蜜蜂球囊菌菌丝和孢子中长链非编码RNA的比较及潜在功能分析

doi:10.3864/j.issn.0578-1752.2021.02.018

中国农业科学 ›› 2021, Vol. 54 ›› Issue (2): 435-448.doi: 10.3864/j.issn.0578-1752.2021.02.018

• 畜牧·兽医·资源昆虫 • 上一篇下一篇

蜜蜂球囊菌菌丝和孢子中长链非编码RNA的比较及潜在功能分析

陈华枝¹(),王杰¹(),祝智威¹,蒋海宾¹,范元婵¹,范小雪¹,万洁琦¹,卢家轩¹,郑燕珍¹,付中民^1,^2,³,徐国钧¹,陈大福^1,^2,³,郭睿^1,^2,³()

¹福建农林大学动物科学学院（蜂学学院）,福州350002
²福建农林大学蜂疗研究所,福州 350002
³福建农林大学蜂产品加工与应用教育部工程研究中心,福州 350002

收稿日期:2020-02-10 接受日期:2020-02-25 出版日期:2021-01-16 发布日期:2021-02-03
通讯作者: 郭睿
作者简介:陈华枝,E-mail： CHZ0720@outlook.com。|王杰,E-mail： wanglegejie@163.com。
基金资助:
国家自然科学基金(31702190);国家现代农业产业技术体系建设专项资金(CARS-44-KXJ7);福建省自然科学基金(2018J05042);福建农林大学硕士生导师团队(郭睿);福建农林大学科技创新专项基金(CXZX2017342);福建农林大学科技创新专项基金(CXZX2017343);福建省大学生创新创业项目(202010389016);福建省大学生创新创业项目(202010389162)

Comparison and Potential Functional Analysis of Long Non-Coding RNAs Between Ascosphaera apis Mycelium and Spore

CHEN HuaZhi¹(),WANG Jie¹(),ZHU ZhiWei¹,JIANG HaiBin¹,FAN YuanChan¹,FAN XiaoXue¹,WAN JieQi¹,LU JiaXuan¹,ZHENG YanZhen¹,FU ZhongMin^1,^2,³,XU GuoJun¹,CHEN DaFu^1,^2,³,GUO Rui^1,^2,³()

¹College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002
²Apitherapy Research Institution, Fujian Agriculture and Forestry University, Fuzhou 350002
³Engineering Research Center of Processing and Application of Bee Products of Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002

Received:2020-02-10 Accepted:2020-02-25 Online:2021-01-16 Published:2021-02-03
Contact: Rui GUO

