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Article(id=1276204297578746707, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1276204178091413862, articleNumber=null, orderNo=null, doi=10.3969/j.issn.1000-2561.2024.12.002, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1720368000000, receivedDateStr=2024-07-08, revisedDate=1722268800000, revisedDateStr=2024-07-30, acceptedDate=null, acceptedDateStr=null, onlineDate=1782200415271, onlineDateStr=2026-06-23, pubDate=1735056000000, pubDateStr=2024-12-25, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1782200415271, onlineIssueDateStr=2026-06-23, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1782200415271, creator=13701087609, updateTime=1782200415271, updator=13701087609, issue=Issue{id=1276204178091413862, tenantId=1146029695717560320, journalId=1235980609244409860, year='2024', volume='45', issue='12', pageStart='2487', pageEnd='2737', issueExtLink='null', onlineDate='null', pubDate='1735056000000', pubDateStr='2024-12-25', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1782200386783, creator='13701087609', updateTime=1782200456354, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1276204470308565242, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1276204178091413862, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1276204470308565243, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1276204178091413862, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=2500, endPage=2514, ext={EN=ArticleExt(id=1276204297947845461, articleId=1276204297578746707, tenantId=1146029695717560320, journalId=1235980609244409860, language=EN, title=Identification and Bioinformatics Analysis of Mango Peroxidase Gene Family, columnId=1236256430337085821, journalTitle=Chinese Journal of Tropical Crops, columnName=Omics & Biotechnology, runingTitle=null, highlight=null, articleAbstract=

Plant peroxidase (POD) plays a role in plant development, hormone signaling, and stress response, but there are few research reports on the POD gene in mango. This study used mango genome data as a reference and employed bioinformatics methods to identify members of the POD gene family from multiple aspects, including protein characteristics, phylogenetic relationships, gene structure, promoter cis acting elements, and gene expression patterns. The expression patterns of POD gene family members under enhanced UV-B irradiation through transcriptome and quantitative real-time PCR (qPCR) experiments were analyzed. The mango POD (MiPOD) gene family had a total of 77 family members, and the genes were then mapped to 17 chromosomes and 2 scaffolds, encoding amino acids with a number of 206~500 aa, Stable proteins were accountted for the majority, most of them were hydrophilic proteins. Most MiPOD were predicted to localize in subcellular within chloroplasts, and classified into seven subgroups using phylogenetic analysis. The gene structure among members of the subgroup were similar. The results of collinearity analysis indicated that the proportion of MiPOD genes involved in segmental duplication was relatively high. It was speculated that it may be related to the expansion of the MiPOD family. The selection pressure analysis indicated that the Ka/Ks values of collinear genes were far less than 1, indicating that MiPODs may be mainly subjected to purifying selection during the evolutionary process. The MiPODs promoter region contained a large number of light responsive, hormone responsive, and stress responsive elements. MiPOD had different expression patterns, which may be related to its different protein functions. MiPOD exhibited different expression patterns during fruit growth and development under enhanced UV-B irradiation, with only MiPOD7 showing significant differences in expression levels among the highly expressed members. MiPOD7 expression levels were significantly higher than those of the control under UV-B stress, suggesting that it may play an important role in the response of mango fruit to UV-B stress. In summary, members of the MiPOD gene family may have evolved through segmental duplication and intron reduction patterns, and perform different functions by sensing different types of signals, thus forming different expression patterns. This research would lay the foundation for further studying the response mechanism of mango POD genes to different signals.

, authors=null, authorsList=Shaopu SHI, Minjie QIAN, Kaibing ZHOU, authorCompany=null, correspAuthors=Kaibing ZHOU, authorNote=null, correspAuthorsNote=null, copyrightStatement=null, 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, fund=null), CN=ArticleExt(id=1276204303085867879, articleId=1276204297578746707, tenantId=1146029695717560320, journalId=1235980609244409860, language=CN, title=杧果过氧化物酶基因家族鉴定与生物信息学分析, columnId=1236256430517440904, journalTitle=热带作物学报, columnName=组学与生物技术, runingTitle=null, highlight=null, articleAbstract=

植物过氧化物酶（POD）参与植物发育、激素信号传导和响应胁迫，但鲜见杧果POD基因的研究报道。本研究以杧果基因组数据为参考，利用生物信息学方法从蛋白质特性、系统进化关系、基因结构、启动子顺式作用元件、基因表达模式等多个方面鉴定POD基因家族成员，通过转录组和实时荧光定量PCR分析POD基因家族成员在增强UV-B照射下的表达模式。杧果POD（MiPOD）基因家族共有77个家族成员，分布于20条染色体与2个碎片片段中，其编码的氨基酸数量为206~500 aa，稳定蛋白占多数，大部分为亲水性蛋白；预测大部分MiPOD亚细胞定位于叶绿体内；根据进化关系分为7个亚组，亚组成员间的基因结构相似；共线性分析结果表明，MiPOD基因参与片段复制的比例较高，推测其可能与MiPOD家族的扩张有关；选择压分析结果表明，共线性基因Ka/Ks值均远小于1，说明MiPOD在进化过程中可能主要受到纯化选择作用；MiPOD基因的启动区域包含大量光响应、激素响应与逆境响应元件；MiPOD在增强UV-B照射下的果实生长发育过程中具有不同的表达模式，其中高表达成员仅MiPOD7的表达量存在显著差异，MiPOD7在UV-B胁迫下的表达量显著高于对照，推测可能在杧果果实响应UV-B胁迫中发挥重要作用。综上所述，MiPOD基因家族成员可能通过片段复制和内含子减少模式进化，并通过感受不同种类的信号而行使不同的功能，从而形成不同的表达模式。本研究为进一步研究杧果POD基因对不同信号的响应机制奠定基础。

, authors=

施绍璞（1999—），男，硕士研究生，研究方向：热带果树生理与栽培。

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* 周开兵（ZHOU Kaibing），E-mail：。
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2.海南大学热带农林学院，海南海口　570228, bio={"content":"

施绍璞（1999—），男，硕士研究生，研究方向：热带果树生理与栽培。

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施绍璞（1999—），男，硕士研究生，研究方向：热带果树生理与栽培。

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figureFileBig=yHOrhKuVfpn4pb3dm0MAxg==, tableContent=null), ArticleFig(id=1276204320567726997, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276204297578746707, language=CN, label=图7, caption=杧果POD基因在果肉不同时期的表达模式, figureFileSmall=9J9vi/rQDoU2VcJVYE9Jfg==, figureFileBig=yHOrhKuVfpn4pb3dm0MAxg==, tableContent=null), ArticleFig(id=1276204320643224470, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276204297578746707, language=EN, label=Fig. 8, caption=qPCR validation of MiPOD4, MiPOD7 and MiPOD63 genes, figureFileSmall=346BQOk1hGrgJhKDVddoJg==, figureFileBig=kjAl/RHOAdqKyIsUSpJcwg==, tableContent=null), ArticleFig(id=1276204320991351703, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276204297578746707, language=CN, label=图8, caption=MiPOD4、MiPOD7、MiPOD63基因的qPCR验证, figureFileSmall=346BQOk1hGrgJhKDVddoJg==, figureFileBig=kjAl/RHOAdqKyIsUSpJcwg==, tableContent=null), ArticleFig(id=1276204321083626392, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276204297578746707, language=EN, label=Tab. 1, caption=

