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浙江大学学报(农业与生命科学版)  2023, Vol. 49 Issue (5): 729-743    DOI: 10.3785/j.issn.1008-9209.2022.07.071
动物科学与动物医学     
利用长链非编码RNAs与mRNAs联合分析半番鸭及番鸭胚胎期性腺发育差异
李丽1,2(),章琳俐1,2,辛清武1,2,缪中纬1,2,朱志明1,2,邱君志3,郝晓娜4,黄勤楼2(),郑嫩珠1,2()
1.福建省农业科学院畜牧兽医研究所, 福建 福州 350013
2.福建省畜禽遗传育种重点实验室, 福建 福州 350013
3.福建农林大学生命科学学院, 福建 福州 350002
4.福建农林大学动物科学学院(蜂学学院), 福建 福州 350002
Combined analysis of embryonic gonadal development differences of mulard duck and muscovy duck using long non-coding RNAs and mRNAs
Li LI1,2(),Linli ZHANG1,2,Qingwu XIN1,2,Zhongwei MIAO1,2,Zhiming ZHU1,2,Junzhi QIU3,Xiaona HAO4,Qinlou HUANG2(),Nenzhu ZHENG1,2()
1.Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, Fujian, China
2.Fujian Key Laboratory of Animal Genetics and Breeding, Fuzhou 350013, Fujian, China
3.College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
4.College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
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摘要:

本研究旨在筛选影响鸭胚胎期性腺发育的关键mRNAs和长链非编码RNAs(long non-coding RNAs, lncRNAs),科学解释半番鸭性腺发育缺陷问题。采集半番鸭(BF1、BF2、BF3)和番鸭(F1、F2、F3)各3个雄性胚胎性腺组织并提取其RNA,通过高通量测序筛选差异基因和lncRNAs,预测靶基因并进行功能注释,最后应用实时荧光定量聚合酶链反应(real-time fluorescence quantitative polymerase chain reaction, qRT-PCR)对测序结果进行验证。结果显示:从半番鸭和番鸭性腺组织中共筛选出1 109个差异基因;相对于番鸭,半番鸭中上调表达基因共857个,下调表达基因共252个,其中,醛酮还原酶家族1成员D1基因(aldo-keto reductase family 1 member D1 gene, AKR1D1)、17β-羟基类固醇脱氢酶3基因(17β-hydroxysteroid dehydrogenase 3 gene, 17β-HSD3)和胆固醇侧链裂解酶基因(cholesterol side-chain cleavage enzyme gene, P450scc)等可能与半番鸭性腺分化发育相关。同时,获得了733个显著差异表达的lncRNAs;相对于番鸭,半番鸭中显著上调的lncRNAs共660个,显著下调的lncRNAs共73个。靶基因预测分析显示,136个下调的lncRNAs和893个上调的lncRNAs可能参与差异基因表达并存在潜在的调控关系,其中,TCONS_00246198靶向17β-HSD3,TCONS_00229529靶向四次穿膜蛋白2基因(tetraspanin-2 gene, TSPAN2),说明以上lncRNAs可能通过靶向关键基因来参与鸭胚胎期性腺发育。qRT-PCR结果显示,差异基因和lncRNAs表达水平与转录组测序中的表达趋势一致,表明通过高通量测序获得的数据较为可靠。RNA结合蛋白免疫沉淀(RNA binding protein immunoprecipitation, RIP)试验结果发现,与IgG相比,TCONS_00246198富集水平达71.51倍,表明TCONS_00246198与17β-HSD3蛋白存在直接或间接的相互作用,即两者可能存在靶向关系。综上所述,本研究获得了一批可能影响鸭胚胎期性腺发育的关键mRNAs和lncRNAs,推测差异lncRNAs可以调控差异基因的表达,为了解鸭胚胎期性腺发育差异及禽类性腺发育机制提供了科学依据。

关键词: 半番鸭番鸭性腺不育长链非编码RNAsmRNAs    
Abstract:

