伊丽莎白安格斯三角梅转录组的SSR、SNP和InDel特征分析

孙利娜; 林茂; 黄旭光; 陈尔; 杨舒婷; 王华新; 龚建英

doi:10.3969/j.issn.2095-1191.2024.03.015

伊丽莎白安格斯三角梅转录组的SSR、SNP和InDel特征分析

1 广西林业科学研究院, 广西南宁 530002;
2 南宁市园林科研所, 广西南宁 530012

基金项目:

广西自然科学基金项目(2020GXNSFAA297064)

广西林业科技推广示范项目(桂林科研[2022]第11号)

广西林业科技推广示范项目(2023GXLK29)

详细信息

作者简介:
孙利娜(1981-),https://orcid.org/0000-0002-5273-6066,副研究员,主要从事园林植物遗传育种研究工作,E-mail:sunlina8958170@126.com

通讯作者:
龚建英(1978-),https://orcid.org/0000-0003-3121-0708,副研究员,主要从事园林植物遗传育种研究工作E-mail:282305221@qq.com

中图分类号: S685.99;S722.3
计量
- 文章访问数: 123
- HTML全文浏览量: 0
- PDF下载量: 4
出版历程
- 收稿日期: 2023-09-20
- 网络出版日期: 2024-06-25

SSR， SNP and InDel characteristics analysis based on transcriptome of Bougainvillea glabra‘Elizabeth Angus’

1 Guangxi Forestry Research Institute, Nanning, Guangxi 530002, China;
2 Research Institute of Landscape Architecture of Nanning, Nanning, Guangxi 530012, China

Funds:

Guangxi Natural Science Foundation(2020GXNSFAA297064)

Guangxi Forestry Science and Technology Promotion Demonstration Project(Guilinkeyan[2022]11)

Guangxi Forestry Science and Technology Promotion Demonstration Project(2023GXLK29)