Primer sequences of mango MiPOD and reference genes

, figureFileSmall=null, figureFileBig=null, tableContent=
基因名称Gene name上游引物序列（5′-3′）Forward primer sequence (5′-3′)下游引物序列（5′-3′）Reverse primer sequence (5′-3′)
MiPOD4TGGAGCTGATGCGCTGAGAGGAGTCCTGCTGCGAGA
MiPOD7GGCGATGAAGACCCGTCTACTCCCGGGGTCCATCTC
MiPOD63AGGGGGTCCAACTTGGGAGGGGCAGGCAAGCTTGTA
Actin7ATCTGCTGGAAGGTGCTGAGCCAAGCAGCATGAAGATCAA
), ArticleFig(id=1276204321142346649, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276204297578746707, language=CN, label=表1, caption=

杧果MiPOD及内参基因引物序列

, figureFileSmall=null, figureFileBig=null, tableContent=
基因名称Gene name上游引物序列（5′-3′）Forward primer sequence (5′-3′)下游引物序列（5′-3′）Reverse primer sequence (5′-3′)
MiPOD4TGGAGCTGATGCGCTGAGAGGAGTCCTGCTGCGAGA
MiPOD7GGCGATGAAGACCCGTCTACTCCCGGGGTCCATCTC
MiPOD63AGGGGGTCCAACTTGGGAGGGGCAGGCAAGCTTGTA
Actin7ATCTGCTGGAAGGTGCTGAGCCAAGCAGCATGAAGATCAA
), ArticleFig(id=1276204321452725146, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276204297578746707, language=EN, label=Tab. 2, caption=

Basic information of MiPOD proteins

, figureFileSmall=null, figureFileBig=null, tableContent=
基因Gene基因编号Gene ID氨基酸长度Amino acids lengh/aa分子量Mw/Da等电点pI不稳定系数Instability index脂肪系数Aliphatic index平均亲水系数GRAVY亚细胞定位Subcellular localization
MiPOD1LOC123210304.133236 686.969.1632.7783.40-0.201chlo
MiPOD2LOC123192310.131935 234.339.0336.8986.87-0.187vacu
MiPOD3LOC123205166.131934 318.339.1930.1489.660.001extr
MiPOD4LOC123213782.131634 590.355.6434.8877.18-0.156extr
MiPOD5LOC123199508.129832 410.859.0647.6683.15-0.159chlo
MiPOD6LOC123218004.134437 771.418.6944.8883.08-0.128extr
MiPOD7LOC123195912.132735 848.816.5339.2285.90-0.098chlo
MiPOD8LOC123198670.132736 320.705.2244.2789.11-0.081chlo
MiPOD9LOC123198727.132635 747.829.4950.3581.41-0.278extr
MiPOD10LOC123230089.134537 469.958.3434.6591.33-0.032extr
MiPOD11LOC123192273.130833 044.479.4233.1481.72-0.147chlo
MiPOD12LOC123229404.132434 440.879.0741.6178.64-0.113chlo
MiPOD13LOC123206033.131934 372.018.6537.4386.65-0.047extr
MiPOD14LOC123202461.131935 009.118.0740.1794.8-0.056extr
MiPOD15LOC123218182.132937 249.808.3447.1785.65-0.332extr
MiPOD16LOC123226583.132735 820.148.7240.0686.79-0.056mito
MiPOD17LOC123207067.131834 336.338.3952.4488.400.001plas
MiPOD18LOC123198011.135439 089.838.6741.6694.52-0.11chlo
MiPOD19LOC123193658.131935 255.278.3540.7085.92-0.195chlo
MiPOD20LOC123203066.131834 354.368.3952.8387.17-0.007plas
MiPOD21LOC123197035.132735 701.978.9630.6387.98-0.067extr
MiPOD22LOC123214042.133236 813.309.4755.5680.84-0.255chlo
MiPOD23LOC123219743.136440 631.725.1231.0083.35-0.332extr
MiPOD24LOC123202454.132735 444.228.3842.3279.88-0.133chlo
MiPOD25LOC123222918.131633 806.128.8143.6085.03-0.011chlo
MiPOD26LOC123219578.150053 555.214.9056.3985.08-0.048chlo
MiPOD27LOC123198397.133137 024.188.5240.9882.27-0.207chlo
MiPOD28LOC123206675.136240 143.476.0747.0485.41-0.235vacu
MiPOD29LOC123216573.132435 850.024.8738.9485.46-0.109extr
MiPOD30LOC123225298.136240 258.656.2247.1185.41-0.235vacu
MiPOD31LOC123199034.132635 561.026.3132.4777.82-0.207chlo
MiPOD32LOC123192578.131934 991.908.5135.8785.36-0.176chlo
MiPOD33LOC123209793.131733 970.844.4038.4889.56-0.071chlo
MiPOD34LOC123227058.132635 337.805.5135.1289.23-0.049extr
MiPOD35LOC123209542.131733 850.524.2537.2886.47-0.074plas
MiPOD36LOC123209512.131934 329.409.5131.8786.58-0.048vacu
MiPOD37LOC123214866.133837 559.815.0330.4892.010.001chlo
MiPOD38LOC123202443.131935 008.016.9932.4592.66-0.066chlo
MiPOD39LOC123229397.132434 302.518.7441.1778.95-0.127chlo
MiPOD40LOC123212289.133136 322.445.7737.5984.26-0.139extr
MiPOD41LOC123218050.132034 294.189.5732.2383.81-0.155chlo
MiPOD42LOC123223873.233337 489.886.2642.8094.26-0.157cyto
MiPOD43LOC123209747.132735 655.417.5438.7087.03-0.116chlo
MiPOD44LOC123209501.131934 287.319.2630.9889.970.009extr
MiPOD45LOC123206024.131934 350.219.3536.3587.55-0.066extr
MiPOD46LOC123199152.129531 997.359.3347.9383.02-0.221chlo
MiPOD47LOC123205164.131934 485.529.1031.2486.02-0.01extr
MiPOD48LOC123229388.132434 240.368.0842.2479.23-0.095chlo
MiPOD49LOC123227347.133635 268.254.9042.0082.530.038chlo
MiPOD50LOC123209792.134637 468.455.1630.4189.340.01plas
MiPOD51LOC123195865.132635 226.116.2036.1581.10-0.001chlo
MiPOD52LOC123194338.132636 009.088.9733.5883.50-0.185E.R.
MiPOD53LOC123207412.136339 765.769.4229.0880.08-0.282vacu
MiPOD54LOC123208596.132735 713.386.2142.6685.26-0.121chlo
MiPOD55LOC123228403.133336 304.475.8340.9988.500.007chlo
MiPOD56LOC123204277.133236 542.95.8037.0885.54-0.039extr
MiPOD57LOC123220857.121624 005.279.6456.4676.30-0.512chlo
MiPOD58LOC123203600.132334 745.635.2038.2294.490.051chlo
MiPOD59LOC123220169.133636 101.694.5045.2492.08-0.009extr
MiPOD60LOC123201256.131935 120.137.0332.9192.66-0.087chlo
MiPOD61LOC123200207.131934 323.39.2629.1887.84-0.009extr
MiPOD62LOC123224408.132435 668.169.1432.6386.14-0.113extr
MiPOD63LOC123209320.131334 095.89.0742.4981.98-0.18extr
MiPOD64LOC123198833.133236 254.845.5933.9480.78-0.162extr
MiPOD65LOC123217588.133036 050.655.8331.90103.730.212extr
MiPOD66LOC123196052.132635 493.485.6938.0484.69-0.002plas
MiPOD67LOC123220530.132235 430.78.7838.9386.02-0.089chlo
MiPOD68LOC123221202.125828 599.135.6334.3079.73-0.416nucl
MiPOD69LOC123209791.134636 809.024.3327.2188.530.008vacu
MiPOD70LOC123200306.233235 716.645.4538.0890.720.133chlo
MiPOD71LOC123193664.132837 120.658.3346.6688.29-0.331cyto
MiPOD72LOC123217656.133837 121.35.5433.7589.440.033chlo
MiPOD73LOC123208597.133337 293.849.1335.9183.42-0.295chlo
MiPOD74LOC123216867.132434 362.678.7446.0778.64-0.102chlo
MiPOD75LOC123202551.137040 646.185.7345.0387.57-0.173E.R.
MiPOD76LOC123210958.132836 885.55.3140.0582.59-0.362chlo
MiPOD77LOC123216420.133736 331.728.9634.0087.42-0.025chlo
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MiPOD蛋白基本信息