摘要/Abstract

摘要：

【背景】蜜蜂球囊菌（Ascosphaera apis,简称球囊菌）是一种专性侵染蜜蜂幼虫的真菌病原,可引起成年蜜蜂数量和蜂群群势的急剧下降。长链非编码RNA（long non-coding RNA,lncRNA）是一类新近发现的非编码RNA,在表观遗传、细胞周期、剂量补偿等众多生命活动中发挥重要生物学功能。【目的】明确球囊菌菌丝和孢子中lncRNA的数量、种类和表达谱差异,并探究共有lncRNA、特有lncRNA和差异表达lncRNA（differentially expressed lncRNA,DElncRNA）在菌丝与孢子中的潜在功能。【方法】利用基于链特异性建库的lncRNA-seq技术对球囊菌的纯化菌丝（AaM）和纯化孢子（AaS）分别进行测序。根据FPKM（Fragment Per Kilobase of per Million mapped reads）法计算lncRNA在AaM和AaS中的表达水平。通过Venn分析筛选AaM与AaS的共有lncRNA和特有lncRNA。按照P≤0.05且|log₂ fold change|≥1的标准筛选AaM vs AaS比较组中的DElncRNA。通过Blast工具将共有lncRNA、特有lncRNA和DElncRNA的上下游基因比对GO和KEGG数据库,以进行功能及通路注释。根据靶向结合关系构建共有lncRNA、特有lncRNA和DElncRNA的竞争性内源RNA（competing endogenous RNA,ceRNA）调控网络并利用Cytoscape软件进行可视化。利用RT-qPCR验证测序数据的可靠性。【结果】AaM和AaS分别测得108 614 646和105 675 408条原始读段（raw reads）,经严格过滤得到107 780 032和104 621 402条有效读段（clean reads）,Q20分别为98.76%和98.72%,Q30分别达到95.84%和95.78%。共鉴定到850个lncRNA。AaM和AaS的共有lncRNA为701个,二者的特有lncRNA分别为39和110个。上述共有lncRNA通过顺式作用调控3 992个上下游基因,它们涉及细胞进程、代谢进程和催化活性等42个功能条目,以及代谢途径、次生代谢物的生物合成和抗生素的生物合成等117条通路;AaM的特有lncRNA和AaS的特有lncRNA通过顺式作用分别调控243和672个上下游基因。AaM vs AaS比较组包含的255个DElncRNA通过顺式作用调控1 479个上下游基因,它们涉及代谢进程、细胞进程和催化活性等41个功能条目,以及代谢途径、次生代谢产物的生物合成和抗生素的生物合成等107条通路。从共有lncRNA、孢子特有lncRNA和DElncRNA中分别预测到41、5和13个微小RNA（microRNA,miRNA）的前体序列。调控网络分析结果显示,菌丝lncRNA、孢子lncRNA形成较为复杂的ceRNA调控网络;菌丝lncRNA可靶向结合8个miRNA,进而调控77个mRNA;孢子lncRNA可靶向结合7个miRNA,进而调控87个mRNA;2个DElncRNA（TCONS_00008630与TCONS_00009302）可靶向结合miR-4968-y,进而调控10个mRNA。RT-qPCR验证结果显示4个DElncRNA的差异表达趋势与测序结果一致,表明测序数据真实可靠。【结论】共有lncRNA、特有lncRNA和DElncRNA可能通过调控上下游基因的表达,作为miRNA的前体,以及充当ceRNA影响菌丝和孢子的物质和能量代谢、自噬、转录、MAPK信号通路、泛素介导的蛋白水解、蛋白酶体以及次生代谢产物的生物合成等生物学过程,从而调节球囊菌的生长、发育、生殖和致病性。

关键词: 蜜蜂球囊菌, 长链非编码RNA, 菌丝, 孢子, 竞争性内源RNA

Abstract:

