利用第三代纳米孔长读段测序技术构建和注释蜜蜂球囊菌的全长转录组

doi:10.3864/j.issn.0578-1752.2021.04.017

中国农业科学 ›› 2021, Vol. 54 ›› Issue (4): 864-876.doi: 10.3864/j.issn.0578-1752.2021.04.017

• 畜牧·兽医·资源昆虫 • 上一篇

利用第三代纳米孔长读段测序技术构建和注释蜜蜂球囊菌的全长转录组

杜宇¹(),祝智威¹(),王杰¹,王秀娜^3,⁴,蒋海宾¹,范元婵¹,范小雪¹,陈华枝¹,隆琦¹,蔡宗兵¹,熊翠玲^1,²,郑燕珍¹,付中民^1,²,陈大福^1,²(),郭睿^1,²()

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福建农林大学生命科学学院,福州350002
⁴福建省病原真菌与真菌毒素重点实验室（福建农林大学）,福州 350002

收稿日期:2020-05-04 接受日期:2020-05-22 出版日期:2021-02-16 发布日期:2021-02-16
通讯作者: 陈大福,郭睿
作者简介:杜宇,E-mail： m18505700830@163.com。|祝智威,E-mail： zzw15235470398@163.com。
基金资助:
国家现代农业产业技术体系建设专项(CARS-44-KXJ7);福建省自然科学基金(2018J05042);福建农林大学杰出青年科研人才计划(xjq201814);福建省病原真菌与真菌毒素重点实验室开放课题郭睿;江西省蜜蜂生物学与饲养重点实验室开放基金(JXKLHBB-2020-04);福建农林大学优秀硕士学位论文资助基金杜宇

Construction and Annotation of Ascosphaera apis Full-Length Transcriptome Utilizing Nanopore Third-Generation Long-Read Sequencing Technology

DU Yu¹(),ZHU ZhiWei¹(),WANG Jie¹,WANG XiuNa^3,⁴,JIANG HaiBin¹,FAN YuanChan¹,FAN XiaoXue¹,CHEN HuaZhi¹,LONG Qi¹,CAI ZongBing¹,XIONG CuiLing^1,²,ZHENG YanZhen¹,FU ZhongMin^1,²,CHEN DaFu^1,²(),GUO Rui^1,²()

¹ College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002
²Apitherapy Research Institution, Fujian Agriculture and Forestry University, Fuzhou 350002
³College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002
⁴Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province (Fujian Agriculture and Forestry University), Fuzhou 350002

Received:2020-05-04 Accepted:2020-05-22 Online:2021-02-16 Published:2021-02-16
Contact: DaFu CHEN,Rui GUO

摘要/Abstract

摘要：

【目的】利用第三代纳米孔（nanopore）长读段测序技术对蜜蜂球囊菌（Ascosphaera apis,简称球囊菌）的纯化菌丝（Aam）和孢子（Aas）进行测序,构建和注释球囊菌的高质量全长转录组。【方法】通过Oxford Nanopore PromethION平台对Aam和Aas进行测序。利用Guppy软件对原始读段（raw reads）进行碱基识别（base calling）,通过过滤短片段和低质量原始读段得到有效读段（clean reads）。通过识别两端引物鉴定全长转录本序列。通过比对Nr、Swissprot、KOG、eggNOG、Pfam、GO和KEGG数据库获得全长转录本的注释信息。分别利用CPC、CNCI、CPAT、Pfam 4种方法对长链非编码RNA（long non-coding RNA,lncRNA）进行预测,取四者的交集作为高可信度的lncRNA。【结果】Aam和Aas的纳米孔测序分别测得6 321 704和6 259 727条原始读段,经质控得到5 669 436和6 233 159条有效读段,其中包含的全长有效读段分别为4 497 102（79.32%）和4 963 101（79.62%）条。共鉴定到9 859和16 795条非冗余全长转录本,N50分别为1 482和1 658 bp,平均长度分别为1 187和1 303 bp,最大长度分别为6 472和6 815 bp。Venn分析结果显示有6 512条非冗余全长转录本为菌丝和孢子所共有,分别有3 347和10 283个非冗余全长转录本为二者特有。此外,在球囊菌菌丝和孢子中共鉴定到20 142条全长转录本,其中分别有20 809、11 151、17 723、12 164、11 340和9 833条全长转录本可注释到Nr、KOG、eggNOG、Pfam、GO和KEGG数据库。注释全长转录本数量最多的物种是球囊菌、Polytolypa hystricis和荚膜组织胞浆菌（Histoplasma capsulatum）。GO数据库注释结果显示,上述全长转录本可注释到45个功能条目,涉及细胞组件、细胞和细胞器等细胞组分相关条目;催化活性、结合和转运器活性等分子功能相关条目;以及细胞进程、代谢进程和单一组织进程等生物学进程相关条目。KEGG数据库注释结果显示,上述全长转录本还可注释到抗生素的生物合成、核糖体、氨基酸的生物合成、碳代谢和剪接体等49条通路。此外,鉴定到648条高可信度的lncRNA,包含480条基因间区lncRNA、119条反义链lncRNA和49条正义链lncRNA。【结论】构建和注释了球囊菌的首个高质量全长转录组,为探究球囊菌转录组的复杂性,完善参考基因组的序列和功能注释信息以及深入开展球囊菌可变剪接体的功能研究提供了关键依据。

