基于纳米孔全长转录组数据完善东方蜜蜂微孢子虫的基因组注释

doi:10.3864/j.issn.0578-1752.2021.06.018

中国农业科学 ›› 2021, Vol. 54 ›› Issue (6): 1288-1300.doi: 10.3864/j.issn.0578-1752.2021.06.018

• 畜牧·兽医·资源昆虫 • 上一篇

基于纳米孔全长转录组数据完善东方蜜蜂微孢子虫的基因组注释

陈华枝¹(),范元婵¹(),蒋海宾¹,王杰¹,范小雪¹,祝智威¹,隆琦¹,蔡宗兵¹,郑燕珍¹,付中民^1,²,徐国钧¹,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

收稿日期:2020-05-06 接受日期:2020-05-28 出版日期:2021-03-16 发布日期:2021-03-25
通讯作者: 郭睿
作者简介:陈华枝,E-mail：CHZ0720@outlook.com。|范元婵,E-mail：fanyc19980201@126.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);福建农林大学优秀硕士学位论文资助基金陈华枝

Improvement of Nosema ceranae Genome Annotation Based on Nanopore Full-Length Transcriptome Data

HuaZhi CHEN¹(),YuanChan FAN¹(),HaiBin JIANG¹,Jie WANG¹,XiaoXue FAN¹,ZhiWei ZHU¹,Qi LONG¹,ZongBing CAI¹,YanZhen ZHENG¹,ZhongMin FU^1,²,GuoJun XU¹,DaFu CHEN^1,²,Rui GUO^1,²()

¹College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002
²Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002

Received:2020-05-06 Accepted:2020-05-28 Online:2021-03-16 Published:2021-03-25
Contact: Rui GUO

摘要/Abstract

摘要：

【目的】利用已获得的纳米孔全长转录组数据对现有的东方蜜蜂微孢子虫（Nosema ceranae）参考基因组的基因序列和功能注释进行完善。【方法】采用TransDecoder软件预测东方蜜蜂微孢子虫基因的开放阅读框（open reading frame,ORF）及相应的氨基酸。利用gffcompare软件将全长转录本与参考基因组注释的转录本进行比较,对基因组注释基因的非编码区向上游或下游延伸,修正基因的边界。利用MISA软件鉴定长度在500 bp以上的全长转录本的简单重复序列（simple sequence repeat,SSR）位点,包括单核苷酸重复、双核苷酸重复、三核苷酸重复、四核苷酸重复、五核苷酸重复、六核苷酸重复、混合SSR等类型。通过Blast工具将鉴定到的新基因和新转录本比对Nr、KOG、eggNOG、GO和KEGG数据库,从而获得功能注释。【结果】共预测出2 353个完整ORF,其中长度分布在0—100个氨基酸的ORF最多,占总ORF数的72.12%。共对东方蜜蜂微孢子虫的2 340个基因进行了结构优化,其中5′端延长的基因有1 182个,3′端延长的基因有1 158个。共鉴定到1 658个SSR,其中单核苷酸重复、双核苷酸重复、三核苷酸重复、四核苷酸重复的数量分别为1 622、23、7和6个;单核苷酸重复类型的SSR密度最大,达到182.32个/Mb,其次为混合SSR、双核苷酸重复和三核苷酸重复,分别达到6.90、2.78和0.73个/Mb。共鉴定出954个新基因,其中分别有951、333、371、422和321个新基因可注释到Nr、KOG、eggNOG、GO和KEGG数据库。此外,还鉴定出6 164条新转录本,其中分别有6 141、2 808、2 932、3 196和2 585条新转录本可注释到Nr、KOG、eggNOG、GO和KEGG数据库。新基因和新转录本注释数量最多的物种均为东方蜜蜂微孢子虫,其次是蜜蜂微孢子虫（Nosema apis）。【结论】研究结果较好地完善了现有的东方蜜蜂微孢子虫参考基因组已注释基因的序列和功能注释,并补充和注释了大量参考基因组未注释的新基因和新转录本。

关键词: 纳米孔测序, 全长转录本, 转录组, 基因组, 蜜蜂, 东方蜜蜂微孢子虫

Abstract:

【Objective】The objective of this study is to improve gene sequence and functional annotation of current reference genome of Nosema ceranae using previously obtained Nanopore full-length transcriptome dataset. 【Method】TransDecoder software was used to predict open reading frames (ORFs) of N. ceranae and corresponding amid acids. Comparison between full-length transcripts and transcripts annotated in reference genome was performed using gffcompare software to extend upstream sequences or downstream sequences of annotated genes’ untranslated regions and correct genes’ boundaries. MISA software was used to explore simple sequence repeat (SSR) loci within transcripts with a length above 500 bp, including single nucleotide repeat, dinucleotide repeat, trinucleotide repeat, tetranucleotide repeat, pentanucleotide repeat, hexanucleotide repeat and mixed SSR. By using Blast tool, novel genes and novel transcripts were aligned to Nr, KOG, eggNOG, GO and KEGG databases to gain functional annotations. 【Result】A total of 2 353 complete ORFs were predicted, and those ORFs with a length distribution among 0-100 aa were the predominant, reaching a ratio of 72.12% among total ORFs. Additionally, structures of 2 340 N. ceranae genes were optimized; 5′ ends of 1 182 genes and 3′ ends of 1 158 genes were respectively prolonged. Moreover, 1 658 SSRs were identified, and the numbers of single nucleotide repeat, dinucleotide repeat, trinucleotide repeat, tetranucleotide repeat were 1 622, 23, seven and six, respectively. The density of single nucleotide repeat was the highest (182.32/Mb), followed by those of mixed SSR, dinucleotide repeat and trinucleotide repeat, reaching 6.90, 2.78 and 0.73/Mb, respectively. Further, 954 novel genes were identified, among them 951, 333, 371, 422 and 321 were respectively annotated to Nr, KOG, eggNOG, GO and KEGG databases. In addition, 6 164 novel transcripts were identified, among them 6 141, 2 808, 2 932, 3 196 and 2 585 were annotated to the aforementioned five databases, respectively. The species annotated by the highest number of new gene and new transcript was N. ceranae followed by Nosema apis. 【Conclusion】Our results well improve sequences and functional annotations of annotated genes in current reference genome of N. ceranae, and supplement and annotate a number of unannotated novel genes and transcripts. Lots of SSR sites were provided for research on molecular markers, information of genes and transcripts on reference genome were supplemented.

Key words: Nanopore sequencing, full-length transcript, transcriptome, genome, honeybee, Nosema ceranae

陈华枝,范元婵,蒋海宾,王杰,范小雪,祝智威,隆琦,蔡宗兵,郑燕珍,付中民,徐国钧,陈大福,郭睿. 基于纳米孔全长转录组数据完善东方蜜蜂微孢子虫的基因组注释[J]. 中国农业科学, 2021, 54(6): 1288-1300.

HuaZhi CHEN,YuanChan FAN,HaiBin JIANG,Jie WANG,XiaoXue FAN,ZhiWei ZHU,Qi LONG,ZongBing CAI,YanZhen ZHENG,ZhongMin FU,GuoJun XU,DaFu CHEN,Rui GUO. Improvement of Nosema ceranae Genome Annotation Based on Nanopore Full-Length Transcriptome Data[J]. Scientia Agricultura Sinica, 2021, 54(6): 1288-1300.