【Background】Ascosphaera apis is a fungal pathogen that exclusively infects honeybee larvae, causing a sharp decrease of the population of adult honeybees and colony population. Long non-coding RNA (lncRNA), a recently discovered non-coding RNA (ncRNA), plays a vital biological role in various activities such as epigenetics, cell cycle and dose compensation.【Objective】This study aimed to clarify the differences of number, type and expression profile of lncRNAs between A. apis mycelium and spore, and investigate the potential role of the common lncRNAs, specific lncRNAs and differentially expressed lncRNAs (DElncRNAs). 【Method】The purified mycelia (AaM) and purified spores (AaS) of A. apis were respectively sequenced using strand specific library-based lncRNA-seq technology. The expression levels of lncRNAs in AaM and AaS were calculated using FPKM (Fragment Per Kilobase of per Million mapped reads) method. Common lncRNAs and specific lncRNAs were filtered out following Venn analysis. DElncRNAs within AaM vs AaS comparison group were screened out following the standard of P≤0.05 and |log₂fold change|≥1. Upstream and downstream genes of common lncRNAs, specific lncRNAs and DElncRNAs were aligned against GO and KEGG databases to obtain function and pathway annotations. The competing endogenous RNA (ceRNA) regulation networks of common lncRNAs, specific lncRNAs and DElncRNAs were constructed following target binding relationships, followed by visualization using Cytoscape software. RT-qPCR was performed to verify the reliability of the sequencing data.【Result】In total, 108 614 646 and 105 675 408 raw reads were gained from AaM and AaS, and after strict filtering, 107 780 032 and 104 621 402 clean reads were obtained, respectively, with Q20 of 98.76% and 98.72%, and Q30 of 95.84% and 95.78%. A total of 850 lncRNAs were identified. Seven hundred and one lncRNAs were shared by AaM and AaS, and there were 39 and 110 specific lncRNAs. Via cis function, these shared lncRNAs could regulate 3 992 upstream and downstream genes involving in 42 functional terms such as cellular process, metabolism process and catalytic activity; and 117 pathways such as metabolism pathway, biosynthesis of secondary metabolites and biosynthesis of antibiotics. Specific lncRNAs for AaM and AaS could respectively regulate 243 and 672 upstream and downstream genes. In AaM vs AaS comparison group, 255 DElncRNAs were identified and found to regulate 1 479 upstream and downstream genes, which were associated with 41 functional terms including cellular process, metabolism process and catalytic activity; and 107 pathways including metabolism pathway, biosynthesis of secondary metabolites and biosynthesis of antibiotics. Forty one, five and 13 miRNA precursors were predicted from common lncRNAs, specific lncRNAs and DElncRNAs. The result of regulatory network analysis showed the formation of ceRNA networks of mycelium lncRNAs and spore lncRNAs; ten lncRNAs in mycelium could bind to eight miRNAs, further targeting 77 mRNAs; while eight lncRNAs in spore could link to seven miRNAs, further targeting 87 mRNAs; two DElncRNAs including TCONS_00008630 and TCONS_00009302 could simultaneously target miR-4968-y, further regulating ten mRNAs. The result of RT-qPCR suggested the differential expression trend of four DElncRNAs were in accordance of that in sequencing result, indicating the reliability of our sequencing data.【Conclusion】Common lncRNAs, specific lncRNAs and DElncRNAs are likely to affect material and energy metabolisms, autophagy, transcription, MAPK signaling pathway, ubiquitin-mediated proteolysis, proteasome and biosynthesis of secondary metabolites, by regulating the expression of upstream and downstream genes, serving as miRNA precursors or ceRNAs, thus regulating the growth, development, reproduction and pathogenicity of A. apis.

Key words: Ascosphaera apis, long non-coding RNA (lncRNA), mycelium, spore, competing endogenous RNA (ceRNA)

陈华枝,王杰,祝智威,蒋海宾,范元婵,范小雪,万洁琦,卢家轩,郑燕珍,付中民,徐国钧,陈大福,郭睿. 蜜蜂球囊菌菌丝和孢子中长链非编码RNA的比较及潜在功能分析[J]. 中国农业科学, 2021, 54(2): 435-448.

CHEN HuaZhi,WANG Jie,ZHU ZhiWei,JIANG HaiBin,FAN YuanChan,FAN XiaoXue,WAN JieQi,LU JiaXuan,ZHENG YanZhen,FU ZhongMin,XU GuoJun,CHEN DaFu,GUO Rui. Comparison and Potential Functional Analysis of Long Non-Coding RNAs Between Ascosphaera apis Mycelium and Spore[J]. Scientia Agricultura Sinica, 2021, 54(2): 435-448.