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基因Gene基因编号Gene ID氨基酸长度Amino acids lengh/aa分子量Mw/Da等电点pI不稳定系数Instability index脂肪系数Aliphatic index平均亲水系数GRAVY亚细胞定位Subcellular localization
MiPOD1LOC123210304.133236 686.969.1632.7783.40-0.201chlo
MiPOD2LOC123192310.131935 234.339.0336.8986.87-0.187vacu
MiPOD3LOC123205166.131934 318.339.1930.1489.660.001extr
MiPOD4LOC123213782.131634 590.355.6434.8877.18-0.156extr
MiPOD5LOC123199508.129832 410.859.0647.6683.15-0.159chlo
MiPOD6LOC123218004.134437 771.418.6944.8883.08-0.128extr
MiPOD7LOC123195912.132735 848.816.5339.2285.90-0.098chlo
MiPOD8LOC123198670.132736 320.705.2244.2789.11-0.081chlo
MiPOD9LOC123198727.132635 747.829.4950.3581.41-0.278extr
MiPOD10LOC123230089.134537 469.958.3434.6591.33-0.032extr
MiPOD11LOC123192273.130833 044.479.4233.1481.72-0.147chlo
MiPOD12LOC123229404.132434 440.879.0741.6178.64-0.113chlo
MiPOD13LOC123206033.131934 372.018.6537.4386.65-0.047extr
MiPOD14LOC123202461.131935 009.118.0740.1794.8-0.056extr
MiPOD15LOC123218182.132937 249.808.3447.1785.65-0.332extr
MiPOD16LOC123226583.132735 820.148.7240.0686.79-0.056mito
MiPOD17LOC123207067.131834 336.338.3952.4488.400.001plas
MiPOD18LOC123198011.135439 089.838.6741.6694.52-0.11chlo
MiPOD19LOC123193658.131935 255.278.3540.7085.92-0.195chlo
MiPOD20LOC123203066.131834 354.368.3952.8387.17-0.007plas
MiPOD21LOC123197035.132735 701.978.9630.6387.98-0.067extr
MiPOD22LOC123214042.133236 813.309.4755.5680.84-0.255chlo
MiPOD23LOC123219743.136440 631.725.1231.0083.35-0.332extr
MiPOD24LOC123202454.132735 444.228.3842.3279.88-0.133chlo
MiPOD25LOC123222918.131633 806.128.8143.6085.03-0.011chlo
MiPOD26LOC123219578.150053 555.214.9056.3985.08-0.048chlo
MiPOD27LOC123198397.133137 024.188.5240.9882.27-0.207chlo
MiPOD28LOC123206675.136240 143.476.0747.0485.41-0.235vacu
MiPOD29LOC123216573.132435 850.024.8738.9485.46-0.109extr
MiPOD30LOC123225298.136240 258.656.2247.1185.41-0.235vacu
MiPOD31LOC123199034.132635 561.026.3132.4777.82-0.207chlo
MiPOD32LOC123192578.131934 991.908.5135.8785.36-0.176chlo
MiPOD33LOC123209793.131733 970.844.4038.4889.56-0.071chlo
MiPOD34LOC123227058.132635 337.805.5135.1289.23-0.049extr
MiPOD35LOC123209542.131733 850.524.2537.2886.47-0.074plas
MiPOD36LOC123209512.131934 329.409.5131.8786.58-0.048vacu
MiPOD37LOC123214866.133837 559.815.0330.4892.010.001chlo
MiPOD38LOC123202443.131935 008.016.9932.4592.66-0.066chlo
MiPOD39LOC123229397.132434 302.518.7441.1778.95-0.127chlo
MiPOD40LOC123212289.133136 322.445.7737.5984.26-0.139extr
MiPOD41LOC123218050.132034 294.189.5732.2383.81-0.155chlo
MiPOD42LOC123223873.233337 489.886.2642.8094.26-0.157cyto
MiPOD43LOC123209747.132735 655.417.5438.7087.03-0.116chlo
MiPOD44LOC123209501.131934 287.319.2630.9889.970.009extr
MiPOD45LOC123206024.131934 350.219.3536.3587.55-0.066extr
MiPOD46LOC123199152.129531 997.359.3347.9383.02-0.221chlo
MiPOD47LOC123205164.131934 485.529.1031.2486.02-0.01extr
MiPOD48LOC123229388.132434 240.368.0842.2479.23-0.095chlo
MiPOD49LOC123227347.133635 268.254.9042.0082.530.038chlo
MiPOD50LOC123209792.134637 468.455.1630.4189.340.01plas
MiPOD51LOC123195865.132635 226.116.2036.1581.10-0.001chlo
MiPOD52LOC123194338.132636 009.088.9733.5883.50-0.185E.R.
MiPOD53LOC123207412.136339 765.769.4229.0880.08-0.282vacu
MiPOD54LOC123208596.132735 713.386.2142.6685.26-0.121chlo
MiPOD55LOC123228403.133336 304.475.8340.9988.500.007chlo
MiPOD56LOC123204277.133236 542.95.8037.0885.54-0.039extr
MiPOD57LOC123220857.121624 005.279.6456.4676.30-0.512chlo
MiPOD58LOC123203600.132334 745.635.2038.2294.490.051chlo
MiPOD59LOC123220169.133636 101.694.5045.2492.08-0.009extr
MiPOD60LOC123201256.131935 120.137.0332.9192.66-0.087chlo
MiPOD61LOC123200207.131934 323.39.2629.1887.84-0.009extr
MiPOD62LOC123224408.132435 668.169.1432.6386.14-0.113extr
MiPOD63LOC123209320.131334 095.89.0742.4981.98-0.18extr
MiPOD64LOC123198833.133236 254.845.5933.9480.78-0.162extr
MiPOD65LOC123217588.133036 050.655.8331.90103.730.212extr
MiPOD66LOC123196052.132635 493.485.6938.0484.69-0.002plas
MiPOD67LOC123220530.132235 430.78.7838.9386.02-0.089chlo
MiPOD68LOC123221202.125828 599.135.6334.3079.73-0.416nucl
MiPOD69LOC123209791.134636 809.024.3327.2188.530.008vacu
MiPOD70LOC123200306.233235 716.645.4538.0890.720.133chlo
MiPOD71LOC123193664.132837 120.658.3346.6688.29-0.331cyto
MiPOD72LOC123217656.133837 121.35.5433.7589.440.033chlo
MiPOD73LOC123208597.133337 293.849.1335.9183.42-0.295chlo
MiPOD74LOC123216867.132434 362.678.7446.0778.64-0.102chlo
MiPOD75LOC123202551.137040 646.185.7345.0387.57-0.173E.R.
MiPOD76LOC123210958.132836 885.55.3140.0582.59-0.362chlo
MiPOD77LOC123216420.133736 331.728.9634.0087.42-0.025chlo
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Ka and Ks analysis of POD replication gene pairs in M. indica L.