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参考文献 35

[1]	WHEELER D A, SRINIVASAN M, EGHOLM M, SHEN Y, CHEN L, MCGUIRE A, HE W, CHEN Y J, MAKHIJANI V, ROTH G T, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature, 2008,452(7189):872-876. doi: 10.1038/nature06884 pmid: 18421352
[2]	XIA Q, ZHOU Z, LU C, CHENG D, DAI F, LI B, ZHAO P, ZHA X, CHENG T, CHAI C, et al. A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science, 2004,306(5703):1937-1940. doi: 10.1126/science.1102210 pmid: 15591204
[3]	The Honeybee Genome Sequencing Consortium. Insights into social insects from the genome of the honeybee Apis mellifera. Nature, 2006,443(7114):931-949. doi: 10.1038/nature05260 pmid: 17073008
[4]	KOCHER S D, LI C, YANG W, TAN H, YI S V, YANG X, HOEKSTRA H E, ZHANG G, PIERCE N E, YU D W. The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes. Genome Biology, 2013,14(12):R142. doi: 10.1186/gb-2013-14-12-r142 pmid: 24359881
[5]	PARK D, JUNG J W, CHOI B S, JAYAKODI M, LEE J, LIM J, YU Y, CHOI Y S, LEE M L, PARK Y, CHOI I Y, YANG T J, EDWARDS O R, NAH G, KWON H W. Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing. BMC Genomics, 2015,16(1):1. doi: 10.1186/1471-2164-16-1
[6]	OLSEN J L, ROUZÉ P, VERHELST B, LIN Y C, BAYER T, COLLEN J, DATTOLO E, DE PAOLI E, DITTAMI S, MAUMUS F, et al. The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature, 2016,530(7590):331-335. doi: 10.1038/nature16548 pmid: 26814964
[7]	ZHANG G Q, XU Q, BIAN C, TSAI W C, YEH C M, LIU K W, YOSHIDA K, ZHANG L S, CHANG S B, CHEN F, et al. The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution. Scientific Reports, 2016,6:19029. doi: 10.1038/srep19029 pmid: 26754549
[8]	PELIN A, SELMAN M, 1 ARIS-BROSOU S, FARINELLI L, CORRADI N. Genome analyses suggest the presence of polyploidy and recent human-driven expansions in eight global populations of the honeybee pathogen Nosema ceranae. Environmental Microbiology, 2015,17(11):4443-4458. doi: 10.1111/1462-2920.12883 pmid: 25914091
[9]	LIU B, ZHOU Y, LI K, HU X, WANG C, CAO G, XUE R, GONG C. The complete genome of cyprinid herpesvirus 2, a new strain isolated from Allogynogenetic crucian carp. Virus Research, 2018,256:6-10. doi: 10.1016/j.virusres.2018.07.016 pmid: 30053416
[10]	RHOADS A, AU K F. PacBio sequencing and its applications. Genomics Proteomics Bioinformatics, 2015,13(5):278-289. doi: 10.1016/j.gpb.2015.08.002 pmid: 26542840
[11]	MAGRINI V, GAO X, ROSA B A, MCGRATH S, ZHANG X, HALLSWORTH-PEPIN K, MARTIN J, HAWDON J, WILSON R K, MITREVA M. Improving eukaryotic genome annotation using single molecule mRNA sequencing. BMC Genomics, 2018,19(1):172. pmid: 29495964
[12]	TANG Y T, GAO X, ROSA B A, ABUBUCKER S, HALLSWORTH- PEPIN K, MARTIN J, TYAGI R, HEIZER E, ZHANG X, BHONAGIRI-PALSIKAR V, et al. Genome of the human hookworm Necator americanus. Nature Genetics, 2014,46(3):261-269. doi: 10.1038/ng.2875
[13]	MITREVA M, JASMER D P, ZARLENGA D S, WANG Z, ABUBUCKER S, MARTIN J, TAYLOR C M, YIN Y, FULTON L, MINX P, et al. The draft genome of the parasitic nematode Trichinella spiralis. Nature Genetics, 2011,43(3):228-235. doi: 10.1038/ng.769 pmid: 21336279
[14]	PENDLETON M, SEBRA R, PANG A W C, UMMAT A, FRANZEN O, RAUSCH T, STÜTZ A M, STEDMAN W, ANANTHARAMAN T, HASTIE A, et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nature Methods, 2015,12(8):780-786. doi: 10.1038/nmeth.3454 pmid: 26121404
[15]	SHIELDS E J, SHENG L, WEINER A K, GARCIA B A, BONASIO R. High-quality genome assemblies reveal long non-coding RNAs expressed in ant brains. Cell Reports, 2018,23(10):3078-3090. doi: 10.1016/j.celrep.2018.05.014 pmid: 29874592
[16]	DACCORD N, CELTON J M, LINSMITH G, BECKER C, CHOISNE N, SCHIJLEN E, VAN DE GEEST H, BIANCO L, MICHELETTI D, VELASCO R, et al. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nature Genetics, 2017,49(7):1099-1106. pmid: 28581499
[17]	DONG L, LIU H, ZHANG J, YANG S, KONG G, CHU S C, CHEN N, WANG D. Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research. BMC Genomics, 2015,16(1):1039. doi: 10.1186/s12864-015-2257-y
[18]	CORNMAN R S, CHEN Y P, SCHATZ M C, STREET S, ZHAO Y, DESANY B, EGHOLM M, HUTCHISON S, PETTIS J S, LIPKIN W I, EVANS J D. Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees. PLoS Pathogens, 2009,5(6):e1000466. doi: 10.1371/journal.ppat.1000466 pmid: 19503607
[19]	陈华枝, 杜宇, 范小雪, 祝智威, 蒋海宾, 王杰, 范元婵, 熊翠玲, 郑燕珍, 付中民, 徐国钧, 陈大福, 郭睿. 基于第三代纳米孔测序技术的东方蜜蜂微孢子虫全长转录组构建及注释. 昆虫学报, 2020,63(12):1461-1472.