关键词: 第三代高通量测序技术, 纳米孔测序, 全长转录本, 参考转录组, 蜜蜂, 蜜蜂球囊菌

Abstract:

【Objective】Purified mycelia sample (Aam) and spore sample (Aas) were sequenced using third-generation nanopore long-read sequencing technology, followed by construction and annotation of high-quality full-length transcriptome.【Method】Aam and Aas were respectively sequenced using Oxford Nanopore PromethION platform. Guppy software was used to conduct base calling of raw reads. Clean reads were obtained after filtering out short fragments and low-quality raw reads. Full-length transcripts were identified by recognizing primers at both ends of clean reads. Full-length transcripts were aligned to Nr, Swissprot, KOG, eggNOG, Pfam, GO and KEGG databases to gain corresponding annotations. Four approaches such as CPC, CNCI, CPAT, and Pfam were used to predict lncRNAs, and the intersection was deemed to be high-reliability lncRNAs.【Result】In total, 6 321 704 and 6 259 727 raw reads were yielded from nanopore sequencing of Aam and Aas, and after quality control, 5 669 436 and 6 233 159 clean reads were obtained, including 4 497 102 (79.32%) and 4 963 101 (79.62%) full-length clean reads. Additionally, 9 859 and 16 795 non-redundant full-length transcripts were identified, with a N50 of 1 482 and 1 658 bp, an average length of 1 187 and 1 303 bp, and a maximum length of 6 472 and 6 815 bp, respectively. Venn analysis showed that 6 512 non-redundant full-length transcripts were shared by Aam and Aas, while 3 347 and 10 283 ones were specific for Aam and Aas, respectively. Besides, a total of 20 142 full-length transcripts were identified in Aam and Aas, among them 20 809, 11 151, 17 723, 12 164, 11 340 and 9 833 full-length transcripts could be annotated to Nr, KOG, eggNOG, Pfam, GO and KEGG databases, respectively. Most of full-length transcripts were annotated to A. apis, Polytolypa hystricis and Histoplasma capsulatum. Moreover, GO database annotation demonstrated that the above-mentioned full-length transcripts could be annotated to 45 functional terms, involving in cell component-associated terms such as cell part, cell and organelle; molecular function-associated terms such as catalytic activity, binding and transporter activity; and biological process-associated terms such as cellular processes, metabolic processes and single-organism processes. KEGG database annotation indicated that these full-length transcripts could be annotated to 49 pathways, including biosynthesis of antibiotics, ribosome, biosynthesis of amino acid, carbon metabolism, spliceosome and so on. In addition, 648 lncRNAs were identified, including 480 long intergenic RNAs (lincRNAs), 119 anti-sense lncRNAs and 49 sense lncRNAs. 【Conclusion】The first high-quality full-length transcriptome was constructed and annotated in this work, which offers a key basis for exploration of the complexity of A. apis transcriptome, improvement of sequence and functional annotation of reference genome and further study on isoforms’ function of A. apis.