The purpose of this study was to screen key mRNAs and long non-coding RNAs (lncRNAs) that affect gonadal development in duck embryos and to explain scientifically gonadal development defects in the mulard duck. Three male embryonic gonadal tissues of the mulard duck (BF1, BF2, BF3) and the muscovy duck (F1, F2, F3) were collected to extract RNA and perform high-throughput sequencing, and differential genes and lncRNAs were screened to predict target genes and perform functional annotations. Finally, the sequencing data were verified by real-time fluorescence quantitative polymerase chain reaction (qRT-PCR). The results showed that a total of 1 109 differentially expressed genes were screened from the gonadal tissues of the mulard duck and the muscovy duck. Compared with the muscovy duck, 857 genes were up-regulated and 252 genes were down-regulated in the mulard duck. Among them, the aldo-keto reductase family 1 member D1 gene (AKR1D1), 17β-hydroxysteroid dehydrogenase 3 gene (17β-HSD3), and cholesterol side-chain cleavage enzyme gene (P450scc) may be related to gonadal differentiation and development in the mulard duck. Meanwhile, 733 significantly differentially expressed lncRNAs were obtained. Compared with the muscovy duck, a total of 660 lncRNAs were significantly up-regulated and 73 lncRNAs were significantly down-regulated in the mulard duck. Target gene prediction analysis showed that a total of 136 down-regulated lncRNAs and 893 up-regulated lncRNAs may be involved in differential gene expression and had potential regulatory relationships, among which, TCONS_00246198 targeted 17β-HSD3, and TCONS_00229529 targeted tetraspanin-2 gene (TSPAN2), suggesting that the above lncRNAs may participate in duck embryonic gonadal development by targeting key genes. The qRT-PCR results showed that the expression levels of differential genes and lncRNAs were consistent with the expression trends in transcriptome sequencing, indicating that the data obtained by high-throughput sequencing are relatively reliable. RNA binding protein immunoprecipitation (RIP) assay results revealed that compared with IgG, the enrichment level of TCONS_00246198 reached 71.51 times. The above results indicate that TCONS_00246198 interacts directly or indirectly with the 17β-HSD3 protein, which means that they may have a targeting relationship. In summary, this study obtains a batch of key mRNAs and lncRNAs that may affect duck embryonic gonadal development, and it is speculated that the differential lncRNAs can regulate the expression of differential genes. This study provides a scientific basis for understanding the differences in duck embryonic gonadal development and the mechanisms of avian gonadal development.

Key words: mulard duck    muscovy duck    gonad    infertility    long non-coding RNAs (lncRNAs)    mRNAs
收稿日期: 2022-07-07 出版日期: 2023-11-03
CLC:  S834.89  
基金资助: 福建省自然科学基金项目(2021J01483);福建省省属公益类项目(2020R10260016);福建省农业科学院英才项目(YC20210046);福建省现代家禽产业技术体系建设专项(2019—2022);福建省“5511”协同创新工程项目(XTCXGC2021008);福建省农业科学院科技创新团队项目(CXTD2021006-2)
通讯作者: 黄勤楼,郑嫩珠     E-mail: 576801792@qq.com;hql202@126.com;zhengnz@163.com
作者简介: 李丽(https://orcid.org/0000-0002-9953-7785),E-mail:576801792@qq.com
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引用本文:

李丽,章琳俐,辛清武,缪中纬,朱志明,邱君志,郝晓娜,黄勤楼,郑嫩珠. 利用长链非编码RNAs与mRNAs联合分析半番鸭及番鸭胚胎期性腺发育差异[J]. 浙江大学学报(农业与生命科学版), 2023, 49(5): 729-743.

Li LI,Linli ZHANG,Qingwu XIN,Zhongwei MIAO,Zhiming ZHU,Junzhi QIU,Xiaona HAO,Qinlou HUANG,Nenzhu ZHENG. Combined analysis of embryonic gonadal development differences of mulard duck and muscovy duck using long non-coding RNAs and mRNAs. Journal of Zhejiang University (Agriculture and Life Sciences), 2023, 49(5): 729-743.

链接本文:

https://www.zjujournals.com/agr/CN/10.3785/j.issn.1008-9209.2022.07.071        https://www.zjujournals.com/agr/CN/Y2023/V49/I5/729

名称

Name

GenBank登录号

GenBank accession No.

引物序列(5→3

Primer sequence (5→3)

扩增长度

Size/bp

退火温度

Annealing temperature/℃

GAPDHXM_005016745.2

F: GGAGCTGCCCAGAACATTATC

R: GCAGGTCAGGTCCACGACA

14160
AKR1D1101802488

F: CGTGTCCTCCCCTCCTTTA

R: CCTCGCTGGATGCTGAAAC

10560
17β-HSD3101799136

F: GGGACTGATCTGTTTCTGTGCT

R: CCATCTCCTGCTCCTGTGA

13860
LOC101794158101794158

F: CCTTTGGCATCGGGATTGGA

R: GCCGGATGACTCTGTTGGA

13860
PTGFRN101794936

F: CACAATGGGAGCTGGCATAAAGT

R: GGTGGGGTCATCTGAAAACTTG

13260
TCONS_00189165XLOC_112996

F: GCTATGAAGAGGAAAAGGGATGTC

R: GCGCTTAAACGAGAGGAACCA

7960
XR_003494977.1106018179

F: GGAACCATAATGTGCCAGCTGAA

R: CCTTGCAGTTGATAAGACGATGGTA

9660
TCONS_00087264101791443

F: GAGCCACAGACACGAAGAGAA

R: GGGGAATCAGTAACCCATAGC

9660
XR_003498542.1113844190

F: GAAGAGGACACCGATCAAGAG

R: GTAACAACCTTCAGCCACTCAAAC

8760
表1  qRT-PCR引物序列信息
图1  半番鸭和番鸭雌雄鉴定bf/BF:半番鸭;b:北京鸭;f/F:番鸭;M:DNA标志物。

样品

Sample

原始读长

Raw read

高质量读长

Clean read

原始碱基数

Raw base

number/Gb

高质量碱基数

Clean base

number/Gb

Q20/%Q30/%

GC含量

GC content/%

比对读长(比对率)

Mapped read

(mapped rate/%)

BF188 347 43687 273 71213.2513.0998.0194.2549.5366 096 582(75.73)
BF2106 246 148104 905 27015.9415.7497.9794.2549.2077 624 844(74.00)
BF388 259 88287 107 52213.2413.0798.1694.7448.7166 689 926(76.56)
F1106 867 756105 328 09015.5915.8098.1594.7448.7867 180 376(63.78)
F292 794 78291 434 96815.2713.7298.2994.9950.0857 816 779(63.23)
F396 607 49495 297 67015.7014.2998.2995.0949.0661 078 250(64.09)
表2  测序数据的质量及比对分析
图2  半番鸭中相对于番鸭的差异表达的lncRNAs

GenBank 登录号

GenBank accession No.