	CHEN H Z, DU Y, FAN X X, ZHU Z W, JIANG H B, WANG J, FAN Y C, XIONG C L, ZHENG Y Z, FU Z M, XU G J, CHEN D F, GUO R. Construction and annotation of the full-length transcriptome of Nosema ceranae based on the third-generation nanopore sequencing technology. Acta Entomologica Sinica, 2020,63(12):1461-1472. (in Chinese)
[20]	陈华枝, 范小雪, 范元婵, 王杰, 祝智威, 蒋海宾, 张文德, 隆琦, 熊翠玲, 郑燕珍, 付中民, 徐国钧, 陈大福, 郭睿. 东方蜜蜂微孢子虫基因的可变剪接及可变腺苷酸化解析. 菌物学报, 2021,40(1):161-173.
	CHEN H Z, FAN X X, FAN Y C, WANG J, ZHU Z W, JIANG H B, ZHANG W D, LONG Q, XIONG C L, ZHENG Y Z, FU Z M, XU G J, CHEN D F, GUO R. Analysis of alternative splicing and alternative polyadenylation of Nosema ceranae genes. Mycosystema, 2021,40(1):161-173. (in Chinese)
[21]	THIEL T, MICHALEK W, VARSHNEY R, GRANER A. Exploiting EST databases for the development and characterization of gene- derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics, 2003,106(3):411-422. pmid: 12589540
[22]	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)
[23]	熊翠玲, 王海朋, 郑燕珍, 付中民, 徐国均, 童新宇, 赵红霞, 陈大福, 郭睿. 基于中华蜜蜂幼虫肠道转录组数据对东方蜜蜂基因组的基因结构优化及新基因鉴定. 中国农业大学学报, 2019,24(3):86-93.
	XIONG C L, WANG H P, ZHENG Y Z, FU Z M, XU G J, TONG X Y, ZHAO H X, CHEN D F, GUO R. Gene structure optimization and identification of novel genes in Apis cerana genome: Based on the transcriptome data obtained from larval gut. Journal of China Agricultural University, 2019,24(3):86-93. (in Chinese)
[24]	CHENG B, FURTADO A, HENRY R J. Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts. Giga Science, 2017,6(11):1-13. doi: 10.1093/gigascience/gix093 pmid: 29048480
[25]	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. doi: 10.1007/s13592-018-0593-z
[26]	BARRETT L W, FLETCHER S, WILTON S D. Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements. Cellular and Molecular Life Sciences, 2012,69(21):3613-3634. pmid: 22538991
[27]	熊翠玲, 童新宇, 陈华枝, 耿四海, 庄天艺, 郑燕珍, 付中民, 陈大福, 赵红霞, 郭睿. 东方蜜蜂微孢子虫的基因结构优化及新基因鉴定. 环境昆虫学报, 2019,41(2):373-379.
	XIONG C L, TONG X Y, CHEN H Z, GENG S H, ZHUANG T Y, ZHENG Y Z, FU Z M, CHEN D F, ZHAO H X, GUO R. Optimization of gene structure and identification of novel genes in Nosema ceranae. Journal of Environmental Entomology, 2019,41(2):373-379. (in Chinese)
[28]	JARNE P, LAGODA P J. Microsatellites, from molecules to populations and back. Trends in Ecology and Evolution, 1996,11(10):424-429. pmid: 21237902
[29]	ZANE L, BARGELLONI L, PATARNELLO T. Strategies for microsatellite isolation: A review. Molecular Ecology, 2002,11(1):1-16. doi: 10.1046/j.0962-1083.2001.01418.x pmid: 11903900
[30]	朱家颖, 吴国星, 杨斌. 基于转录组数据高通量发掘黄粉甲微卫星引物. 昆虫学报, 2013,56(7):724-728.
	ZHU J Y, WU G X, YANG B. High-throughput discovery of SSR genetic markers in the yellow mealworm beetle, Tenebrio molitor (Coleoptera: Tenebrionidae), from its transcriptome database. Acta Entomologica Sinica, 2013,56(7):724-728. (in Chinese)
[31]	罗梅, 张鹤, 宾淑英, 林进添. 基于转录组数据高通量发掘扶桑绵粉蚧微卫星引物. 昆虫学报, 2014,57(4):395-400.
	LUO M, ZHANG H, BIN S Y, LIN J T. High-throughput discovery of SSR genetic markers in the mealybug, Phenacoccus solenopsis (Hemiptera: Pseudococcidae), from its transcriptome database. Acta Entomologica Sinica, 2014,57(4):395-400. (in Chinese)
[32]	李汶东, 熊翠玲, 王鸿权, 侯志贤, 童新宇, 张璐, 付中民, 郑燕珍, 陈大福, 郭睿. 基于RNA-seq数据大规模挖掘蜜蜂球囊菌的SSR分子标记. 福建农林大学学报(自然科学版), 2017,46(4):434-438.
	LI W D, XIONG C L, WANG H Q, HOU Z X, TONG X Y, ZHANG L, FU Z M, ZHENG Y Z, CHEN D F, GUO R. Large scale development of SSR molecular markers of Ascosphaera apis based on RNA-seq data. Journal of Fujian Agriculture and Forestry University (Natural Science Edition), 2017,46(4):434-438. (in Chinese)
[33]	熊翠玲, 张璐, 付中民, 王鸿权, 侯志贤, 童新宇, 李汶东, 郑燕珍, 陈大福, 郭睿. 基于RNA-seq数据大规模开发中华蜜蜂幼虫的SSR分子标记. 环境昆虫学报, 2017,39(1):68-74.
	XIONG C L, ZHANG L, FU Z M, WANG H Q, HOU Z X, TONG X Y, LI W D, ZHENG Y Z, CHEN D F, GUO R. Large-scale development of SSR primers for Apis cerana cerana larvae based on its RNA-seq datasets. Journal of Environmental Entomology, 2017,39(1):68-74. (in Chinese)
[34]	郭睿, 陈华枝, 庄天艺, 熊翠玲, 郑燕珍, 付中民, 陈恒, 陈大福. 利用转录组数据开发意大利蜜蜂的SSR分子标记. 安徽农业大学学报, 2018,45(3):404-408.
	GUO R, CHEN H Z, ZHUANG T Y, XIONG C L, ZHENG Y Z, FU Z M, CHEN H, CHEN D F. Exploitation of SSR markers for Apis mellifera ligustica based on transcriptome data. Journal of Anhui Agricultural University, 2018,45(3):404-408. (in Chinese)
[35]	张鹏飞, 周晓榕, 庞保平, 谭瑶, 常静, 高利军. 基于转录组数据高通量发掘沙葱萤叶甲微卫星引物. 应用昆虫学报, 2016,53(5):1058-1064.
	ZHANG P F, ZHOU X R, PANG B P, TAN Y, CHANG J, GAO L J. High-throughput discovery of microsatellite markers in Galeruca daurica (Coleoptera: Chrysomelidae) from a transcriptome database. Chinese Journal of Applied Entomology, 2016,53(5):1058-1064. (in Chinese)