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同源基因对Homologous gene pairsKaKsKa/Ks同源基因对Homologous gene pairsKaKsKa/Ks
MiPOD1-MiPOD640.110 485 6960.396 608 7900.278 576 015MiPOD62-MiPOD210.177 426 9290.867 003 8150.204 643 770
MiPOD29-MiPOD80.062 280 7820.446 430 7810.139 508 261MiPOD71-MiPOD210.678 326 9073.459 458 0930.196 078 949
MiPOD22-MiPOD90.059 334 4560.501 415 7050.118 333 860MiPOD40-MiPOD270.403 654 0552.424 788 8440.166 469 776
MiPOD10-MiPOD90.280 094 0782.698 917 6120.103 780 151MiPOD30-MiPOD280.003 627 5770.007 822 7570.463 721 005
MiPOD22-MiPOD100.296 061 575--MiPOD55-MiPOD310.265 556 5681.557 210 9100.170 533 463
MiPOD74-MiPOD110.307 184 8822.333 449 1920.131 644 127MiPOD32-MiPOD380.099 218 2970.419 437 7680.236 550 697
MiPOD41-MiPOD110.207 223 8741.814 371 5180.114 212 482MiPOD74-MiPOD340.314 930 444--
MiPOD34-MiPOD110.335 617 419--MiPOD41-MiPOD340.318 098 4263.253 800 0020.097 762 132
MiPOD15-MiPOD710.020 716 3190.211 246 5210.098 067 029MiPOD37-MiPOD720.075 223 3310.345 009 4160.218 032 690
MiPOD43-MiPOD160.118 546 6680.372 057 2510.318 624 802MiPOD40-MiPOD560.128 669 0610.677 209 4510.189 998 915
MiPOD16-MiPOD490.427 998 9852.465 920 9390.173 565 575MiPOD74-MiPOD410.291 442 294--
MiPOD20-MiPOD170.001 375 201--MiPOD43-MiPOD490.414 263 4533.461 702 5320.119 670 437
MiPOD63-MiPOD200.236 277 5712.819 182 5290.083 810 668MiPOD62-MiPOD710.706 101 1342.213 947 2380.318 933 135
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杧果POD复制基因对的Ka、Ks分析

