD多为酸性蛋白。每个蛋白的酸碱氨基酸比例与理论等电点对应, 除Sa2-ODD32、Sa2-ODD5、Sa2-ODD3和Sa2-ODD2之外, 其余蛋白所含碱性氨基酸比例均低于酸性氨基酸比例, 进一步提示大多数Sa2-ODD为酸性蛋白。对39条Sa2-ODD蛋白稳定系数的预测结果显示, 不稳定系数大于40的有25条, 不稳定系数小于40的为14条, 提示这些Sa2-ODD中, 不稳定蛋白居多。这些Sa2-ODD除Sa2-ODD24的总平均亲水性大于0, 为0.011, 其余总平均亲水性均为负值, 提示Sa2-ODD多为亲水性蛋白。
对这39条Sa2-ODD基因进行氨基酸序列相似性比较, 发现氨基酸序列间的两两(pairwise) 相似度从16.52% (Sa2-ODD36与Sa2-ODD37) 到96.86% (Sa2-ODD6与Sa2-ODD16) 不等, 提示序列间变异较大, 与文献[14, 15]报道一致。
7 白鼠尾草2-ODD基因编码蛋白的信号肽、亚细胞定位和跨膜结构域预测
信号肽预测显示, 除Sa2-ODD1和Sa2-ODD4具有信号肽外, 其余Sa2-ODD都不具有信号肽。
亚细胞定位预测显示, Sa2-ODD1和Sa2-ODD4都定位在细胞外, 与信号肽预测结果一致; Sa2-ODD7、Sa2-ODD9、Sa2-ODD11、Sa2-ODD12、Sa2-ODD13、Sa2-ODD16、Sa2-ODD17、Sa2-ODD18、Sa2-ODD19、Sa2-ODD20、Sa2-ODD21、Sa2-ODD22、Sa2-ODD23、Sa2-ODD24、Sa2-ODD26、Sa2-ODD27、Sa2-ODD28、Sa2-ODD29、Sa2-ODD31、Sa2-ODD32、Sa2-ODD34、Sa2-ODD35、Sa2-ODD36和Sa2-ODD38都定位在细胞质内; Sa2-ODD30和Sa2-ODD33定位在细胞核内; Sa2-ODD8、Sa2-ODD10和Sa2-ODD39定位在细胞质和细胞核内; Sa2-ODD14和Sa2-ODD15定位在细胞质和细胞质膜上; Sa2-ODD6定位在细胞质和细胞质膜上, 还穿过细胞膜定位在细胞外; Sa2-ODD2定位在线粒体上; Sa2-ODD3定位在细胞质膜和细胞外; Sa2-ODD5定位在细胞外和线粒体上; Sa2-ODD25定位在细胞质和叶绿体上; Sa2-ODD37定位在细胞外和细胞质中。
跨膜结构域预测显示, Sa2-ODD2、Sa2-ODD3、Sa2-ODD5、Sa2-ODD6、Sa2-ODD14和Sa2-ODD17具有跨膜结构域。
8 白鼠尾草2-ODD基因编码蛋白的二级和三级结构预测
利用在线分析软件SOPMA对白鼠尾草2-ODD基因的蛋白序列进行二级结构预测(表 4), 结果显示白鼠尾草2-ODD基因的蛋白序列由4个结构组件组成, 以无规则卷曲为主导, α-螺旋次之, 延伸链居第三, β-折叠所占比例最少。其中Sa2-ODD7、Sa2-ODD18、Sa2-ODD19、Sa2-ODD20和Sa2-ODD21中, α-螺旋所占比例最多; Sa2-ODD6中, 延伸链所占比例大于α-螺旋。
白鼠尾草2-ODD基因编码蛋白的三级结构预测采用Phyre2线串法的从头计算模式完成, 所有三级结构都在 > 90%的置信度下建模, 结果如图 4所示。2-ODD基因编码蛋白的功能域中包含1个扭曲的双股β螺旋核心折叠结构域, 包括8条β-折叠股, 每2条连续的β-折叠股之间以反向平行方式排列, 最终4对β-折叠股形成1个扁桶状的DSBH结构[8]。
9 白鼠尾草2-ODD基因的系统进化分析
为了研究白鼠尾草2-ODD基因家族的系统进化关系, 使用MEGA 11软件的Neighbor-joining算法, 用氨基酸序列构建39个白鼠尾草2-ODD基因与132个丹参2-ODD基因的系统进化树。根据丹参2-ODD基因的分组规则[11], 171个2-ODD基因被分成了3大类15组(图 5), 其中红色区域为DOXA亚家族(XV), 成员最少; 黄色区域为DOXB亚家族(XIV), 成员居中; 蓝色区域为DOXC亚家族(I-XIII), 绝大多数2-ODD基因都属于DOXC类。DOXB类的成员, 都属于P4H (prolyl 4-hydroxylase, 脯氨酰4-羟基化酶, XIV)。