Differential analysis of transcriptomes in Boettcherisca peregrine pupae at three developmental stages

Abstract

Abstract: Objective To investigate the differential expression of transcriptomes in Boettcherisca peregrine pupae at three developmental stages. Methods Total RNA was extracted from B. peregrine pupae at stages of day 1(MY1), day 5(MY2) and day 10(MY3), reverse-transcribed into cDNA, and sequenced. Gene differential expression was analyzed with edgeR software. GO enrichment analysis was made for genes with differential expression. Analysis of KEGG(Kyoto Encyclopedia of Genes and Genomes) metabolic pathway was made for Universal Gene (Unigene). The simple sequence repeat(SSR) of Unigene was detected with MISA. Results A total of 38 727 Unigenes were obtained after differential expression analysis on cDNA at the three stages. The numbers of genes with differential expression between each two stages were 1 263-2 430, with an overall number of 5 283. Pattern clustering analysis revealed similar expression patterns of those genes at the three stages. A total of 8 856 Unigenes and 336 pathways were annotated for B. peregrine pupae. A total of 12 146 SSR were detected from 8 645 Unigenes(22.3%), comprising predominantly of single-nucleotide repeats(69.23%), then the three-nucleotide repeat(21.0%). Of the SSR, the A/T occurred most frequently, followed by AAC/GTT and AG/GT. Conclusions There are significant differences in gene expression in B. peregrine pupae at different developmental stages.

Key words: Boettcherisca peregrine, Pupa, Transcriptome, Differential expression of genes

CLC Number:

R384.21

Hao ZHOU, Qi-yan WANG, Hong-ling ZHANG, Zheng REN, Jia-lin DAI, Yu-bo LIU, Jie WANG, Jiang HUANG. Differential analysis of transcriptomes in Boettcherisca peregrine pupae at three developmental stages[J]. CHINESE JOURNAL OF PARASITOLOGY AND PARASITIC DISEASES, 2017, 35(3): 274-279.

Figures/Tables 6

Fig. 1

Table 1

Fig. 2

Fig. 3

Fig. 4

Table 2

References 22

1	李学博, 巩强, 万立华, 等. 利用嗜尸性蝇类辅助推断死亡时间1例[J]. 中国法医学杂志, 2013, 28(3): 248-249.
2	蔡继峰 . 现代法医昆虫学[M]. 北京: 人民卫生出版社, 2011: 6.
3	谢丹, 彭钰龙, 郭亚东, 等. 法医昆虫学死亡时间的推断与Daubert规则之思考[J]. 法医学杂志, 2013, 29(4): 290-294.
4	Gaudry E, Myskowiak JB, Chauvet B, et al. Activity of the forensic entomology department of the French Gendarmerie[J]. Forensic Sci Int, 2001, 120(1/2): 68-71.
5	杨玲, 蔡继峰, 兰玲梅, 等. 石家庄地区夏秋季常见嗜尸性昆虫群落演替规律[J]. 法医学杂志, 2010, 26(4): 253-256.
6	Prado e Castro C, García MD, Martins da Silva P, et al. Coleoptera of flies forensic interest: a study of seasonal community composition and succession in Lisbon, Portugal[J]. Forensic Sci Int, 2013, 232(1-3): 73-83.
7	Cherix D, Wyss C, Pape T. Occurrences of flesh flies(Diptera ∶Sarcophagidae) on human cadavers in Switzerland, and their importance as forensic indicators[J]. Forensic Sci Int, 2012, 220(1-3): 158-163.
8	Ansorge WJ. Next-generation DNA sequencing techniques[J].N Biotechnol, 2009, 25(4): 195-203.
9	祁云霞, 刘永斌, 荣威恒. 转录组研究新技术: RNA-Seq及其应用[J]. 遗传, 2011, 33(11): 1191-1202.
[10]	Chen YH, Chen JH, Luo YM.Complementary biodiesel combination from tung and medium-chain fatty acid oils[J]. Renew Energy, 2012, 44(4): 305-310.
[11]	Tuskan GA, Difazio S, Jansson S, et al. The genome of black cottonwood, Populus trichocarpa(Torr. & Gray)[J]. Science, 2006, 313(5793): 1596-1604.
[12]	Wilhelm BT, Landry JR.RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing[J]. Methods, 2009, 48(3): 249-257.
[13]	陈斌, 龚正达, 张丽云, 等. 利用siRNA高通量测序技术筛查蚊子体内携带的RNA病毒[J]. 生物信息学, 2011, 9(3): 189-191.
[14]	陈禄仕. 中国尸食性蝇类[M]. 贵阳: 贵州科技出版社, 2013: 118-119.
[15]	Siriwattanarungsee S, Sukontason KL, Kuntalue B, et al. Morphology of the puparia of the housefly, Musca domestica (Diptera ∶ Muscidae) and blowfly, Chrysomya megacephala (Diptera ∶ Calliphoridae)[J]. Parasitol Res, 2005, 96(3): 166-170.
[16]	陈禄仕. 贵阳市郊嗜尸蝇类群落组成及生长观察[J]. 中国法医学杂志, 2011, 26(3): 204-206.
[17]	王贺. 铜绿蝇蛹发育形态学用于死后间隔时间推断的研究[D]. 石家庄: 河北医科大学, 2007.
[18]	Davies K, Harvey ML.Internal morphological analysis for age estimation of blow fly pupae (Diptera ∶ Calliphoridae) in postmortem interval estimation[J]. J Forensic Sci, 2013, 58(1): 79-84.
[19]	Zajac BK, Amendt J, Horres R, et al. De novo transcriptome analysis and highly sensitive digital gene expression profiling of Calliphora vicina(Diptera ∶ Calliphoridae) pupae using MACE(Massive Analysis of cDNA Ends)[J]. Sci Int Genet, 2015, 15: 137-146.
[20]	夏冰, 刘玉铭, 王启燕, 等. 大头金蝇卵不同发育时间形态变化及基因表达差异研究[J]. 中国寄生虫学与寄生虫病杂志, 2014, 32(4): 295-298.
[21]	韩宇, 刘春, 魏丽婉, 等. 家蚕酪氨酸羟化酶基因BmTh的表达及功能[J]. 昆虫学报, 2010, 53(9): 949-956.
[22]	张建珍. 昆虫几丁质代谢与植物保护[J]. 中国农业科学, 2014, 47(7): 1301-1302.