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同源基因对Homologous gene pairsKaKsKa/Ks同源基因对Homologous gene pairsKaKsKa/Ks
MiPOD1-MiPOD640.110 485 6960.396 608 7900.278 576 015MiPOD62-MiPOD210.177 426 9290.867 003 8150.204 643 770
MiPOD29-MiPOD80.062 280 7820.446 430 7810.139 508 261MiPOD71-MiPOD210.678 326 9073.459 458 0930.196 078 949
MiPOD22-MiPOD90.059 334 4560.501 415 7050.118 333 860MiPOD40-MiPOD270.403 654 0552.424 788 8440.166 469 776
MiPOD10-MiPOD90.280 094 0782.698 917 6120.103 780 151MiPOD30-MiPOD280.003 627 5770.007 822 7570.463 721 005
MiPOD22-MiPOD100.296 061 575--MiPOD55-MiPOD310.265 556 5681.557 210 9100.170 533 463
MiPOD74-MiPOD110.307 184 8822.333 449 1920.131 644 127MiPOD32-MiPOD380.099 218 2970.419 437 7680.236 550 697
MiPOD41-MiPOD110.207 223 8741.814 371 5180.114 212 482MiPOD74-MiPOD340.314 930 444--
MiPOD34-MiPOD110.335 617 419--MiPOD41-MiPOD340.318 098 4263.253 800 0020.097 762 132
MiPOD15-MiPOD710.020 716 3190.211 246 5210.098 067 029MiPOD37-MiPOD720.075 223 3310.345 009 4160.218 032 690
MiPOD43-MiPOD160.118 546 6680.372 057 2510.318 624 802MiPOD40-MiPOD560.128 669 0610.677 209 4510.189 998 915
MiPOD16-MiPOD490.427 998 9852.465 920 9390.173 565 575MiPOD74-MiPOD410.291 442 294--
MiPOD20-MiPOD170.001 375 201--MiPOD43-MiPOD490.414 263 4533.461 702 5320.119 670 437
MiPOD63-MiPOD200.236 277 5712.819 182 5290.083 810 668MiPOD62-MiPOD710.706 101 1342.213 947 2380.318 933 135
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杧果过氧化物酶基因家族鉴定与生物信息学分析
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施绍璞 1, 2 , 钱敏杰 1, 2 , 周开兵 1, 2, *
热带作物学报 | 组学与生物技术 2024,45(12): 2500-2514
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热带作物学报 |组学与生物技术 2024 , 45 (12) : 2500 -2514
杧果过氧化物酶基因家族鉴定与生物信息学分析
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施绍璞1, 2, 钱敏杰1, 2, 周开兵1, 2, *
作者信息
  • 1.海南大学三亚南繁研究院，海南三亚　572025
  • 2.海南大学热带农林学院，海南海口　570228
通讯作者:
* 周开兵（ZHOU Kaibing），E-mail：。
Identification and Bioinformatics Analysis of Mango Peroxidase Gene Family
Shaopu SHI1, 2, Minjie QIAN1, 2, Kaibing ZHOU1, 2, *
Affiliations
  • 1.Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, Hainan 572025, China
  • 2.Tropical Agriculture and Forestry College, Hainan University, Haikou, Hainan 570228, China
出版时间: 2024-12-25 doi: 10.3969/j.issn.1000-2561.2024.12.002
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植物过氧化物酶（POD）参与植物发育、激素信号传导和响应胁迫，但鲜见杧果POD基因的研究报道。本研究以杧果基因组数据为参考，利用生物信息学方法从蛋白质特性、系统进化关系、基因结构、启动子顺式作用元件、基因表达模式等多个方面鉴定POD基因家族成员，通过转录组和实时荧光定量PCR分析POD基因家族成员在增强UV-B照射下的表达模式。杧果POD（MiPOD）基因家族共有77个家族成员，分布于20条染色体与2个碎片片段中，其编码的氨基酸数量为206~500 aa，稳定蛋白占多数，大部分为亲水性蛋白；预测大部分MiPOD亚细胞定位于叶绿体内；根据进化关系分为7个亚组，亚组成员间的基因结构相似；共线性分析结果表明，MiPOD基因参与片段复制的比例较高，推测其可能与MiPOD家族的扩张有关；选择压分析结果表明，共线性基因Ka/Ks值均远小于1，说明MiPOD在进化过程中可能主要受到纯化选择作用；MiPOD基因的启动区域包含大量光响应、激素响应与逆境响应元件；MiPOD在增强UV-B照射下的果实生长发育过程中具有不同的表达模式，其中高表达成员仅MiPOD7的表达量存在显著差异，MiPOD7在UV-B胁迫下的表达量显著高于对照，推测可能在杧果果实响应UV-B胁迫中发挥重要作用。综上所述，MiPOD基因家族成员可能通过片段复制和内含子减少模式进化，并通过感受不同种类的信号而行使不同的功能，从而形成不同的表达模式。本研究为进一步研究杧果POD基因对不同信号的响应机制奠定基础。

杧果  /  POD基因家族  /  生物信息学分析

Plant peroxidase (POD) plays a role in plant development, hormone signaling, and stress response, but there are few research reports on the POD gene in mango. This study used mango genome data as a reference and employed bioinformatics methods to identify members of the POD gene family from multiple aspects, including protein characteristics, phylogenetic relationships, gene structure, promoter cis acting elements, and gene expression patterns. The expression patterns of POD gene family members under enhanced UV-B irradiation through transcriptome and quantitative real-time PCR (qPCR) experiments were analyzed. The mango POD (MiPOD) gene family had a total of 77 family members, and the genes were then mapped to 17 chromosomes and 2 scaffolds, encoding amino acids with a number of 206~500 aa, Stable proteins were accountted for the majority, most of them were hydrophilic proteins. Most MiPOD were predicted to localize in subcellular within chloroplasts, and classified into seven subgroups using phylogenetic analysis. The gene structure among members of the subgroup were similar. The results of collinearity analysis indicated that the proportion of MiPOD genes involved in segmental duplication was relatively high. It was speculated that it may be related to the expansion of the MiPOD family. The selection pressure analysis indicated that the Ka/Ks values of collinear genes were far less than 1, indicating that MiPODs may be mainly subjected to purifying selection during the evolutionary process. The MiPODs promoter region contained a large number of light responsive, hormone responsive, and stress responsive elements. MiPOD had different expression patterns, which may be related to its different protein functions. MiPOD exhibited different expression patterns during fruit growth and development under enhanced UV-B irradiation, with only MiPOD7 showing significant differences in expression levels among the highly expressed members. MiPOD7 expression levels were significantly higher than those of the control under UV-B stress, suggesting that it may play an important role in the response of mango fruit to UV-B stress. In summary, members of the MiPOD gene family may have evolved through segmental duplication and intron reduction patterns, and perform different functions by sensing different types of signals, thus forming different expression patterns. This research would lay the foundation for further studying the response mechanism of mango POD genes to different signals.