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参考文献 64

[1]	CALDERÓN R A, RIVERA G, SÁNCHEZ L A, ZAMORA L G. Chalkbrood (Ascosphaera apis) and some other fungi associated with Africanized honey bees (Apis mellifera) in Costa Rica. Journal of Apicultural Research, 2004,43(4):187-188.
[2]	WOOD M. Microbes help bees battle chalkbrood. Agricultural Research, 1998,46(8):16-17.
[3]	ARONSTEINK K A, MURRAY D. Chalkbrood disease in honey bees. Journal of Invertebrate Pathology, 2010,103(Suppl.1):20-29.
[4]	KAPRANOV P, CHENG J, DIKE S, NIX D A, DUTTAGUPTA R, WILLINGHAM A T, STADLER P F, HERTEL J, HACKERMÜLLER J, HOFACKER I L, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science, 2007,316(5830):1484-1488. pmid: 17510325
[5]	PONTIER D B, GRIBNAU J. Xist regulation and function explored. Human Genetics, 2011,130(2):223-236. pmid: 21626138
[6]	KINO T, HURT D E, ICHIJO T, NADER N, CHROUSOS G P. Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Science Signaling, 2010, 3(107): ra8. pmid: 20124551
[7]	HEO J B, SUNG S. Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science, 2011,331(6013):76-79.
[8]	TSAI M C, MANOR O, WAN Y, MOSAMMAPARAST N, WANG J K, LAN F, SHI Y, SEGAL E, CHANG H Y. Long noncoding RNA as modular scaffold of histone modification complexes. Science, 2010,329(5992):689-693.
[9]	MERCER T R, MATTICK J S. Structure and function of long noncoding RNAs in epigenetic regulation. Nature Structural and Molecular Biology, 2013,20(3):300-307.
[10]	LI M, SUN X, CAI H, SUN Y, PLATH M, LI C, LAN X, LEI C, LIN F, BAI Y, CHEN H. Long non-coding RNA ADNCR suppresses adipogenic differentiation by targeting miR-204. Biochimica et Biophysica Acta, 2016,1859(7):871-882.
[11]	ST LAURENT G, WAHLESTEDT C, KAPRANOV P. The landscape of long noncoding RNA classification. Trends in Genetics, 2015,31(5):239-251. pmid: 25869999
[12]	LI Z X, HAN K W, ZHANG D F, CHEN J G, XU Z, HOU L J. The role of long noncoding RNA in traumatic brain injury. Neuropsychiatric Disease and Treatment, 2019,15:1671-1677.
[13]	郭睿, 王海朋, 陈华枝, 熊翠玲, 郑燕珍, 付中民, 赵红霞, 陈大福. 蜜蜂球囊菌的microRNA鉴定及其调控网络分析. 微生物学报, 2018,58(6):1077-1089.
	GUO R, WANG H P, CHEN H Z, XIONG C L, ZHENG Y Z, FU Z M, ZHAO H X, CHEN D F. Identification of Ascosphaera apis microRNAs and investigation of their regulation networks. Acta Microbiologica Sinica, 2018,58(6):1077-1089. (in Chinese)
[14]	KOPP F, MENDELL J T. Functional classification and experimental dissection of long noncoding RNAs. Cell, 2018,172(3):393-407.
[15]	KIM W, MIGUEL-ROJAS C, WANG J, TOWNSEND J P, TRAIL F. Developmental dynamics of long noncoding RNA expression during sexual fruiting body formation in Fusarium graminearum. mBio, 2018,9(4):e01292-18.
[16]	HIRIART E, VERDEL A. Long noncoding RNA-based chromatin control of germ cell differentiation: a yeast perspective. Chromosome Research, 2013,21(6/7):653-663.
[17]	CHEN D F, CHEN H Z, DU Y, ZHOU D D, GENG S H, WANG H P, WAN J Q, XIONG C L, ZHENG Y Z, GUO R. Genome-wide identification of long non-coding RNAs and their regulatory networks involved in Apis mellifera ligustica response to Nosema ceranae infection. Insects, 2019,10(8):245.
[18]	WILUSZ J E, SUNWOO H, SPECTOR D L. Long noncoding RNAs: Functional surprises from the RNA world. Genes and Development, 2009,23(13):1494-1504. doi: 10.1101/gad.1800909 pmid: 19571179
[19]	FAN G Q, WANG Z, ZHAI X Q, CAO Y B. ceRNA cross-talk in paulownia witches’ broom disease. International Journal of Molecular Sciences, 2018,19(8):2463.