摘要

摘要: 【目的】基于转录组测序数据分析伊丽莎白安格斯三角梅SSR、SNP和InDel位点特征，为开发三角梅分子标记、选育无刺或少刺品种、品种鉴定及亲缘关系分析提供理论依据。【方法】以伊丽莎白安格斯三角梅3个时期的枝刺和茎段为材料，对其进行转录组测序，采用Trinity对获得的高质量测序数据进行序列组装，利用MISA和GATK3对SSR、SNP和InDel进行特征分析。【结果】18个样本转录组测序平均获得45905982 bp Raw data，质控过滤后获得45640193 bp Clean data，拼接后获得312812条转录本和144512条Unigenes，有54516个SSR位点分布于40820条Unigenes上，发生频率为28.25%，平均分布距离为2.67 kb，包含1个以上SSR位点的Unigenes 10269条，占Unigenes总数的4.25%。在重复基元类型中，单核苷酸、二核苷酸和三核苷酸重复数量占优势，其中单核苷酸重复数量最多（39904个，占比73.20%），其次为二核苷酸重复（8169个，占比14.98%）和三核苷酸重复（5899个，占比10.82%），五核苷酸重复最少（31个，占比0.06%）。单核苷酸~六核苷酸重复类型共检测到98种重复基元，出现频率为0.01%~25.71%，其中出现频率最高的基元为A/T（37151个），占SSR位点总数的68.15%。SSR各类型重复基元的重复次数集中在5~23次，SSR序列的长度10~60 bp，平均长度为20.38 bp。共检测到231248个SNP位点和99580个InDel位点，其中SNP位点平均分布距离为1.59 kb，InDel位点平均分布距离为0.68 kb，且均以含1个位点的Unigenes数量最多，Unigenes数量随SNP和InDel位点数量的增加而逐渐减少。【结论】伊丽莎白安格斯三角梅转录组中SSR位点数量多、类型丰富，分布特征明显，可用于开发大量SSR标记，SNP和InDel位点发生频率低于模式植物，有待深度挖掘。
- 伊丽莎白安格斯三角梅 /
- 转录组 /
- SSR /
- SNP /
- InDe
Abstract: 【Objective】The characteristics of SSR， SNP and InDel sites in Bougainvillea glabra ‘Elizabeth Angus’ were analyzed based on transcriptome sequencing data to provide theoretical basis for developing molecular markers， breeding thornless or less thorn varieties， variety identification and kinship analysis of B. spectabilis Willd. 【Method】The branch thorn and stem segment at three development stages of B. glabra‘ Elizabeth Angus’ were used to transcriptomed， The obtained high-quality sequencing data were sequenced and assembled by Trinity， and SSR， SNP and InDel were characterized using MISA and GATK3. 【Result】A total of 45905982 bp raw data were obtained from the transcriptome of 18 samples， and 45640193 bp clean data were obtained after quality control filtration. 312812 transcripts and 144512 unigenes were obtained after splicing， and 54516 SSR sites were distributed on 40820 unigenes， the frequency was 28.25%， the average distance was 2.67 kb， and 10269 unigenes contained more than one SSR locus， accounting for 4.25% of the total number of unigenes. Among the repeat unit types， the numbers of mononucleotide， dinucleotide and trinucleotide repeats were dominant， mononucleotide type had the largest number of repeat motifs （39904，73.20%）， the second was dinucleotide repeats （8169，14.98%） and trinucleotide repeats （5899，10.82%）， the pentanucleotide repeats was the least （31，0.06%）. A total of 98 repetitive motifs were detected from mononucleotide to hexanucleotide repeat types， with an occurrence frequency of 0.01%-25.71%. Among them， the most frequent motif was A/T （37151）， accounting for 68.15% of the total SSR sites. The motif repeats of SSR mainly concentrated in 5-23 times and the length of SSR sequences was mainly 10-60 bp， the average length was 20.38 bp. A total of 231248 SNP sites and 99580 InDel sites were detected， with an average distribution distance of 1.59 kb SNP site and 0.68 kb InDel site respectively， and the number of unigenes contained one site was the largest， and the number of unigenes gradually decreased with increa-sing the number of SNP and InDel sites.【 Conclusion】B. glabra‘ Elizabeth Angus’ transcriptome has abundant SSR sites， rich types and obvious distribution characteristics， which can be used to develop a large number of SSR markers. SNP and InDel sites occur less frequently than model plants， which requires further mining.
- Bougainvillea glabra' Elizabeth Angus' /
- transcriptome /
- SSR /
- SNP /
- InDel

HTML全文

参考文献(35)

杜方. 2014. 百合不同器官转录组分析及SSR 标记开发应用[D]. 杭州:浙江大学.[Du F. 2014. Transcriptome analysis of different Lily organs and development and applications of SSR markers[D]. Hangzhou:Zhejiang University.]

郭聪,陈燕,王莹,谈峰,柯裴蓓,沙文锋,李玉娟. 2021. 美国红枫转录组SSR 序列分析[J]. 中南林业科技大学学报, 41(7):132-141.[Guo C,Chen Y,Wang Y,Tan F,Ke P B, Sha W F,Li Y J. 2021. Sequence analysis of SSR in transcriptome of American red maple[J]. Journal of Central South University of Forestry & Technology,41(7):132 141.] doi: 10.14067/j.cnki.1673-923x.2021.07.016.

郭栋梁,黄石连,王静,韩冬梅,李建光. 2022. 基于SSR 分子标记的龙眼种质资源遗传多样性分析及其指纹图谱构建[J]. 中国农学通报,38(36):67-73.[Guo D L,Huang S L,Wang J,Han D M,Li J G. 2022. Longan germplasms resources:Genetic diversity analysis and fingerprint construction based on SSR markers[J]. Chinese Agricultural Science Bulletin,38(36):67-73.]

郭云. 2022. 基于SSR 的叶子花属分子身份证构建及观赏性状分析[D]. 洛阳:河南科技大学.[Guo Y. 2022. Molecular identification of Bougainvillea varieties based on SSR markers and analysis of ornamental characters[D]. Luoyang:Henan University of Science and Technology.]