mango  /  POD gene family  /  bioinformatics analysis
施绍璞, 钱敏杰, 周开兵. 杧果过氧化物酶基因家族鉴定与生物信息学分析. 热带作物学报, 2024 , 45 (12) : 2500 -2514 . DOI: 10.3969/j.issn.1000-2561.2024.12.002
Shaopu SHI, Minjie QIAN, Kaibing ZHOU. Identification and Bioinformatics Analysis of Mango Peroxidase Gene Family[J]. Chinese Journal of Tropical Crops, 2024 , 45 (12) : 2500 -2514 . DOI: 10.3969/j.issn.1000-2561.2024.12.002
正文
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过氧化物酶（EC 1.11.1.X，POD）可以定义为通过将过氧化氢还原为水来催化各种底物氧化的酶。根据辅基的种类不同，这些蛋白质可分为血红素酶或非血红素酶。大多数血红素POD属于两大家族：动物POD和非动物POD[1]。非动物POD超家族可分为Ⅰ、Ⅱ和Ⅲ类，即细菌POD（Ⅰ类）、分泌性POD（Ⅱ类）和分泌性植物POD（Ⅲ类）[2]。
Ⅲ类POD作为植物特异性氧化还原酶，其功能众多，参与木质化、细胞伸长、种子萌发和胁迫防御[3-4]，Ⅲ类POD几乎参与了植物生长发育的各个环节。在介导木质合成方面，拟南芥缺失AtPRX2和AtPRX25的突变体的总木质素含量显著降低，AtPRX2、AtPRX25和AtPRX71的缺失甚至引发了木质素结构的改变[5]，对AtPRX71功能的进一步探究发现，AtPRX71有助于加强细胞壁，从而限制细胞的生长[6]；杨树组织内木质素含量随着Ⅲ类POD的CWPO-C基因表达量的改变而变化，抑制CWPO-C的表达，杨树中木质素含量降低了约45%[7]。在调节青蒿素合成方面，除了发现了与青蒿素含量变化呈正相关的POD基因Aa528和Aa540，也发现了对青蒿素含量负向调节的POD基因Aa547，但Aa547的表达量与木质素含量正向相关[8]。拟南芥PRX2、PRX8、PRX35和PRX73正向调节拟南芥根的伸长与营养生长[9]；小麦中的一个Ⅲ类POD基因TaPer12-3A参与了小麦的萌发与休眠；TaPer12-3A参与赤霉酸和脱落酸的生物合成和分解代谢途径，其表达量的下降促进了小麦种子的休眠，上调表达促进小麦的发芽[10]。
植物遭受生物胁迫与非生物胁迫时，POD基因会被诱导表达，参与植物胁迫响应。73个已鉴定的拟南芥Ⅲ类POD，有38.4%的基因参与了逆境胁迫的响应过程[11-12]，例如AtPrx64在铝胁迫中上调表达，增强植株对铝胁迫的耐受性[13]；当杨树受到病原体感染时，PdePrx12的表达受到抑制，导致H2O2含量增加，从而增强抗病性[14]；过表达CsPrx25重新构建植株的ROS平衡，提高过氧化氢含量，并促进细胞壁木质素积累，从而增强了柑橘对溃疡病的抗性水平[15]；在水稻中，抑制OsPrx30的表达有助于提高对细菌性枯萎病的抗性[16]；过表达GsPOD40增强了大豆植株的抗旱性，其在干旱胁迫下表现出增强的光合作用和抗氧化酶活性，从而减轻ROS诱导的氧化损伤[17]；在小麦中TaPRX-2A在干旱胁迫与盐胁迫诱导下均呈现上调表达，过表达TaPRX-2A，相关过氧化酶活性上升，ROS含量与膜脂过氧化程度下降，提高了小麦对干旱与盐胁迫的抗性[18-19]。
杧果（Mangifera indica L.）为漆树科（Anacardiaceae R. Br.）杧果属果树，分布于90多个国家，在热带与亚热带地区栽培杧果具有重要的经济价值[20]，但生物胁迫与非生物胁迫都严重影响杧果的产量与品质。在干旱胁迫下，杧果叶片光合速率随干旱胁迫的程度加剧而下降[21]，果实的大小与果实的坐果率随着下降[22-24]；低温胁迫下的杧果叶片膜透性不断上升，叶片损伤明显，同时抑制叶片的光合作用，进而对果实品质与产量造成不利影响[25-26]；杧果果实在感病后导致的内源乙烯含量大幅上升，进而引起叶片、枝条、花序的畸形生长，造成大幅减产[27]；杧果果实组织中较低的抗氧化酶活性易导致芒果果肉中形成“海绵组织”而影响品质，使杧果果实失去商品价值[28]；在模拟增强UV-B照射下，杧果果实的品质下降，果肉细胞的膜脂过氧化加剧，同时在处理前期增强了POD的酶活性[29]。由于POD基因家族Ⅲ类成员的表达在芒果遭遇上述逆境时发挥着重要的主动防御作用，因此，系统鉴定和分析杧果POD基因家族Ⅲ类成员将为杧果抗逆生理机制与抗逆品种选育等研究奠定基础。
1　材料与方法
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1.1　材料
实验地点为海南省三亚市海棠区升昌村芒果园，杧果园年平均降水量约1700 mm，年平均气温约25 ℃，花园土壤为砖砂土。选择10棵生长稳定茁壮的成熟台农1号杧果树作为试验材料。实验组于距树冠40 cm高度处均匀交叉安装4个UV-B灯，人工模拟光照强度为96 J/(m2·d)的增强UV-B照射处理，对照组为自然光照射。单株小区，重复5次。选择2023年花后30、50、91 d进行取样，在每棵树的中部外围四周选择5个大小一致且适中的果实作为取样果，取完样后及时放入液氮中速冻，带回实验室于超低温冰箱（–80 ℃）中保存备用。
杧果（Mangifera indica L.）基因组及注释数据下载于NCBI（https://www.ncbi.nlm.nih.gov/datasets/taxonomy/29780/）数据库，拟南芥[Arabidopsis thaliana (L.) Heynh.] POD（AtPOD）基因家族序列下载于tair（https://www.arabidopsis.org/）数据库。
1.2　方法
1.2.1　杧果POD基因家族成员鉴定
以AtPOD基因家族成员蛋白序列作为参考，利用TBtools软件，运行本地Blast，与杧果蛋白序列进行比对检索，得到103条蛋白序列，将其作为杧果过氧化物酶（MiPOD）候选序列。登录NCBI数据库，利用在线工具NCBI blastp（https://blast.ncbi.nlm.nih.gov/Blast.cgi），以Swiss-Prot数据库（http://www.gpmaw.com/html/swissprot.html）作为参考，对MiPOD候选序列进行比对，去除多余基因。利用InterPro（https://www.ebi.ac.uk/interpro/）和NCBI batch wab CD-search tool（https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi）在线分析工具，与已知POD保守结构域（PF00141）进行比对，剔除保守结构域不相符的基因，从而获得正确的MiPOD基因家族成员，并对已筛选出的基因进行重命名。
1.2.2　蛋白质特性分析
利用在线工具ProtParam（http://web.expasy.org/protparam/）预测MiPOD蛋白特性，包括氨基酸数、分子量（MW）、等电点（pI）等，利用WoLF PSORT软件（https://wolfpsort.hgc.jp/）进行亚细胞定位预测。
1.2.3　杧果POD家族基因结构和保守结构域分析
将筛选后MiPOD蛋白序列提交到NCBI batch wab CD-search tool（https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi）进行保守结构域分析，使用MEME（https://meme-suite.org/meme/tools/meme）在线工具分析MiPOD蛋白的保守基序，设置分析motif数值为6；利用Tbtools软件进行可视化处理。
