红白锦鲤皮肤转录组测序分析
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摘要
为进一步开发红白锦鲤Cyprinus carpio haematopterus肤色基因资源,采用Illumina PE150高通量测序技术对体长为(28.34±3.12)cm的红白锦鲤的白色和红色皮肤组织进行了转录组测序,获得116.26 Gb Clean Date,并与Nr、GO、KEGG、KOG、Pfam、Swiss-Prot、eggNOG等7个数据库进行BLAST信息比对,共获得10 476个注释基因。结果表明:Nr数据库注释成功比例最高,为35.62%;通过功能、通路富集分析,差异基因富集在包括激动蛋白细胞骨架调节/黏着斑通路在内的132个代谢途径;随机选取9个差异基因进行qRT-PCR验证发现,红白锦鲤皮肤差异表达基因的表达趋势与RNA-seq定量结果一致,表明转录组测序结果是可靠的。本研究中获得的转录组数据可为今后观赏鱼肤色关键基因开发及功能分析等研究提供基础数据。
Illumina PE150 high-throughput sequencing technology was used to sequence the transcriptome of white skin and red skin tissue of Cyprinus carpio haematopterus with body length of(28.34±3.12)cm in order to further develop gene resources of red and white koi carp Cyprinus carpio haematopterus. The 116.26 Gb Clean Date obtained were compared with seven databases of Nr, GO, KEGG, KOG, Pfam, Swiss-Prot, and eggNOG. A total of 10 476 annotated genes were obtained, with the maxiaml percent of annotation success(35.62%) in Nr database. The functional and pathway enrichment analysis revealed that differential genes were enriched in 132 metabolic pathways including regulation of actin cytoskeleton and focal adhesion pathway. qRT-PCR of 9 differentially expressed genes selected randomly showed that the expression of differentially expressed genes in the skin of Cyprinus carpio haematopterus was consistent with the quantitative results of RNA-seq, indicating that the transcriptome sequencing were reliable. The transcriptome data obtained in this study can provide basic data for future research on key gene development and functional analysis of ornamental fish skin color.
Illumina PE150 high-throughput sequencing technology was used to sequence the transcriptome of white skin and red skin tissue of Cyprinus carpio haematopterus with body length of(28.34±3.12)cm in order to further develop gene resources of red and white koi carp Cyprinus carpio haematopterus. The 116.26 Gb Clean Date obtained were compared with seven databases of Nr, GO, KEGG, KOG, Pfam, Swiss-Prot, and eggNOG. A total of 10 476 annotated genes were obtained, with the maxiaml percent of annotation success(35.62%) in Nr database. The functional and pathway enrichment analysis revealed that differential genes were enriched in 132 metabolic pathways including regulation of actin cytoskeleton and focal adhesion pathway. qRT-PCR of 9 differentially expressed genes selected randomly showed that the expression of differentially expressed genes in the skin of Cyprinus carpio haematopterus was consistent with the quantitative results of RNA-seq, indicating that the transcriptome sequencing were reliable. The transcriptome data obtained in this study can provide basic data for future research on key gene development and functional analysis of ornamental fish skin color.
引文
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[2] Mininni A N,Milan M,Ferraresso S,et al.Liver transcriptome analysis in gilthead sea bream upon exposure to low temperature[J].BMC Genomics,2014,15:765.
[3] Lockhart D J,Winzeler E A.Genomics,gene expression and DNA arrays[J].Nature,2000,405(6788):827-836.
[4] Garg R,Patel R K,Tyagi A K,et al.De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification[J].DNA Research,2011,18(1):53-63.
[5] Hussainzada N,Lewis J A,Baer C E,et al.Whole adult organism transcriptional profiling of acute metal exposures in male zebrafish[J].BMC Pharmacology and Toxicology,2014(15):15-29.
[6] 聂洪涛,姜力文,郑梦鸽,等.大竹蛏高通量转录组测序数据组装和分析[J].大连海洋大学学报,2017,32(6):658-663.
[7] 赵永利,夏明哲,吴蓉蓉,等.基于高通量测序的花斑裸鲤转录组及功能分析[J].青海大学学报,2018,36(1):1-8.
[8] Pereiro P,Balseiro P,Romero A,et al.High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454-pyrosequencing for the discovery of antiviral immune genes[J].PLoS One,2012,7(5):e35369.
[9] 刘思嘉,田菲,张存芳,等.鲤在低温胁迫下肝胰腺转录组测序分析[J].生物技术通报,2018,34(11):168-178.
[10] Renaut S,Nolte A W,Bernatchez L.Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp.,Salmonidae)[J].Molecular Ecology,2010,19(S1):115-131.
[11] 黄勇,高小婵,孙西红.基于RNA-Seq高通量测序技术的大鲵转录组分析[J].基因组学与应用生物学,2018,37(9):3759-3768.
[12] 赵文,高峰英,石振广.达氏鳇肌肉组织转录组测序和功能分析[J].水产学报,2014,38(9):1255-1262.
[13] 史东杰,梁拥军,孙砚胜,等.锦鲤“御三家”新品系的选育[J].水产科技情报,2014,41(3):152-154.
[14] Murakami M,Ohi M,Ishikawa S,et al.Adaptive expression of uncoupling protein 1 in the carp liver and kidney in response to changes in ambient temperature[J].Comparative Biochemistry and Physiology Part A:Molecular & Integrative Physiology,2015,185:142-149.
[15] 张春兰,赵文,徐立蒲,等.微生态制剂和着色剂对锦鲤体色的影响[J].大连海洋大学学报,2011,26(4):328-332.
[16] 史东杰,梁拥军,许金华,等.微生态制剂对锦鲤生长性能、肌肉组成、体色及非特异性免疫的影响[J].河南农业科学,2017,46(1):144-148.
[17] 崔培,姜志强,王雪,等.不同蛋白水平的虾青素饲料对锦鲤体色、生长及免疫的影响[J].上海海洋大学学报,2012,21(3):382-388.
[18] 何志刚,王冬武,邓时铭,等.不同饲料对锦鲤体色和着色成本的影响[J].中国饲料添加剂,2015(8):23-25.
[19] 何志刚,王冬武,曾国清,等.不同饲料对红白锦鲤生长、体色和血液生化指标的影响[J].广东农业科学,2015,42(20):107-111.
[20] 孙向军,罗琳,姜志强,等.饲料脂肪水平对锦鲤体色和几项免疫指标的影响[J].大连海洋大学学报,2011,26(5):397-401.
[21] 王巍,胡红霞,孙向军,等.锦鲤酪氨酸酶基因序列分析及其在不同锦鲤品系不同组织中的表达[J].水产学报,2012,36(11):1658-1666.
[22] 赵刚,龚全,刘亚,等.基于Illumina高通量测序的岩原鲤转录组分析[J].西南农业学报,2016,29(7):1743-1749.