郝广婧,祁银燕,张得芳,朱春云. 2019. 基于转录组的黑果枸杞SSR 分布特征分析及引物设计[J]. 分子植物育种,17(13):4342-4350.[Hao G J,Qi Y Y,Zhang D F,Zhu C Y. 2019. Analysis of SSR distribution characteristics and primer design of Lycium ruthenicum Murr. based on transcriptome[J]. Molecular Plant Breeding,17(13):4342 4350.] doi: 10.13271/j.mpb.017.004342.

胡小文,孔冉,刘洋,徐志军,苏俊波. 2022. 利用转录组测序开发甘蔗SNP分子标记[J]. 南方农业学报,53(9):2527 2536.[Hu X W,Kong R,Liu Y,Xu Z J,Su J B. 2022. SNP molecular marker development based on sugarcane transcriptome sequencing[J]. Journal of Southern Agriculture,53(9):2527-2536.] doi: 10.3969/j.issn.2095-1191.2022.09.015.

黄彦晶. 2011. 三角梅(Bongainvillea brasiliensis Raeusch.)种质资源的ISSR 分析[D]. 福州:福建农林大学.[Huang Y J. 2011. ISSR analysis of germplasm resources of Bongainvillea brasiliensis Raeusch.[D]. Fuzhou:Fujian Agriculture and Forestry University.]

李房英,黄彦晶,吴少华. 2011. 三角梅种质资源的ISSR 分析[J]. 热带作物学报,32(9):1692-1696.[Li F Y,Huang Y J,Wu S H. 2011. ISSR analysis of germplasm resources of Bougainvillea spectabilis Willd[J]. Journal of Tropical Crops,32(9):1692-1696.] doi: 10.3969/j.issn.1000-2561.2011.09.022.

刘慧青,谢丽琼,王贤磊,李群,宁雪飞. 2022. 精细定位甜瓜白粉病抗性基因Pm-M[J]. 植物遗传资源学报,23(1):217-225.[Liu H Q,Xie L Q,Wang X L,Li Q,Ning X F. 2022. Fine mapping of a powdery mildew resistance gene Pm-MR1 12.1 in melon[J]. Journal of Plant Genetic Resources, 23(1):217-225.] doi: 10.13430/j.cnki.jpgr.20210506001.

陆丹,牛楠,李玥莹. 2010. SSR 标记技术在植物基因组研究上的应用[J]. 沈阳师范大学学报(自然科学版),28(1):83-85.[Lu D,Niu N,Li Y Y. 2010. Application of SSR markers in plant genome research[J]. Journal of Shenyang Normal University(Natural Science Edition),28(1):83 85.] doi: 10.3969/j.issn.1673-5862.2010.01.024.

孙利娜,李进华,甘四明,唐庆,李冰,刘雁玲,马坚炜,廖美兰,黄欣,林茂. 2021. 基于ISSR 分子标记的叶子花亲缘关系分析和指纹图谱构建[J]. 广西植物,41(2):251-265.[Sun L N,Li J H,Gan S M,Tang Q,Li B,Liu Y L,Ma J W,Liao M L,Huang X,Lin M. 2021. Analysis of genetic relationship and construction of fingerprints in Bougainvillea based on ISSR molecular marker[J]. Guihaia,41(2):251-265.] doi: 10.11931/guihaia.gxzw201904001.

孙利娜,林茂,陈升侃,孙开道,陈尔,李进华,唐庆,甘四明. 2019. 宝巾花宝巾花基于转录组测序的SSR标记的开发和应用[J]. 分子植物育种,17(24):8170-8177.[Sun L N, Lin M,Chen S K,Sun K D,Chen E,Li J H,Tang Q,Gan S M. 2019. Development and application of SSR markers derived from RNAseq data in Bougainvillea[J]. Molecular Plant Breeding,17(24):8170-8177.] doi: 10.13271/j.mpb.017.008170.