1.2.4　MiPOD蛋白系统发育树的构建
使用MEGA 11软件，以neighbor-joining（NJ）方法创建MiPOD蛋白序列的系统发育树，Bootstrap值为1000。
1.2.5　MiPOD基因家族启动子顺式作用元件分析及功能预测
根据杧果基因组序列信息，利用TBtools软件提取MiPOD基因家族序列上游长度为2000 bp的启动子序列，并将其上传到PlantCARE（http://bioinformatics.psb.ugent.be/webtools/plantcare/html/）进行预测分析，通过TBtools软件进行可视化处理。
1.2.6　染色体分布和物种内共线性、选择压分析
使用TBtools软件进行杧果物种内共线性分析。利用杧果全基因组注释信息获取所有基因密度信息和MiPOD家族成员在染色上的位置，使用基因组全序列文件，计算染色体GC值与gap位置，使用自然梯度（natural gradient descent, NG）法计算同源基因对的Ka和Ks值，并进行选择压分析。
1.2.7　 MiPOD家族成员的表达模式分析
根据本实验室所测的杧果转录组数据，提取花后30、50、91 d果肉的RNA进行转录组测序，每个时期各3个生物学重复。RNA经纯化并检验合格后建立cDNA文库。库检合格后，不同文库按照目标下机数据量进行pooling，使用Illumina平台进行测序。将测序后的原始数据raw data过滤后得到clean reads，与参考基因组对比后，进行基因表达定量分析。差异基因的筛选条件为|log2Fold Change|>=1，且FDR<0.05。使用Clusters of Orthologous Groups of proteins（COG）、Kyoto Encyclopedia of Genes and Genomes（KEGG）、nonredundant protein sequences（NR）、SwissProt和Gene Ontology（GO）等5个主要数据库进行基因功能注释，并从中提取MiPOD基因的FPKM值，利用TBtools软件绘制基因在不同生长发育阶段的表达热图。选取MiPOD4、MiPOD7、MiPOD63进行qPCR分析，用Prime 3（https://bioinfo.ut.ee/primer3-0.4.0）在线工具设计qRT-PCR特异性引物（表1），由铂尚生物技术（上海）有限公司合成引物。使用SteadyPure植物RNA提取试剂盒（杭州艾科瑞生物科技有限公司）提取果肉RNA，使用Evo M-MLV反转录预混型试剂盒（杭州艾科瑞生物科技有限公司）完成逆转录，操作按照试剂盒说明书进行。用2×Q3 SYBR qPCR Master mix（Universal）（TOLOBIO）和德国耶拿的qTOWER3仪器进行qRT-PCR验证。使用2-ΔΔCt法计算基因的相对表达量。
2　结果与分析
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2.1　MiPOD基因家族成员鉴定及系统进化分析
利用AtPOD基因家族的氨基酸序列在杧果蛋白全序列中初步筛选出103条候选序列，通过NCBI数据库进行Blastp分析，结合保守结构域分析，去除不含PF00141与secretory_peroxidase结构域的序列后，最终获得77个MiPOD基因家族成员，命名为MiPOD1-77（表2）。
全部MiPOD家族成员编码氨基酸数量在206~500 aa之间，相对分子质量介于24 005.27~53 555.21 Da之间，等电点（pI）介于4.25~9.64之间，因而编码的肽链长度、大小和电离性质等差异明显。不稳定系数介于27.21~56.46之间，有44个成员不稳定系数小于40，属于稳定蛋白，其余33个成员属于不稳定蛋白。12个MiPOD的平均亲水系数大于0，属于疏水蛋白；其余家族成员的平均亲水系数均小于0，属于亲水性蛋白。37个MiPOD定位于叶绿体内，2个MiPOD定位于细胞质内，2个MiPOD定位于内质网内，23个MiPOD定位于细胞壁中，1个MiPOD定位于线粒体中，1个MiPOD定位于细胞核内，5个MiPOD定位于质膜上，另外6个MiPOD定位于液泡膜上。
基于NJ法构建MiPOD基因家族进化树（图1），该基因家族分为7亚组，将其命名为A~G组。A组中包含MiPOD77/58两个基因，B组包含MiPOD26/28/30/53/58/68六个基因，且A组与B组首先从进化树中分离出来。G组中包含的MiPOD家族成员最多，共有23个MiPOD基因；D组次之，共有17个MiPOD基因。A组的基因数量较之其他亚组的基因数量差距较大，说明杧果中存在多样化的POD家族，也可能是杧果在进化过程中存在基因丢失。
2.2　 MiPOD基因结构、保守基序及保守结构域分析
基因结构可视化分析结果如图2所示。MiPOD基因家族成员所含外显子与内含子的数量并不均一，家族成员含有0~6个不等的内含子，但进化关系相近的成员间趋于相同。A组的MiPOD58含有4个外显子与3个内含子，MiPOD77仅含有2个外显子与1个内含子；B、E、F组均含有4个外显子，3个内含子；C组均含有4个外显子，3个内含子；D组含有0~6个内含子，其中多为4个外显子，3个内含子；G组含有3个外显子，但MiPOD11含有7个外显子。总之，77个MiPOD基因中，有37个（48.1%）家族成员的基因结构为4个外显子与3个内含子。
保守基序分析结果如图3所示。亲缘关系越近的成员其基序结构越相似，绝大部分的MiPOD基因家族成员均包含motif1-6，且均以N→C端按序排列，但MiPOD57缺失motif1与motif2，MiPOD11缺失motif3，MiPOD42存在2个motif1，MiPOD68缺失motif1；motif4-6在MiPOD更为保守，这可能表明motif4-6在POD蛋白功能中有更为重要的作用。
保守结构域作为蛋白质三级结构的基本结构单位，是蛋白功能的重要单元。杧果POD家族成员蛋白保守结构域分析结果如图4所示，所有的杧果POD家族成员均包含1个共同的结构域，在进化过程中并没有出现变化，由此表明secretory_peroxidase结构域决定了POD蛋白的功能。
2.3　MiPOD家族成员染色体分布、物种内共线性和选择压分析
染色体定位分析表明，MiPODs分布在20条不同染色体与2条碎片片段上。MiPOD家族成员在染色体上的分布并不均匀，Chr1、Chr2上集中了大量的MiPOD基因，而在Chr3、Chr4、Chr11、Chr13、Chr17、Chr20和2条碎片片段的基因密度较高的区域中仅包含1个MiPOD基因。
共线性分析表明，27个MiPOD基因（35%）参与了串联复制，共产生了7个串联复制基因簇，分布于Chr1、Chr2、Chr14、Chr16、Chr18等5个染色体上；33个基因（42.8%）间共发现了26对同源基因，这些基因分布于18条染色体与2条碎片片段上（图5）。说明除了Chr7与Chr13外的片段复制在杧果POD基因家族进化复制的过程中起主导作用。
同源基因间的Ka/Ks值均远小于1（表3），说明进化过程中主要受到纯化选择压力的影响。
2.4　顺式作用元件分析
对MiPOD基因家族成员启动子中与光响应、激素响应和逆境响应相关的顺式作用元件进行可视化分析，结果如图6所示。每一个MiPOD家族成员启动子均包含大量的光响应元件（ARE、GT1-motif、TCT-motif、TCCC-motif、AT1-motif、G-Box、Box 4、MRE、ATC-motif、AE-box、ACE、I-box、GATA-motif、chs-CMA1a、chs-Unit 1 m1、ATCT-motif、LAMP-element、GA-motif、Gap-box、chs-CMA2a、LS7、Box II、Sp1、3-AF1 binding site、TGGCA、P-box、CAG-motif、ACA-motif、GGA-motif、L-box、GTGGC-motif、GATT-motif）。