基因ID Gene ID	基因位置 Gene locus	正负链 Plus and minus strand	末端 End	原位置 Original site	优化后位置 Optimized site
Gene1175	NW_020169317.1:49652-50638	-	3′	50341	50638
Gene326	NW_020169413.1:1478-3041	-	3′	2683	3041
Gene503	NW_020169431.1:1208-2193	-	5′	1461	1208
Gene503	NW_020169431.1:1208-2193	-	3′	1634	2193
Gene1591	NW_020169298.1:96744-98975	+	5′	96746	96744
Gene1591	NW_020169298.1:96744-98975	+	3′	98671	98975
Gene588	NW_020169310.1:2436-3030	+	3′	2741	3030
Gene350	NW_020169307.1:13073-18338	-	5′	17277	13073
Gene36	NW_020169296.1: 54153-55245	-	5′	54289	54153
Gene2363	NW_020169300.1:40046-41314	-	5′	40510	40046

MISA搜索项目 MISA searching item	数量 Number
搜索基因 Searching gene	8021
搜索基因的总序列长度 Total sequence length of searching gene (bp)	8265494
鉴定到的SSR位点 Identified SSR loci	1658
鉴定到的SSR总序列长度 Total sequence length of identified SSRs (bp)	1405
含有1个以上SSR的基因 Genes containing more than one SSR	212
混合SSR Mixed SSR	65
单核苷酸重复Single nucleotide repeat	1622
双核苷酸重复Dinucleotide repeat	23
三核苷酸重复Trinucleotide repeat	7
四核苷酸重复Tetranucleotide repeat	6

基于纳米孔全长转录组数据完善东方蜜蜂微孢子虫的基因组注释

Improvement of Nosema ceranae Genome Annotation Based on Nanopore Full-Length Transcriptome Data

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