基因名称 Gene name	引物名 Primer name	引物序列（5′→ 3′） Primer sequences（5′→ 3′）	长度/bp Length/bp	退火温度/℃ Tm/℃
TH	TH-F： TH-R：	ATGGTGCTGGTCTCTTGTCC ATACCCAACGACGGAACTTG	3 625	60
CBM-14	CBM-14-F： CBM-14-R：	AAACACCACGGAAATCATCC CCAGAAGCAATCATCCCAAT	663	60
Tubulin	Tubulin-F： Tubulin-R：	GCTTCCTCATCTTCCACTCGTTC GATGTCGTAGATAGCCTCGTTGTC	1 353	60

代谢通路ID Metabolic pathway ID	代谢通路 Metabolic pathway	被注释的数量 Annotated number	所占比例/% Percentage/%
ko01100	生化代谢Metabolic pathways	1 353	15.28
ko01110	次生代谢产物的生物合成Biosynthesis of secondary metabolites	438	4.95
ko05016	亨廷顿氏舞蹈症Huntington's disease	405	4.57
ko01120	微生物的代谢Microbial metabolism in	273	3.08
ko05010	阿尔茨海默病Alzheimer's disease	254	2.87
ko05200	恶性肿瘤通路Alzheimer's disease	229	2.59
ko00230	嘌呤代谢Purine metabolism	214	2.42
ko00190	氧化磷酸化Oxidative phosphorylation	212	2.39
ko05012	帕金森病Parkinson's disease	199	2.25
ko05166	HTLV-I感染HTLV-I infection	198	2.24

[1]	XU Xinjie, LI Jing, WU Yike, YANG Feng, SHAN Wenxin, ZHANG Zhiding, YE Changjiang, SUN Entao. RNA sequencing analysis of gene expression in Dermatophagoides farinae post-exposure to horseradish and the underlying mechanisms [J]. CHINESE JOURNAL OF PARASITOLOGY AND PARASITIC DISEASES, 2025, 43(1): 112-118.
[2]	ZHANG Chi, CHEN Jiating, XIN Zixuan, YANG Lili, YANG Zihan, PENG Hongjuan. Transcriptome analysis of mice brain chronically infected with Toxoplasma gondii and validation of the kynurenine pathway associated with depression [J]. CHINESE JOURNAL OF PARASITOLOGY AND PARASITIC DISEASES, 2023, 41(3): 270-278.
[3]	QIN Xin, ZHU Feng, ZHANG Kun, ZHANG Jian. Analysis of immune genes of anopheline mosquitoes induced by Plasmodium yoelii hemolymph sporozoites [J]. CHINESE JOURNAL OF PARASITOLOGY AND PARASITIC DISEASES, 2021, 39(4): 449-454.
[4]	WANG Long-jiang, LI Jin, YIN Kun, XU Chao, LIU Gong-zhen, HUANG Bing-cheng, WEI Qing-kuan, SUN Hui. Comparative analysis of transcriptomes in Toxoplasma gondii before and after invasion in human foreskin fibroblasts [J]. CHINESE JOURNAL OF PARASITOLOGY AND PARASITIC DISEASES, 2021, 39(4): 480-486.
[5]	LI Xue-bo1，NING Shu-hua2，ZHANG Gui-qin3，YU Hong-li3，WANG Qing-shan4，Li Hong-wei4 *. Species Identification of Puparium Samples of Common Sarcosaphagous Flies Based on Molecular Marker Analysis [J]. , 2015, 33(1): 7-35-39.