[20]	QIN X, EVANS J D, ARONSTEIN K A, MURRAY K D, WEINSTOCK G M. Genome sequences of the honey bee pathogens Paenibacillus larvae and Ascosphaera apis. Insect Molecular Biology, 2006,15(5):715-718. pmid: 17069642
[21]	SPILTOIR C F. Life cycle of Ascosphaera apis (Pericystis apis). American Journal of Botany, 1955,42(6):501-508.
[22]	FLORES J M, SPIVAK M, GUTIÉRREZ I. Spores of Ascosphaera apis contained in wax foundation can infect honeybee brood. Veterinary Microbiology, 2005,108(1/2):141-144.
[23]	SKOU J P. More details in support of the class Ascosphaeromycetes. Mycotaxon, 1988,31(1):191-198.
[24]	ANDERSON D, GIACON H SEARCH ARTICLES BY 'GIACON H' GIACON H, GIBSON N SEARCH ARTICLES BY 'GIBSON N' GIBSON N. Detection and thermal destruction of the chalkbrood fungus (Ascosphaera apis) in honey. Journal of Apicultural Research, 1997,36(3/4):163-168.
[25]	SHANG Y F, XIAO G H, ZHENG P, CEN K, ZHAN S, WANG C S. Divergent and convergent evolution of fungal pathogenicity. Genome Biology and Evolution, 2016,8(5):1374-1387. pmid: 27071652
[26]	郭睿, 耿四海, 熊翠玲, 郑燕珍, 付中民, 王海朋, 杜宇, 童新宇, 赵红霞, 陈大福. 意大利蜜蜂工蜂中肠发育过程中长链非编码RNA的差异表达分析. 中国农业科学, 2018,51(18):3600-3613.
	GUO R, GENG S H, XIONG C L, ZHENG Y Z, FU Z M, WANG H P, DU Y, TONG X Y, ZHAO H X, CHEN D F. Differential expression analysis of long non-coding RNAs during the developmental process of Apis mellifera ligustica worker’s midgut. Scientia Agricultura Sinica, 2018,51(18):3600-3613. (in Chinese)
[27]	FLÓREZ-ZAPATA N M V, REYES-VALDÉS M H, MARTÍNEZ O. Long non-coding RNAs are major contributors to transcriptome changes in sunflower meiocytes with different recombination rates. BMC Genomics, 2016,17:490.
[28]	YANG L, LONG Y P, LI C, CAO L, GAN H Y, HUANG K L, JIA Y J. Genome-wide analysis of long noncoding RNA profile in human gastric epithelial cell response to Helicobacter pylori. Japanese Journal of Infectious Diseases, 2015,68(1):63-66.
[29]	GUO R, CHEN D F, XIONG C L, HOU C S, ZHENG Y Z, FU Z M, LIANG Q, DIAO Q Y, ZHANG L, WANG H Q, HOU Z X, KUMAR D. First identification of long non-coding RNAs in fungal parasite Nosema ceranae. Apidologie, 2018,49(5):660-670.
[30]	WANG Z Q, ZHAO Y W, ZHANG Y. Viral lncRNA: A regulatory molecule for controlling virus life cycle. Noncoding RNA Research, 2017,2(1):38-44.
[31]	GUO R, CHEN D F, XIONG C L, HOU C S, ZHENG Y Z, FU Z M, DIAO Q Y, ZHANG L, WANG H Q, HOU Z X, LI W D, DHIRAJ K, LIANG Q. Identification of long non-coding RNAs in the chalkbrood disease pathogen Ascospheara apis. Journal of Invertebrate Pathology, 2018,156:1-5. pmid: 29894727
[32]	GUO R, CHEN D F, CHEN H Z, FU Z M, XIONG C L, HOU C S, ZHENG Y Z, GUO Y, WANG H P, DU Y, DIAO Q Y. Systematic investigation of circular RNAs in Ascosphaera apis, a fungal pathogen of honeybee larvae. Gene, 2018,678:17-22.
[33]	陈大福, 郭睿, 熊翠玲, 梁勤, 郑燕珍, 徐细建, 黄枳腱, 张曌楠, 张璐, 李汶东, 童新宇, 席伟军. 胁迫意大利蜜蜂幼虫肠道的球囊菌的转录组分析. 昆虫学报, 2017,60(4):401-411.
	CHEN D F, GUO R, XIONG C L, LIANG Q, ZHENG Y Z, XU X J, HUANG Z J, ZHANG Z N, ZHANG L, LI W D, TONG X Y, XI W J. Transcriptomic analysis of Ascosphaera apis stressing larval gut of Apis mellifera ligustica (Hyemenoptera: Apidae). Acta Entomologica Sinica, 2017,60(4):401-411. (in Chinese)
[34]	张曌楠, 熊翠玲, 徐细建, 黄枳腱, 郑燕珍, 骆群, 刘敏, 李汶东, 童新宇, 张琦, 梁勤, 郭睿, 陈大福. 蜜蜂球囊菌的参考转录组de novo组装及SSR分子标记开发. 昆虫学报, 2017,60(1):34-44.
	ZHANG Z N, XIONG C L, XU X J, HUANG Z J, ZHENG Y Z, LUO Q, LIU M, LI W D, TONG X Y, ZHANG Q, LIANG Q, GUO R, CHEN D F. De novo assembly of a reference transcriptome and development of SSR markers for Ascosphaera apis. Acta Entomologica Sinica, 2017,60(1):34-44. (in Chinese)