孙利娜,周群,黄妹平,周长品,徐世松,杨舒婷,杜铃,甘四明,唐庆. 2019. 基于SSR标记构建宝巾花品种的分子指纹[J]. 南京林业大学学报(自然科学版),43(6):60-66.[Sun L N,Zhou Q,Huang M P,Zhou C P,Xu S S, Yang S T,Du L,Gan S M,Tang Q. 2019. Using the SSR fluorescent labling to establish SSR fingerprint for 131 cultivars in Bougainvillea(Nyctaginaceae)[J]. Journal of Nanjing Forestry University(Natural Sciences Edition),43(6):60 66.] doi: 10.3969/j.issn.1000-2006.201812045.

王静毅,刘菊华,王卓,金志强,徐碧玉. 2019. 香蕉根系转录组SSR位点信息分析[J]. 中国农学通报,35(28):38-43.[Wang J Y,Liu J H,Wang Z,Jin Z Q,Xu B Y. 2019. Bioinformatic analysis of simple sequence repeat(SSR) loci in banana(Musa acuminata L.) root transcriptome[J]. Chinese Agricultural Science Bulletin,35(28):38-43.]

王淋,敖敦,包文泉,张淑宁,陈俊兴,李凤鸣,孟繁庆,杨钰莹,白玉娥. 2021. 基于SSR分子标记的桃品种鉴别及指纹图谱构建[J]. 中南林业科技大学学报,41(6):131-138.[Wang L,Ao D,Bao W Q,Zhang S N,Chen J X,Li F M, Meng F Q,Yang Y Y,Bai Y E. 2021. Research on the identification of main peach varieties and construction of fingerprint based on SSR markers[J]. Journal of Central South University of Forestry & Technology,41(6):131 138.] doi: 10.14067/j.cnki.1673-923x.2021.06.014.

王晓映,张方玉,万星,王成琪,刘燚,肖本泽. 2023. 基于分子标记和表型性状的水稻地方品种遗传多样性研究[J]. 植物遗传资源学报,24(3):636-647.[Wang X Y,Zhang F Y,Wan X, Wang C Q,Liu Y,Xiao B Z. 2023. Diversity of rice landraces revealed by molecular markers and phenotypic traits[J]. Journal of Plant Genetic Resources,24(3):636-647.] doi: 10.13430/j.cnki.jpgr.20221018002.

王艺儒,索玉静,傅建敏. 2022. 小果甜柿果实转录组的SSR、SNP和InDel 特征分析[J]. 西北农林科技大学学报(自然科学版),50(7):147-154.[Wang Y R,Suo Y J,Fu J M. 2022. SSR,SNP and InDel analysis based on transcriptome data of Diospyros kaki 'Xiaoguo-tianshi' fruit[J]. Journal of Northwest A&F University(Natural Science Edition),50(7):147-154.] doi: 10.13207/j.cnki.jnwafu.2022.07.017.

乌日娜,徐舶,石凤翎. 2022. 基于转录组数据的直立型扁蓿豆SSR 序列特征分析[J]. 西北农林科技大学学报(自然科学版),50(5):1-8.[Wu R N,Xu B,Shi F L. 2022. Analysis of SSR characteristics for Medicago ruthenica 'Zhilixing'based on transcriptome data[J].Journal of Nothwest A&F University(Natural Science Edition),50(5):1-8.] doi: 10.13207/j.cnki.jnwafu.2022.05.001.

武晓燕,唐源江,曹雯静. 2012. 三角梅SRAP-PCR 反应体系的建立及引物筛选[J]. 华中师范大学学报(自然科学版),46(3):335-339.[Wu X Y,Tang Y J,Cao W J. 2012. Optimization of SRAP-PCR reaction system and primer screening in Bougainvillea[J]. Journal of Central China Normal University (Natural Science),46(3):335-339.] doi: 10.19603/j.cnki.1000-1190.2012.03.018.

武晓燕. 2013. 叶子花属观赏种质资源的遗传多样性分子评价及亲缘关系分析[D]. 泉州:华侨大学.[Wu X Y. 2014. Studies on genetic diversity and phylogenetic relationship of ornamental germplasm resources in Bougainvillea[D]. Quanzhou:Huaqiao University.]

