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

Abstract

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

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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References 35

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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

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

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