[35]	陈大福, 郭睿, 熊翠玲, 梁勤, 郑燕珍, 徐细建, 张曌楠, 黄枳腱, 张璐, 王鸿权, 解彦玲, 童新宇. 中华蜜蜂幼虫肠道响应球囊菌早期胁迫的转录组学. 中国农业科学, 2017,50(13):2614-2623.
	CHEN D F, GUO R, XIONG C L, LIANG Q, ZHENG Y Z, XU X J, ZHANG Z N, HUANG Z J, ZHANG L, WANG H Q, XIE Y N, TONG X Y. Transcriptome of Apis cerana cerana larval gut under the stress of Ascosphaera apis. Scientia Agricultura Sinica, 2017,50(13):2614-2623. (in Chinese)
[36]	LANGMEAD B, TRAPNELL C, POP M, SALZBERG S L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 2009,10(3):R25.
[37]	KIM D, PERTEA G, TRAPNELL C, PIMENTEL H, KELLEY R, SALZBERG S L. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology, 2013,14(4):R36. pmid: 23618408
[38]	TRAPNELL C, ROBERTS A, GOFF L, PERTEA G, KIM D, KELLEY D R, PIMENTEL H, SALZBERG S L, RINN J L, PACHTER L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols, 2012,7(3):562-578. doi: 10.1038/nprot.2012.016 pmid: 22383036
[39]	KONG L, ZHANG Y, YE Z Q, LIU X Q, ZHAO S Q, WEI L P, GAO G. CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Research, 2007,35:W345-349.
[40]	SUN L, LUO H T, BU D C, ZHAO G G, YU K T, ZHANG C H, LIU Y N, CHEN R S, ZHAO Y. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Research, 2013,41(17):e166. doi: 10.1093/nar/gkt646 pmid: 23892401
[41]	ROBINSON M D, MCCARTHY D J, SMYTH G K. EdgeR: A bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 2010,26(1):139-140. pmid: 19910308
[42]	SHAO J, CHEN H, YANG D, JIANG M, ZHANG H, WU B, LI J, YUAN L, LIU C. Genome-wide identification and characterization of natural antisense transcripts by strand-specific RNA sequencing in Ganoderma lucidum. Scientific Reports, 2017,7(1):5711. pmid: 28720793
[43]	陈华枝, 祝智威, 蒋海宾, 王杰, 范元婵, 范小雪, 万洁琦, 卢家轩, 熊翠玲, 郑燕珍, 付中民, 陈大福, 郭睿. 蜜蜂球囊菌菌丝和孢子中微小RNA及其靶mRNA的比较分析. 中国农业科学, 2020,53(17):3606-3619.
	CHEN H Z, ZHU Z W, JIANG H B, WANG J, FAN Y C, FAN X X, WAN J Q, LU J X, XIONG C L, ZHENG Y Z, FU Z M, CHEN D F, GUO R. Comparative analysis of microRNAs and corresponding target mRNAs in Ascosphaera apis mycelium and spore. Scientia Agricultura Sinica, 2020,53(17):3606-3619. (in Chinese)
[44]	熊翠玲, 陈华枝, 陈大福, 郑燕珍, 付中民, 徐国钧, 杜宇, 王海朋, 耿四海, 周丁丁, 刘思亚, 郭睿. 意大利蜜蜂工蜂中肠的环状RNA及其调控网络分析. 昆虫学报, 2018,61(12):1363-1375.
	XIONG C L, CHEN H Z, CHEN D F, ZHENG Y Z, FU Z M, XU G J, DU Y, WANG H P, GENG S H, ZHOU D D, LIU S Y, GUO R. Analysis of circular RNAs and their regulatory networks in the midgut of Apis mellifera ligustica workers. Acta Entomologica Sinica, 2018,61(12):1363-1375. (in Chinese)
[45]	ALLEN E, XIE Z, GUSTAFSON A M, CARRINGTON J C. MicroRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell, 2005,121(2):207-221. doi: 10.1016/j.cell.2005.04.004 pmid: 15851028
[46]	ATIANAND M K, FITZGERALD K A. Long non-coding RNAs and control of gene expression in the immune system. Trends in Molecular Medicine, 2014,20(11):623-631. pmid: 25262537
[47]	QURESHI I A, MEHLER M F. Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease. Nature Reviews. Neuroscience, 2012,13(8):528-541. doi: 10.1038/nrn3234 pmid: 22814587
[48]	PAULI A, VALEN E, LIN M F, GARBER M, VASTENHOUW N L, LEVIN J Z, FAN L, SANDELIN A, RINN J L, REGEV A, SCHIER A F. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Research, 2012,22(3):577-591. doi: 10.1101/gr.133009.111 pmid: 22110045