Key words: third-generation high-throughput sequencing technology, nanopore sequencing, full-length transcript, reference transcriptome, honeybee, Ascosphaera apis

杜宇,祝智威,王杰,王秀娜,蒋海宾,范元婵,范小雪,陈华枝,隆琦,蔡宗兵,熊翠玲,郑燕珍,付中民,陈大福,郭睿. 利用第三代纳米孔长读段测序技术构建和注释蜜蜂球囊菌的全长转录组[J]. 中国农业科学, 2021, 54(4): 864-876.

DU Yu,ZHU ZhiWei,WANG Jie,WANG XiuNa,JIANG HaiBin,FAN YuanChan,FAN XiaoXue,CHEN HuaZhi,LONG Qi,CAI ZongBing,XIONG CuiLing,ZHENG YanZhen,FU ZhongMin,CHEN DaFu,GUO Rui. Construction and Annotation of Ascosphaera apis Full-Length Transcriptome Utilizing Nanopore Third-Generation Long-Read Sequencing Technology[J]. Scientia Agricultura Sinica, 2021, 54(4): 864-876.

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参考文献 44

[1]	CHEN D F, GUO R, XU X J, XIONG C L, LIANG Q, ZHENG Y Z, LUO Q, ZHANG Z N, HUANG Z J, KUMAR D, XI W J, ZOU X, LIU M. Uncovering the immune responses of Apis mellifera ligustica larval gut to Ascosphaera apis infection utilizing transcriptome sequencing. Gene, 2017,621:40-50.
[2]	GUO R, CHEN D F, DIAO Q Y, XIONG C L, ZHENG Y Z, HOU C S. Transcriptomic investigation of immune responses of the Apis cerana cerana larval gut infected by Ascosphaera apis. Journal of Invertebrate Pathology, 2019,166:107210.
[3]	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.
[4]	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.
[5]	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)
[6]	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)
[7]	郭睿, 陈大福, 黄枳腱, 梁勤, 熊翠玲, 徐细建, 郑燕珍, 张曌楠, 解彦玲, 童新宇, 侯志贤, 江亮亮, 刀晨. 球囊菌胁迫中华蜜蜂幼虫肠道过程中病原的转录组学研究. 微生物学报, 2017,57(12):1865-1878.
	GUO R, CHEN D F, HUANG Z J, LIANG Q, XIONG C L, XU X J, ZHENG Y Z, ZHANG Z N, XIE Y L, TONG X Y, HOU Z X, JIANG L L, DAO C. Transcriptome analysis of Ascosphaera apis stressing larval gut of Apis cerana cerana. Acta Microbiologica Sinica, 2017,57(12):1865-1878. (in Chinese)
[8]	郭睿, 李汶东, 陈大福, 熊翠玲, 郑燕珍, 付中民, 徐细建, 黄枳腱, 骆群. 意大利蜜蜂幼虫肠道内球囊菌及其纯培养的高表达基因差异分析. 微生物学通报, 2018,45(2):368-375.
	GUO R, LI W D, CHEN D F, XIONG C L, ZHENG Y Z, FU Z M, XU X J, HUANG Z J, LUO Q. Highly-expressed gene differences between Ascosphaera apis stressing the larval gut of Apis mellifera ligustica and the pure culture of Ascosphaera apis. Microbiology China, 2018,45(2):368-375. (in Chinese)
[9]	陈大福, 王鸿权, 李汶东, 熊翠玲, 郑燕珍, 付中民, 徐细建, 黄枳腱, 郭睿. 胁迫中华蜜蜂幼虫肠道的球囊菌及其体外培养的高表达基因分析. 福建农林大学学报 (自然科学版), 2017,46(5):562-568.
	CHEN D F, WANG H Q, LI W D, XIONG C L, ZHENG Y Z, FU Z M, XU X J, HUANG Z J, GUO R. Analysis of highly expressed genes of Ascosphaera apis infecting the gut of Apis cerana cerana larvae and its in vitro culture. Journal of Fujian Agriculture and Forestry University (Natural Science Edition), 2017,46(5):562-568. (in Chinese)
[10]	郭睿, 陈华枝, 童新宇, 熊翠玲, 郑燕珍, 付中民, 解彦玲, 王海朋, 赵红霞, 陈大福. 蜜蜂球囊菌基因结构优化及新基因鉴定. 中国农业大学学报, 2019,24(1):61-68.
	GUO R, CHEN H Z, TONG X Y, XIONG C L, ZHENG Y Z, FU Z M, XIE Y L, WANG H P, ZHAO H X, CHEN D F. Structural optimization of annotated genes and identification of novel genes in Ascosphaera apis. Journal of China Agricultural University, 2019,24(1):61-68. (in Chinese)
[11]	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)
[12]	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, KUMAR D, LIANG Q. Identification of long non-coding RNAs in the chalkbrood disease pathogen Ascospheara apis. Journal of Invertebrate Pathology, 2018,156:1-5.
[13]	GUO R, CHEN D F, CHEN H Z, FU Z M, XIONG C L, HOU C S, ZHENG Y Z, GUO Y L, 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.