肖炳光,邱杰,曹培健, 桂毅杰, 卢秀萍, 李永平, 樊龙江. 2014. 利用基因组简约法开发烟草SNP标记及遗传作图[J]. 作物学报,40(3):397-404.[Xiao B G,Qiu J,Cao P J,Gui Y J,Lu X P, Li Y P, Fan L J. 2014. Development and genetic mapping of SNP markers via genome complexity reduction in tobacco[J]. Acta Agronomica Sinica,40(3):397-404..doi: 10.3724/SP.J.1006.2014.00397]

徐哲,钱华丽,陈小磊,张磊,董家红,季鹏章. 2023. 不同种质资源天麻转录组的SSR、SNP 和InDel 特征分析[J/OL]. 分子植物育种. https://kns.cnki.net/kcms/detail/46.1068.S.20221102.1748.006.html" target="_blank"> https://kns.cnki.net/kcms/detail/46.1068.S.20221102.1748.006.html.[Xu Z,Qian H L,Chen X L, Zhang L,Dong J H,Ji P Z. 2023. SSR,SNP and InDel characteristics of Gastrodia elata transcriptome from different germplasm resources[J/OL]. Molecular Plant Breeding. https://kns.cnki.net/kcms/detail/46.1068.S.20221102.1748.006.html" target="_blank"> https://kns.cnki.net/kcms/detail/46.1068.S.20221102.1748.006.html.]

姚国琼,杨帆,严苓方,孙正海,李伟. 2023. 基于转录组SSR的三角梅遗传多样性分析[J/OL]. 分子植物育种. http://kns.cnki.net/kcms/detail/46.1068.S.20220228.2219.017.html" target="_blank"> http://kns.cnki.net/kcms/detail/46.1068.S.20220228.2219.017.html.[Yao G Q,Yang F,Yan L F,Sun Z H,Li W. 2023. Analysis of Bougainvillea glabra Choisy genetic diversity based on SSR of transcriptome[J/OL]. Molecular Plant Breeding, http://kns.cnki.net/kcms/detail/46.1068.S.20220228.2219.017.html" target="_blank"> http://kns.cnki.net/kcms/detail/46.1068.S.20220228.2219.017.html.]

叶鹏,李显煌,唐军荣,李斌,张贵良,刘成,雷瀚,辛培尧. 2019. 云南金花茶转录组SSR 的分布及其序列特征[J]. 中南林业科技大学学报,39(9):86-91.[Ye P,Li X H, Tang J R,Li B,Zhang G L,Liu C,Lei H,Xin P Y. 2019. Distribution and characteristics of SSR in transcriptome of Camellia fascicularis[J]. Journal of Central South University of Forestry & Technology,39(9):86-91.] doi:10. 14067/j.cnki.1673-923x.2019.09.014.

张林甦,刘承贵,蒙慧彤,夏亚兰. 2018. 基于蛇足石杉转录组的SNP 和SSR 多态性分析[J]. 黔南民族医专学报,31(4):235-238.[Zhang L S,Liu C G,Meng H T,Xia Y L. 2018. Mining and analyzing SNP and SSR molecular markers based on transcriptome sequences of Huperzia serrata[J]. Journal of Qiannan Medical College for Nationalities, 31(4):235-238.]

张玲玲. 2011. 三角梅遗传多样性及亲缘关系RAPD 研究[D]. 成都:四川农业大学.[Zhang L L. 2011. Research about RAPD of genetic relationship and geneticdiversity for Bougainvillea spectabilis[D]. Chengdu:Sichuan Agricultural University.]

张小红,彭琼,鄢铮. 2022. 基于甘薯耐盐转录组测序的SSR 和SNP 特征分析[J]. 农学学报,12(11):55-61.[Zhang X H,Peng Q,Yan Z. 2022. SSR and SNP in salt tolerant sweet potato:Characteristics analysis based on transcriptome sequencing[J]. Journal of Agriculture,12(11):55-61.]

赵彤,常圣鑫,冷青云,徐世松,尹俊梅,牛俊海. 2019. 基于三角梅转录组测序的SSR分子标记的开发[J]. 分子植物育种,17(13):4331-4341.[Zhao T,Chang S X,Leng Q Y, Xu S S,Yin J M. 2019. Development of SSR molecular markers based on transcriptome sequencing of Bougainvillea[J]. Molecular Plant Breeding,17(13):4331-4341.] doi: 10.13271/j.mpb.017.004331.