基因名称

Gene name

FPKM值 FPKM valuelog2 (FC)

p

p-value

padj
半番鸭 Mulard duck番鸭 Muscovy duck
101792001THSD430.576 36021.438 52.38×10-238.19×10-19
101805128MACROD223.394 99020.716 15.52×10-243.80×10-19
101792143TSPAN410.613 14020.461 31.06×10-212.44×10-17
101791830RPL7A1 032.393 00020.430 91.73×10-212.98×10-17
101794364PTBP341.773 16019.867 64.27×10-204.91×10-16
101794113TCF414.043 13019.581 08.10×10-206.97×10-16
101790148PRKAR1B21.604 88019.434 57.84×10-206.97×10-16
101 798636BMPR1A30.705 36019.327 01.58×10-191.09×10-15
101799292MXRA783.668 07019.209 64.22×10-192.64×10-15
101803865LOC101803865190.221 80019.199 01.21×10-185.13×10-15
101796808LRP2037.974 58-20.637 31.44×10-71.92×10-5
101790849BBS907.721 36-19.545 72.49×10-73.06×10-5
101803047AUTS202.290 90-19.088 01.13×10-61.06×10-4
101793582TEAD109.605 26-18.878 11.53×10-61.36×10-4
101795217ACTN1012.786 68-18.458 21.95×10-45.97×10-3
101798600SLC4A404.550 25-18.312 77.69×10-65.08×10-4
101803985TBC1D502.929 80-18.191 82.24×10-46.58×10-3
101790849BBS902.916 37-18.165 62.27×10-46.64×10-3
101791925GAK012.974 59-18.117 05.60×10-169.41×10-13
101794936PTGFRN021.933 99-17.955 56.66×10-158.34×10-12
表3  差异倍数前10位的差异基因

转录本号

Transcript ID

转录本名称

Transcript name

FPKM值 FPKM valuelog2 (FC)

p

p-value

padj
半番鸭 Mulard duck番鸭 Muscovy duck
TCONS_00036148LOC101796976-OT257.680 6020.229 81.18×10-44.07×10-3
TCONS_00258829LINC4586131.759 7019.484 81.56×10-191.09×10-15
TCONS_00260238LINC464294.465 7018.437 03.71×10-179.82×10-14
TCONS_00258290LOC101805096-OT15.334 5018.284 43.62×10-62.73×10-4
TCONS_00203531LOC113845374-OT57.646 8017.936 79.07×10-151.10×10-11
TCONS_00258785LINC456419.433 6016.873 34.84×10-122.03×10-9
TCONS_00262674LOC113842089-OT114.538 8016.850 83.31×10-132.17×10-10
TCONS_00036199LOC101796281-OT29.120 5016.749 44.36×10-41.07×10-2
XR_003494977.1LOC10601817922.879 7016.701 06.73×10-133.89×10-10
TCONS_00258797LINC457917.896 5016.600 11.55×10-127.73×10-10
TCONS_00032957PHF21B-OT102.490 1-17.482 12.30×10-142.37×10-11
TCONS_00087264ESRRG-OT200.921 4-15.881 61.61×10-104.31×10-8
TCONS_00250319LOC101789623-OT101.653 1-14.860 81.80×10-32.95×10-2
TCONS_00054873TRHR-OT101.634 7-14.786 38.36×10-53.16×10-3
TCONS_00254443LOC113841128-OT601.830 1-14.273 02.08×10-46.24×10-3
TCONS_00254482LINC4324010.620 7-14.202 63.15×10-34.43×10-2
TCONS_00110367APELA-OT103.733 0-13.559 65.12×10-36.24×10-2
TCONS_00200982LINC345200.893 3-13.375 15.94×10-64.11×10-4
TCONS_00153334NR5A2-OT100.515 0-13.217 46.14×10-37.04×10-2
TCONS_00190897LINC333800.230 9-13.158 07.03×10-41.50×10-2
表4  差异倍数前10位的差异表达的lncRNAs
图3  差异lncRNAs靶向差异mRNAs的维恩图
图4  差异基因和差异lncRNAs靶基因的GO富集过程A.差异基因;B.差异lncRNAs(表达相关性);C.差异lncRNAs(位置关系)。
图5  差异基因和差异lncRNAs靶基因的KEGG富集过程
图6  qRT-PCR验证半番鸭和番鸭胚胎期性腺组织中差异表达基因和lncRNAs
图7  17β -HSD3蛋白对lncRNAs TCONS_00246198的富集分析
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