[14]	LU H Y, GIORDANO F, NING Z M. Oxford Nanopore MinION sequencing and genome assembly. Genomics Proteomics and Bioinformatics, 2016,14(5):265-279.
[15]	WORKMAN R E, TANG A D, TANG P S, JAIN M, TYSON J R, RAZAGHI R, ZUZARTE P C, GILPATRICK T, PAYNE A, QUICK J, et al. Nanopore native RNA sequencing of a human poly (A) transcriptome. Nature Methods, 2019,16(12):1297-1305.
[16]	LEA W A, PARNELL S C, WALLACE D P, CALVET J P, ZELENCHUK L V, ALVAREZ N S, WARD C J. Human-specific abnormal alternative splicing of wild-type PKD1 induces premature termination of polycystin-1. Journal of the American Society of Nephrology, 2018,29(10):2482-2492.
[17]	CHEN S Y, DENG F L, JIA X B, LI C, LAI S J. A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing. Scientific Reports, 2017,7:7648.
[18]	BAYEGA A, OIKONOMOPOULOS S, ZORBAS E, WANG Y C, GREGORIOU M E, TSOUMANI K T, MATHIOPOULOS K D, RAGOUSSIS J. Transcriptome landscape of the developing olive fruit fly embryo delineated by Oxford Nanopore long-read RNA-Seq. bioRxiv, 2018. doi: https://doi.org/10.1101/478172.
[19]	CHAO Q, GAO Z F, ZHANG D, ZHAO B G, DONG F Q, FU C X, LIU L J, WANG B C. The developmental dynamics of the Populus stem transcriptome. Plant Biotechnology Journal, 2019,17(1):206-219.
[20]	ZHU C H, LI X F, ZHENG J Y. Transcriptome profiling using Illumina- and SMRT-based RNA-seq of hot pepper for in-depth understanding of genes involved in CMV infection. Gene, 2018,666:123-133.
[21]	TOMBÁCZ D, BALÁZS Z, CSABAI Z, MOLDOVÁN N, SZŰCS A, SHARON D, SNYDER M, BOLDOGKŐI Z. Characterization of the dynamic transcriptome of a herpesvirus with long-read single molecule real-time sequencing. Scientific Reports, 2017,7:43751.
[22]	TOMBÁCZ D, BALÁZS Z, CSABAI Z, SNYDER M, BOLDOGKOI Z. Long-read sequencing revealed an extensive transcript complexity in herpesviruses. Frontiers in Genetics, 2018,9:259.
[23]	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 Ascospheara apis mycelium and spore. Scientia Agricultura Sinica, 2020,53(17):3606-3619. (in Chinese)
[24]	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的比较及其潜在功能分析. 中国农业科学, 2021,54(2):435-448.
	CHEN H Z, WANG J, ZHU Z W, JIANG H B, FAN Y C, FAN X X, WAN J Q, LU J X, ZHENG Y Z, FU Z M, XU G J, CHEN D F, GUO R. Comparison and potential functional analysis of long non-coding RNAs between Ascosphaera apis mycelium and spore. Scientia Agricultura Sinica, 2021,54(2):435-448. (in Chinese)
[25]	CHEN H Z, FAN X X, DU Y, FAN Y C, WANG J, JIANG H B, XIONG C L, ZHENG Y Z, CHEN D F, GUO R. Nanopore-based long-read transcriptome data of Nosema ceranae-infected and un-infected western honeybee workers’ midguts. bioRxiv, 2020. doi: https://doi.org/10.1101/2020.03.21.001958.
[26]	DU Y, FAN Y C, CHEN H Z, WANG J, XIONG C L, ZHENG Y Z, CHEN D F, GUO R. A full-length transcriptome dataset of normal and Nosema ceranae-challenged midgut tissues of eastern honeybee workers. bioRxiv, 2020. doi: https://doi.org/10.1101/2020.03.18. 997981.
[27]	JENJAROENPUN P, WONGSURAWAT T, PEREIRA R, PATUMCHAROENPOL P, USSERY D W, NIELSEN J, NOOKAEW I. Complete genomic and transcriptional landscape analysis using third-generation sequencing: A case study of Saccharomyces cerevisiae CEN.PK113-7D. Nucleic Acids Research, 2018,46(7):e38.
[28]	BOLDOGKOI Z, MOLDOVAN N, BALAZS Z, SNYDER M, TOMBACZ D. Long-read sequencing-A powerful tool in viral transcriptome research. Trends in Microbiology, 2019,27(7):578-592.