DOXC类分成了13个小组, 分别是功能未知的I组, S3H (salicylic acid 3-hydroxylase, 水杨酸3-羟化酶, II)、H6H (hyoscyamine 6β-hydroxylase, 莨菪碱6β-羟基化酶, III)、ACO (1-aminocyclopropane carboxylic acid oxidase, 1-氨基环丙烷羧酸氧化酶, IV)、FLS/ANS (flavonol synthase/anthocyanin synthase, 黄酮醇合成酶/花青素合成酶, V)、CODM/NCS (codeine O-demethylase/norcoclaurine synthase, 可待因-O-脱甲基酶/去甲乌药碱合成酶, VI)、D4H/GSLOH/BX6 (desacetoxyvindoline-4-hydroxylase/GSLOH/BENZOXAZINLESS6, VII)、GA2ox (gibberellin 2-oxidase, 赤霉素2-氧化酶, VIII)、GA3ox (gibberellin 3β-oxidase, 赤霉素3β-氧化酶, IX)、GA20ox (gibberellin 20-oxidase, 赤霉素20-氧化酶, X)、DAO (dioxygenase for auxin oxidation, XI)、AOP (glucosinolate biosynthesis, 葡萄糖异硫氰酸合成酶, XII) 和F3H (flavanone 3-hydroxylase, 黄烷酮3-羟化酶, XIII)。根据DOXC亚家族的成员组成, 可以推测该亚家族的成员可能参与了植物黄酮、生物碱和生长素类物质的代谢过程。
10 白鼠尾草2-ODD基因的表达分析
为了研究白鼠尾草2-ODD家族基因在地上和地下部位的表达模式, 利用高通量测序技术, 对白鼠尾草的根和叶进行了表达谱测序。基于表达谱数据, 对白鼠尾草2-ODD基因的表达模式进行分析(图 6), 发现绝大多数2-ODD基因在根中的表达量明显高于叶中的表达量; Sa2-ODD7、Sa2-ODD8、Sa2-ODD9、Sa2-ODD22、Sa2-ODD29、Sa2-ODD32和Sa2-ODD38基因在叶中表达量较高; Sa2-ODD11、Sa2-ODD23、Sa2-ODD27和Sa2-ODD34基因在根和叶中的表达量相当, 相较于其他基因, 这4个基因的表达量相对偏低。以上基因表达特征结果显示, Sa2-ODD基因家族中的成员可能参与了白鼠尾草不同代谢产物的调控, 并且其功能存在分化。
讨论
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2-ODD是一个庞大的基因家族, 拟南芥(Arabidopsis thaliana) 和丹参基因组中都包含超过130条2-ODD基因[11]。该家族成员在翻译后修饰、去甲基化、植物激素合成和特殊次生代谢产物生物合成过程中发挥着重要作用[8]。本研究从白鼠尾草转录组数据库中筛选获得39条具有完整结构的2-ODD基因家族成员, 其中6条属于DOXB亚家族, 提示它们可能与白鼠尾草响应信号肽类激素以及细胞壁形成有关; 33条属于DOXC亚家族, 提示白鼠尾草中的大部分2-ODD基因参与了该植物的次生代谢过程, 且可能参与了黄酮、生物碱和生长素类物质的代谢过程; 暂未发现DOXA亚家族成员, 这可能与转录组基因信息不如基因组信息全面有关。GO注释结果显示, 6条DOXB亚家族成员中的3条(Sa2-ODD1、Sa2-ODD2和Sa2-ODD5) 与细胞组分相关; 33条DOXC亚家族成员中, 有13条与分子功能相关, 4条与生物过程相关。这些结果进一步加强了白鼠尾草2-ODD基因功能的推测。
基于生物信息学方法, 对白鼠尾草中鉴定得到的2-ODD基因家族成员进行理化特性和序列特征分析。理化特性分析结果显示, 该家族基因编码氨基酸数量平均为320个氨基酸, 多为酸性和亲水性蛋白, 并且大多数基因所编码的蛋白定位在细胞质中, 这与大多数文献报道结果一致[16, 17]。序列相似性比较显示, 白鼠尾草2-ODD基因家族成员的序列保守性为16.52%~96.86%, 序列间差异较大, 这也与2-ODD基因文献[14, 15]报道一致。以上结果表明, 不同物种中的2-ODD基因在理化特性上具有较高的相似性, 但在基因序列上存在较大差异。