[49]	WANG Z, JIANG Y, WU H, XIE X, HUANG B. Genome-wide identification and functional prediction of long non-coding RNAs involved in the heat stress response in Metarhizium robertsii. Frontiers in Microbiology, 2019,10:2336. doi: 10.3389/fmicb.2019.02336 pmid: 31649657
[50]	YORIMITSU T, KLIONSKY D J. Autophagy: Molecular machinery for self-eating. Cell Death and Differentiation, 2005,12(Suppl. 2):1542-1552.
[51]	FAN C L, CHANG A N, LIU T B. Role of autophagy in the reproduction of pathogenic fungi. Acta Microbiologica Sinica, 2019,59(2):224-234.
[52]	LIU X H, ZHAO Y H, ZHU X M, ZENG X Q, HUANG L Y, DONG B, SU Z Z, WANG Y, LU J P, LIN F C. Autophagy-related protein MoAtg14 is involved in differentiation, development and pathogenicity in the rice blast fungus Magnaporthe oryzae. Scientific Reports, 2017,7:40018. pmid: 28067330
[53]	DENG Y Z, RAMOS-PAMPLONA M, NAQVI N I. Autophagy- ssisted glycogen catabolism regulates asexual differentiation in Magnaporthe oryzae. Autophagy, 2009,5(1):33-43. doi: 10.4161/auto.5.1.7175 pmid: 19115483
[54]	WANG P, GRANADOS R R. Observations on the presence of the peritrophic membrane in larval Trichoplusia ni and its role in limiting baculovirus infection. Journal of Invertebrate Pathology, 1998,72(1):57-62. doi: 10.1006/jipa.1998.4759 pmid: 9647702
[55]	SURESH B, LEE J, KIM K S, RAMAKRISHNA S. The importance of ubiquitination and deubiquitination in cellular reprogramming. Stem Cells International, 2016,2016:6705927. doi: 10.1155/2016/6705927 pmid: 26880980
[56]	BIDOCHKA M J, KHACHATOURIANS G G. The implication of metabolic acids produced by Beauveria bassiana in pathogenesis of the migratory grasshopper, Melanoplus sanguinipes. Journal of Invertebrate Pathology, 1991,58(1):106-117. doi: 10.1016/0022-2011(91)90168-P
[57]	GOTZ P, MATHA V, VILCINSKAS A. Effects of the entomopathogenic fungus Metarhizium anisopliae and its secondary metabolites on morphology and cytoskeleton of plasmatocytes isolated from the greater wax moth, Galleria mellonella. Journal of Invertebrate Pathology, 1997,43(12):1149-1159.
[58]	JENSEN A B, ARONSTEIN K, FLORES J M, VOJVODIC S, PALACIO M A, SPIVAK M. Standard methods for fungal brood disease research. Journal of Apicultural Research, 2013, 52(1): 10.3896/IBRA.1.52.1.13. doi: 10.3896/IBRA.1.52.1.13 pmid: 24198438
[59]	BROWN A J P, BUDGE S, KALORITI D, TILLMANN A, JACOBSEN M D, YIN Z, ENE I V, BOHOVYCH I, SANDAI D, KASTORA S, POTRYKUS J, BALLOU E R, CHILDERS D S, SHAHANA S, LEACH M D. Stress adaptation in a pathogenic fungus. Journal of Experimental Biology, 2014,217(1):144-155.
[60]	SO K K, KIM D H. Role of MAPK signaling pathways in regulating the hydrophobin cryparin in the chestnut blight fungus Cryphonectria parasitica. Mycobiology, 2017,45(4):362-369. doi: 10.5941/MYCO.2017.45.4.362 pmid: 29371804
[61]	JIANG C, ZHANG X, LIU H Q, XU J R. Mitogen-activated protein kinase signaling in plant pathogenic fungi. PLoS Pathogens, 2018,14(3):e1006875. pmid: 29543901
[62]	NI X, GAO J X, YU C J, WANG M, SUN J N, LI Y Q, CHEN J. MAPKs and acetyl-CoA are associated with Curvularia lunata pathogenicity and toxin production in maize. Journal of Integrative Agriculture, 2018,17(1):139-148.
[63]	SALMENA L, POLISENO L, TAY Y, KATS L, PANDOLFI P P. A ceRNA hypothesis: The rosetta stone of a hidden RNA language? Cell, 2011,146(3):353-358. pmid: 21802130
[64]	HUANG M J, ZHAO J Y, XU J J, LI Y, ZHUANG Y F, ZHANG X L. LncRNA ADAMTS9-AS2 controls human mesenchymal stem cell chondrogenic differentiation and functions as a ceRNA. Molecular Therapy-Nucleic Acids, 2019,18:533-545. pmid: 31671346