[29]	邓泱泱, 荔建琦, 吴松锋, 朱云平, 陈耀文, 贺福初. nr数据库分析及其本地化. 计算机工程, 2006,32(5):71-73, 76.
	DENG Y Y, LI J Q, WU S F, ZHU Y P, CHEN Y W, HE F C. Integrated nr database in protein annotation system and its localization. Computer Engineering, 2006,32(5):71-73, 76. (in Chinese)
[30]	The UniProt Consortium. UniProt: The universal protein knowledgebase. Nucleic Acids Research, 2017,45(D1):D158-D169.
[31]	KOONIN E V, FEDOROVA N D, JACKSON J D, JACOBS A R, KRYLOV D M, MAKAROVA K S, MAZUMDER R, MEKHEDOV S L, NIKOLSKAYA A N, RAO B S, et al. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biology, 2004,5(2):R7.
[32]	POWELL S, FORSLUND K, SZKLARCZYK D, TRACHANA K, ROTH A, HUERTA-CEPAS J, GABALDÓN T, RATTEI T, CREEVEY C, KUHN M, JENSEN L J, VON MERING C, BORK P. eggNOG v4.0: Nested orthology inference across 3686 organisms. Nucleic Acids Research, 2014,42(Database issue):D231-D239.
[33]	FINN R D, BATEMAN A, CLEMENTS J, COGGILL P, EBERHARDT R Y, EDDY S R, HEGER A, HETHERINGTON K, HOLM L, MISTRY J, SONNHAMMER E L L, TATE J, PUNTAM. Pfam: The protein families database. Nucleic Acids Research, 2014,42(Database issue):D222-D230.
[34]	ASHBURNER M, BALL C A, BLAKE J A, BOTSTEIN D, BUTLER H, CHERRY J M, DAVIS A P, DOLINSKI K, DWIGHT S S, EPPIG J T, et al. Gene ontology: Tool for the unification of biology. Nature Genetics, 2000,25(1):25-29.
[35]	KANEHISA M, GOTO S, KAWASHIMA S, OKUNO Y, HATTORI M. The KEGG resource for deciphering the genome. Nucleic Acids Research, 2004,32(Database issue):D277-D280.
[36]	熊翠玲, 耿四海, 王心蕊, 刘思亚, 陈大福, 郑燕珍, 付中民, 杜宇, 王海朋, 陈华枝, 周丁丁, 郭睿. 意大利蜜蜂工蜂中肠的长链非编码RNA的预测、分析及鉴定. 应用昆虫学报, 2018,55(6):1034-1044.
	XIONG C L, GENG S H, WANG X R, LIU S Y, CHEN D F, ZHENG Y Z, FU Z M, DU Y, WANG H P, CHEN H Z, ZHOU D D, GUO R. Prediction, analysis and identification of long non-coding RNA in the midguts of Apis mellifera ligustica workers. Chinese Journal of Applied Entomology, 2018,55(6):1034-1044. (in Chinese)
[37]	KONG L, ZHANG Y, YE Z Q, LIU X Q, ZHAO S Q, WEI L, GAO G. CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Research, 2007,35(Web Server issue):W345-W349.
[38]	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.
[39]	WANG L, PARK H J, DASARI S, WANG S, KOCHER J P, LI W. CPAT: Coding-potential assessment tool using an alignment-free logistic regression model. Nucleic Acids Research, 2013,41(6):e74.
[40]	CHEN D F, DU Y, FAN X X, ZHU Z W, JIANG H B, WANG J, FAN Y C, CHEN H Z, ZHOU D D, XIONG C L, ZHENG Y Z, XU X J, LUO Q, GUO R. Reconstruction and functional annotation of Ascosphaera apis full-length transcriptome via PacBio single-molecule long-read sequencing. bioRxiv, 2019. doi: https://doi.org/10.1101/770040.
[41]	MAGI A, SEMERARO R, MINGRINO A, GIUSTI B, D’AURIZIO R. Nanopore sequencing data analysis: State of the art, applications and challenges. Briefings in Bioinformatics, 2018,19(6):1256-1272.
[42]	ARONSTEIN K A, MURRAY K D. Chalkbrood disease in honey bees. Journal of Invertebrate Pathology, 2010,103(Suppl.1):S20-S29.
[43]	李江红, 郑志阳, 陈大福, 梁勤. 影响蜜蜂球囊菌侵染蜜蜂幼虫的因素及侵染过程观察. 昆虫学报, 2012,55(7):790-797.
	LI J H, ZHENG Z Y, CHEN D F, LIANG Q. Factors influencing Ascosphaera apis infection on honeybee larvae and observation on the infection process. Acta Entomologica Sinica, 2012,55(7):790-797. (in Chinese)
[44]	TAUBER J P, EINSPANIER R, EVANS J D, MCMAHON D P. Co-incubation of dsRNA reduces proportion of viable spores of Ascosphaera apis, a honey bee fungal pathogen. Journal of Apicultural Research, 2020,59(5):791-799.