58个MiPOD基因的启动子上存在脱落酸响应元件（ABRE），37个MiPOD基因启动子序列存在生长素响应元件（TGA-element、Aux RR-core、TGA-box），43个MiPOD基因启动子序列存在赤霉素响应元件（GARE-motif、P-box、TATC-box），50个MiPOD基因启动子序列存在茉莉酸甲酯响应元件（CGTCA-motif、TGACG-motif），37个MiPOD基因启动子序列存在水杨酸响应元件（TCA-element）。
67个MiPOD基因的启动子序列存在抗氧化反应元件（ARE），仅有MiPOD8、MiPOD27启动子序列上存在厌氧诱导的类增强子元件（GC-motif），31个MiPOD基因的启动子序列存在防御与逆境应答元件（TC-rich repeats），40个MiPOD基因的启动子序列中存在干旱胁迫应答元件（MBS），27个MiPOD基因的启动子序列中存在冷害胁迫应答元件（LTR），5个MiPOD基因的启动子序列中存在机械伤害反应元件（WUN-motif）。
综上，不同MiPOD基因家族成员启动子区域所含的顺式作用元件类型差异较大，MiPOD60的启动子序列中所含元件数目最多，包括脱落酸、水杨酸、赤霉素、茉莉酸甲酯、抗氧化、防御与逆境应答等34个顺式作用元件，说明其功能较多，可能在杧果生长发育过程中发挥重要的作用。
2.5　 MiPOD基因表达模式分析
根据转录组FPKM值绘制的热图（图7）发现，19个MiPOD基因在杧果果实生长发育与增强UV-B照射下均无表达，41个MiPOD基因在杧果果实生长发育与增强UV-B照射下的表达量较低，其余17个MiPOD基因在增强UV-B照射下呈现不同的表达模式。MiPOD1、MiPOD8、MiPOD42、MiPOD63在增强UV-B照射下的表达无明显变化。与对照相比，MiPOD7、MiPOD15、MiPOD22、MiPOD25、MiPOD27、MiPOD30、MiPOD48、MiPOD64、MiPOD71在花后50 d上调表达，MiPOD7的表达量较高且显著高于对照，MiPOD4、MiPOD41、MiPOD52、MiPOD75在花后50 d下调表达，MiPOD52在花后91 d下调表达。
为了进一步验证MiPOD基因在增强UV-B照射下的表达模式，选择MiPOD4、MiPOD7、MiPOD63进行qPCR分析，结果如图8所示。在增强UV-B照射下，MiPOD4在花后50 d下调表达（与对照相比），在花后91 d的表达量与对照无显著差异；与对照相比，MiPOD7在花后50 d上调表达且差异显著，而花后90 d的表达量无显著差异；MiPOD63的表达量随生长周期下降，且与对照无显著差异。3个基因的相对表达模式与转录组较为相符。
3　讨论
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本研究在杧果的基因组中鉴定出77个杧果POD基因家族成员，其编码的氨基酸数量、相对分子量和等电点等理化性质差异明显，与前人对木薯POD基因的研究相似[30]。MiPOD基因家族成员数量与拟南芥（73）和菠萝（78）相似[12,31]，少于木薯（91）、大豆（124）、马铃薯（124）[17,30,32]，远少于烟草（210）[33]，这表明与其他植物相比，MiPOD基因家族并没有较大的扩张。基因家族扩展主要通过3种模式：多个基因的片段复制、单个基因的串联复制和全基因组复制，本研究鉴定出33个MiPOD基因家族成员参与片段复制，多于参与串联复制的基因，推测片段复制在MiPOD基因家族的进化扩增过程中发挥重要作用。
拟南芥与马铃薯POD家族成员的内含子与外显子模式中，占比较大的均为3个内含子、4个外显子[12,32]。本研究结果表明，48.1%的MiPOD基因的结构与其一致，其余的绝大部分家族成员基因的内含子数量小于3。因此，推测原始MiPOD的基因结构为3个内含子、4个外显子模式，内含子数量减少是MiPOD基因进化的主要模式。
脱落酸、生长素、油菜素内酯、细胞分裂素等植物激素在植物响应逆境胁迫的过程起到信号传导的作用，介导响应逆境胁迫的代谢物质合成[34]，杧果与大豆的POD基因家族启动子含有相似的激素与逆境响应元件[17]，激素响应元件中包含多种介导逆境胁迫胁迫的植物激素，推测MiPOD基因家族成员会在不同类型逆境条件下被诱导表达，响应逆境胁迫，行使抗氧化功能。
MiPOD家族成员在增强UV-B照射下具有不同的表达模式，77.9%（60）的基因不表达或表达量极低，这些基因可能受其他胁迫的调控，剩余22.1%（17）基因的表达受UV-B胁迫的影响。在花后50 d上调或下调表达，在花后91 d，除MiPOD25下调表达外，其余基因均无明显变化；MiPOD7、MiPOD15、MiPOD22、MiPOD25、MiPOD27、MiPOD30、MiPOD48、MiPOD64、MiPOD71在花后50 d时与对照相比呈现上调表达，MiPOD7显著上调，可能在杧果果实响应UV-B胁迫中起到重要作用。结合启动子顺式作用元件分析，呈现上调表达的基因启动子中包含最多的分别是脱落酸响应元件（10）、茉莉酸甲酯响应元件（20），在响应UV-B胁迫中，MiPOD基因可能强烈响应脱落酸和茉莉酸甲酯的诱导。
qPCR相对定量结果验证了MiPOD4、MiPOD7、MiPOD63的表达模式，进一步说明了MiPOD7在响应UV-B胁迫中发挥重要作用。部分相对定量结果与转录组结果不一致，可能是存在MiPOD特异的时空表达。
本研究从杧果全基因组中鉴定到77个MiPOD基因，分析其理化性质、保守结构域、保守基序、系统进化、同源关系、顺式作用元件及在UV-B胁迫下的表达模式，初步筛选出MiPOD7可能在杧果果实响应UV-B胁迫中具有重要作用，本研究为进一步研究杧果POD基因对不同信号的响应机制奠定基础。
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2024年第45卷第12期
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doi: 10.3969/j.issn.1000-2561.2024.12.002
  • 接收时间：2024-07-08
  • 首发时间：2026-06-23
  • 出版时间：2024-12-25
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  • 收稿日期：2024-07-08
  • 修回日期：2024-07-30
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海南省自然科学基金项目(321RC465)
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    1.海南大学三亚南繁研究院，海南三亚　572025
    2.海南大学热带农林学院，海南海口　570228

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* 周开兵（ZHOU Kaibing），E-mail：。
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Number of
species		 占总种数比例
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total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
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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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