系统进化分析结果显示, F3H相关的基因被分成了3组, 分别在进化树的不同位置, 这与文献[11]报道中的聚类结果有所差异, 这可能与序列相似度以及参与进化树构建的基因数目不同有关。
通过表达谱分析发现, Sa2-ODD基因在根和叶中均有表达, 大多数Sa2-ODD基因(28个) 在根中表达量较高, 这与白鼠尾草根中丹参酮类物质积累较多的分布模式一致[5], 与丹参中丹参酮类物质的积累方式也相符, 进一步提示Sa2-ODD基因可能参与丹参酮类物质的合成。刘文超等[14]曾克隆得到丹参中的Sm2-ODD1基因, 该基因在丹参各个器官中都有表达, 但表达水平具有组织特异性, 根中表达量最高, 叶中表达量最低。Xu等[11]发现了丹参中与丹参酮IIA合成相关的一条Sm2-ODD基因(SMil_00012032, 图 5红色圆形标记), 通过进化树比较, 发现白鼠尾草中与该基因最接近的是Sa2-ODD23基因, 但是Sa2-ODD23基因在白鼠尾草根和叶中的表达量均较低, 且根和叶中的表达量没有差异(图 6)。Song等[6]通过进一步研究丹参中的2-ODD基因, 没有找到与SMil_00012032相近的基因, 研究者发现了丹参中与丹参酮IIA合成直接相关的Sm2-ODD14基因(SMil_00018668, 图 5红色三角形标记), 该基因具有催化呋喃环芳构化的作用, 能将隐丹参酮直接转变为丹参酮IIA, 且该基因在丹参根中的表达量明显高于叶中的表达量, 与丹参酮IIA的分布规律一致。通过进化树分析, 发现白鼠尾草中与该基因最接近的是Sa2-ODD21基因, Sa2-ODD21基因的表达模式与Sm2-ODD14一致, 均是根中的表达量明显高于叶中的表达量(图 6), 而且白鼠尾草中丹参酮IIA的积累也是地下部分明显多于地上部分[5]。由此推测, Sa2-ODD21基因可能与白鼠尾草中丹参酮IIA的生物合成有关, 值得进一步研究关注。综上所述, 本研究可为深入挖掘白鼠尾草2-ODD基因的功能奠定基础。
作者贡献: 秦晓静负责数据分析和文章撰写; 胡佳栋负责样品采集和转录组测序; 房振西参与数据分析; 陈万生负责实验统筹和论文审阅; 李卿负责实验设计、指导和论文修改。
利益冲突: 所有作者均声明不存在利益冲突。
基金
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  • 国家自然科学基金项目(32070327)
  • 国家自然科学基金项目(31770329)
  • 国家重点研发计划项目(2019YFC1711100)
文献
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2022年第57卷第12期
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doi: 10.16438/j.0513-4870.2022-0648
  • 接收时间：2022-05-26
  • 首发时间：2025-12-24
  • 出版时间：2022-12-12
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  • 收稿日期：2022-05-26
  • 修回日期：2022-06-15
基金
国家自然科学基金项目(32070327)
国家自然科学基金项目(31770329)
国家重点研发计划项目(2019YFC1711100)
作者信息
    1.上海中医药大学中药研究所, 中药资源与生物技术中心, 上海 201203
    2.中国人民解放军海军军医大学第二附属医院, 药剂科, 上海 200003

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2种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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