LncRNA名称 LncRNA ID	引物名称 Primer name	引物序列 Primer sequence
TCONS_00006988	F	CTCCAGTTGTGCGTTCAT
TCONS_00006988	R	GTTGTCACCGTCTCTTCC
TCONS_00003707	F	GGAATGAATGATGCCAACTT
TCONS_00003707	R	GTAGACCGAGGAAGAACAG
TCONS_00001814	F	ACAAGGAGGAAGTCAAGGA
TCONS_00001814	R	CGAGCATAAGCAGTAGAGAT
TCONS_00007359	F	CCATCGCCACGGATATTC
TCONS_00007359	R	CCAGAGCACATCAACATCA
actin	F	CAGGAAAGGCTATGTTCGC
actin	R	ATTACCGAGGAGCAAGACG

蜜蜂球囊菌菌丝和孢子中长链非编码RNA的比较及潜在功能分析

Comparison and Potential Functional Analysis of Long Non-Coding RNAs Between Ascosphaera apis Mycelium and Spore

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样品 Sample	原始读段 Raw reads	有效读段 Clean reads	99.9%碱基正确率Q20	99.99%碱基正确率Q30
AaM	108 614 646	107 780 032	98.76%	95.84%
AaS	105 675 408	104 621 402	98.72%	95.78%

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