基于RNA-Seq对猪心组织新转录本解析及可变剪接和SNP分析

doi:10.11843/j.issn.0366-6964.2025.04.016

摘要/Abstract

摘要：

为完善和优化猪基因组注释信息，本研究利用RNA-Seq测序技术，开展猪心肌组织的新转录本预测、可变剪接事件和SNP变异位点分析。本研究以藏猪(抗逆性强)和长白猪为研究对象，选取6月龄健康去势公猪各3头，采集其心肌组织样本，进行建库与测序。通过数据分析，挖掘新转录本和新基因，进一步分析可变剪接事件和SNP变异，对新基因和差异可变剪接进行富集分析。结果显示，共发现930个新基因，5 993个新转录本，富集分析显示，病毒粒子组装和病毒生命周期等条目，NF-κ B信号通路和Hedgehog信号等通路被显著富集。外显子跳跃(SE)占可变剪接类型的比例最高，筛选了159个显著的差异剪接基因，主要富集在收缩纤维、AMPK通路和昼夜节律等通路中。藏猪的变异位点均大于长白猪，同义突变数量共有311 117个位点；外显子和3'端非翻译区分别有418 136和356 478个变异位点。在极端环境下，藏猪心肌组织可能通过NF-κ B和AMPK信号通路进行免疫调节，参与细胞的代谢及凋亡，改善心肌损伤，抑制高寒低氧应激。

关键词: 藏猪, 长白猪, 新转录本, 可变剪接, SNP分析

Abstract:

The study aimed to improve and optimize the annotation information of pig genome. In this study, the RNA-Seq technology was used, novel transcript was predicted, alternative splicing events, and SNP mutation sites in porcine myocardium were analyzed. Specifically, the myocardium tissue samples from six-month old healthy castrated Tibetan and Landrace boars (3 for each) were collected respectively, then novel transcripts, alternative splicing events and SNP variation sites were analyzed and their GO and KEGG enrichment analysis were performed based on RNA-Seq sequencing and bioinformatics. The results showed that a total of 930 new genes and 5 993 new transcripts were found. The enrichment analysis showed that the virion assembly and viral life cycle terms, NF-kappa B and Hedgehog signaling pathways were significantly enriched. Skipped exon (SE) accounted for the highest proportion of alternative splicing types, and 159 significant differential splicing genes were screened, mainly enriched in contractile fiber, AMPK signaling pathway and circadian rhythm. The variation loci of Tibetan pigs were greater than that of Landrace pigs, and the number of SILENT was 311 117 loci. There were 418 136 and 356 478 variation loci in EXON and UTR_3_PRIME, respectively. Under extreme environment, Tibetan pig myocardial tissue may regulate immune through NF-κ B and AMPK signaling pathways, participate in cell metabolism and apoptosis, improve myocardial injury, and inhibit hypoxia stress.

Key words: Tibetan pig, Landrace pig, new transcript, alternative splicing, SNP analysis

中图分类号:

S828.8+9

姚博元, 杨志文, 孙亚朋, 杨雅楠, 张雅茹, 王欣荣. 基于RNA-Seq对猪心组织新转录本解析及可变剪接和SNP分析[J]. 畜牧兽医学报, 2025, 56(4): 1664-1675.

YAO Boyuan, YANG Zhiwen, SUN Yapeng, YANG Yanan, ZHANG Yaru, WANG Xinrong. Analysis of Novel Transcripts, Alternative Splicing, and SNP in Porcine Heart Tissue Based on RNA-Seq Technology[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(4): 1664-1675.

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cDNA文库 cDNA library	原始读段/bp Raw reads	过滤后读段/bp Clean reads	GC含量/% GC content	Q20碱基比例/% Q20 proportion	Q30碱基比例/% Q30 proportion
T1	42 211 434	39 818 300	49.42	98.02	94.80
T2	41 241 174	39 380 526	50.88	98.46	95.72
T3	41 558 884	39 827 352	50.63	98.48	95.78
L1	45 231 614	43 418 250	51.25	98.48	95.77
L2	45 315 072	43 168 132	51.13	97.90	94.01
L3	46 542 644	43 527 574	50.46	98.80	96.57

cDNA文库 cDNA library	比对率 Mapped ratio	单一比对率 Uniquely mapped ratio	多重比对率 Multiple mapped ratio	正链比对率 Positive strand mapped ratio	负链比对率 Negative strand mapped ratio
T1	91.96	89.00	2.96	44.46	44.54
T2	91.19	88.01	3.18	43.91	44.10
T3	91.29	88.07	3.22	43.91	44.16
L1	91.71	88.66	3.05	44.22	44.43
L2	91.27	87.76	3.52	43.78	43.98
L3	93.05	89.36	3.70	44.56	44.79

数据库 Database	注释转录本总数/个 Total number of annotated transcripts
GO	1 241
KEGG	923
总计Total	5 993

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