邹勇,黄科,姜玉松,刘奕清. 2016. 白姜转录组中的SSR位点信息分析[J]. 作物杂志,(3):171-174.[Zou Y,Huang K, Jiang Y S,Liu Y Q. 2016. SSR information transcriptome of white ginger (Zingber officinale Roscoe)[J]. Crops,(3):171-174.] doi: 10.16035/j.issn.1001-7283.2016.03.032.

Ching A,Caldwell K,Jung M,Dolan M,Smith O,Tingey S, Morgante M,Rafalski A. 2002. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines[J]. BMC Genetics,3:19. doi:10.1186/1471-2156 3-19.

Grabherr M G,Haas B J,Yassour M,Levin J Z,Thompson D A,Amit I,Adiconis X,Fan L,Raychowdhury R,Zeng Q D,Chen Z,Mauceli E,Hacohen N,Gnirke A, Rhind N, di Palma F, Birren B W, Nusbaum C, Lindblad-Toh K, Friedman N,Regev A. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome[J]. Nature Biotechnology,29(7):644-652. doi: 10.1038/nbt.1883.

McCouch S R,Zhao K,Wright M,Tung C W,Ebana K,Thomson M,Reynolds A,Wang D,DeClerck G,Md. L A, McClung A,Eizenga G,Bustamante C. 2010. Development of genome-wide SNP assays for rice[J]. Breeding Science,60(5):524-535. doi: 10.1270/jsbbs.60.524.

Nasu S,Suzuki J,Ohta R,Hasegawa K,Yui R,Kitazawa N, Monna L,Minobe Y. 2002. Search for and analysis of single nucleotide polymorphisms(SNPs) in rice (Oryza sativa,Oryza rufipogon) and establishment of SNP markers[J]. DNA Research:An International Journal for Rapid Publication of Reports on Genes and Genomes,9(5):163 171. doi: 10.1093/dnares/9.5.163.

Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S. 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.):Frequency,length variation,transposon associations,and genetic marker potential[J]. Genome Research,11(8):1141-1452. doi: 10.1101/gr.184001.

Wang R,Xu S,Jiang Y M,Jiang J W,Li X D,Liang L J,He J, Peng F,Xia B. 2013. De novo sequence assembly and characterization of Lycoris aurea transcriptome using GS FLX titanium platform of 454 pyrosequencing[J]. PLoS One, 8(4):e60449. doi: 10.1371/journal.pone.0060449.

施引文献(1)

期刊类型引用(1)

舒国荣，田金红，杨林，王大玮. 云南栘木衣果实转录组SSR、SNP、InDel特征分析. 西部林业科学. 2024(05): 84-91+99 .

百度学术

其他类型引用(0)

资源附件(0)

计量

文章访问数: 123
HTML全文浏览量: 0
PDF下载量: 4
被引次数: 1

伊丽莎白安格斯三角梅转录组的SSR、SNP和InDel特征分析

作者简介: 孙利娜(1981-),https://orcid.org/0000-0002-5273-6066,副研究员,主要从事园林植物遗传育种研究工作,E-mail:sunlina8958170@126.com

通讯作者: 龚建英(1978-),https://orcid.org/0000-0003-3121-0708,副研究员,主要从事园林植物遗传育种研究工作E-mail:282305221@qq.com

计量

出版历程

SSR， SNP and InDel characteristics analysis based on transcriptome of Bougainvillea glabra‘Elizabeth Angus’

期刊类型引用(1)

其他类型引用(0)

计量

出版历程

目录

作者简介:
孙利娜(1981-),https://orcid.org/0000-0002-5273-6066,副研究员,主要从事园林植物遗传育种研究工作,E-mail:sunlina8958170@126.com

通讯作者:
龚建英(1978-),https://orcid.org/0000-0003-3121-0708,副研究员,主要从事园林植物遗传育种研究工作E-mail:282305221@qq.com