样品 Sample	原始读段数 Number of raw reads	碱基数 Number of bases	居中长度 N50 (bp)	平均长度 Mean length (bp)	最大长度 Maximum length (bp)	平均质量值 Mean Q score
球囊菌菌丝Aam	6 321 704	6 271 320 854	1 094	992	9 421	Q10
球囊菌孢子Aas	6 259 727	6 553 996 867	1 157	1 047	13 060	Q10

样品 Sample	全长转录本数 Number of full-length transcripts	碱基数 Number of bases	居中长度 N50 (bp)	平均长度 Mean length (bp)	最大长度 Maximum length (bp)
球囊菌菌丝Aam	9 859	11 706 153	1 482	1 187	6 472
球囊菌孢子Aas	16 795	21 899 133	1 658	1 303	6 815

利用第三代纳米孔长读段测序技术构建和注释蜜蜂球囊菌的全长转录组

Construction and Annotation of Ascosphaera apis Full-Length Transcriptome Utilizing Nanopore Third-Generation Long-Read Sequencing Technology

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样品 Sample	有效读段数 Number of clean reads	全长有效读段数 Number of full-length clean reads	全长有效读段数的占比 Percentage of full-length clean reads (%)
球囊菌菌丝Aam	5 669 436	4 497 102	79.32
球囊菌孢子Aas	6 233 159	4 963 101	79.62

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