松萝凤梨转录组基因内部微卫星序列信息分析
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- 英文论文题名：Analysis of Genic Microsatellite Information in Transcriptome of Tillandsia usneoides
- 论文作者：金亮 ; 田丹青 ; 俞信英 ; 葛亚英 ; 林延慧 ; 潘晓韵 ; 王炜勇
- 英文论文作者：JIN Liang ; TIAN Dan-qing ; YU Xin-ying ; GE Ya-ying ; LIN Yan-hui ; PAN Xiao-yun ; WANG Wei-yong ; Bromeliad R&D and Promotion Center of National Engineering Research Center for Floriculture ; Research and Development Centre of Flower ; Zhejiang Academy of Agricultural Sciences
- 年：2016
- 作者机构：浙江省农业科学院花卉研究开发中心国家花卉工程技术研究中心凤梨研发与推广中心;
- 论文关键词：松萝凤梨 ; 空气凤梨 ; 转录组 ; 基因内部微卫星 ; 功能注释
- 英文论文关键词：Tillandsia usneoides ; epiphytic Tillandsia ; Transcriptome ; Genic SSR ; Functional annotation
- 会议召开时间：2016-07-19
- 会议录名称：中国观赏园艺研究进展2016
- 语种：中文
- 分类号：S682.3
- 学会代码：EGYP
- 会议名称：2016年中国观赏园艺学术研讨会
- 会议地点：中国湖南长沙
- 主办单位：中国园艺学会观赏园艺专业委员会、国家花卉工程技术研究中心
- 学会名称：中国园艺学会
- 页数：7
- 文件大小：753k
- 原文格式：O
- 会议级别：全国
摘要
对松萝凤梨(Tillandsia usneoides)开展转录组测序分析,共获得62779条单基因簇(Unigene;4.72Gb)。利用MISA软件筛选出17964个基因内部微卫星(genic SSR)位点,分布于14196条Unigene中,出现频率为28.61%,平均分布距离为7.14kb。优势重复基序为单核苷酸、二核苷酸和三核苷酸,分别占总SSR位点的39.36%、22.30%和29.40%。二核苷酸重复中以AG/CT为优势重复基元,占总位点的17.38%,三核苷酸重复以CCG/CGG和AGG/CCT为主,分别占4.63%和4.41%。对含有genic SSR序列注释发现:3001个Unigenes具有KOG注释;6958个Unigenes具有GO注释;1654个Unigenes具有KEGG直系同源(KO)系统注释。这些Unigenes涉及了许多重要的生物功能和代谢途径,这预示着这些潜在的标记可能与重要的生物功能有关。这些信息将为松萝凤梨分子标记开发以及相关基因组研究奠定基础。
A total of 62779 unigenes(4.72Gb) were obtained by using transcriptome sequenceing analysis in Tillandsia usneoides.A total of 17964 genie simple sequence repeat(genie SSR) loci that occurred in 14196 unigenes were identified by MISA software,and the frequency of these genie SSRs was 28.61%and mean distance was 7.14 kb in the unigenes.Mononucleotide,dinucleotide and trinucleotide were major types,accounting for 39.36%,22.30%and 29.40%,respectively.The dinucleotide repeat motifs of AG/CT were the predominant repeat types(17.38%).The trinucleotide repeat motifs of CCG/CGG and AGG/CCT were the predominant repeat types(4.63%and 4.41%).The unigenes containing genie SSR were annotated by Clusters of Orthologous Groups(COG/KOG),Gene Ontology(GO) database and Kyoto Encyclopedia of Genes and Genomes(KEGG) Orthology(KO) system,respectively.There were 3001 unigenes assigned into KOG classifications.There were 6958 unigenes classified into and GO terms.There were 1654 SSR unigenes involved in KO system.A large number of unigenes were annotated with crucial genes that were associated with important biological functions.The numerous genie SSRs identified in this study will contribute to marker development and research on genomics of T.usneoides.
A total of 62779 unigenes(4.72Gb) were obtained by using transcriptome sequenceing analysis in Tillandsia usneoides.A total of 17964 genie simple sequence repeat(genie SSR) loci that occurred in 14196 unigenes were identified by MISA software,and the frequency of these genie SSRs was 28.61%and mean distance was 7.14 kb in the unigenes.Mononucleotide,dinucleotide and trinucleotide were major types,accounting for 39.36%,22.30%and 29.40%,respectively.The dinucleotide repeat motifs of AG/CT were the predominant repeat types(17.38%).The trinucleotide repeat motifs of CCG/CGG and AGG/CCT were the predominant repeat types(4.63%and 4.41%).The unigenes containing genie SSR were annotated by Clusters of Orthologous Groups(COG/KOG),Gene Ontology(GO) database and Kyoto Encyclopedia of Genes and Genomes(KEGG) Orthology(KO) system,respectively.There were 3001 unigenes assigned into KOG classifications.There were 6958 unigenes classified into and GO terms.There were 1654 SSR unigenes involved in KO system.A large number of unigenes were annotated with crucial genes that were associated with important biological functions.The numerous genie SSRs identified in this study will contribute to marker development and research on genomics of T.usneoides.
引文
1.丁久玲,郑凯,俞禄生.2008.不同浓度氮肥对松萝凤梨生长的影响[J].安徽农业科学,(26):11444-11445.
2.贾新平,孙晓波,邓衍明,等.2014.鸟巢蕨转录组高通量测序及分析[J].园艺学报,41(11):2329-2341.
3.巩檑,程永芳,甘晓燕,等.2015.马铃薯转录组ESTSSR挖掘及其多样性分析[J].分子植物育种,(07):1535-1544.
4.李俊霖,李鹏,王恒蓉,等.2013.特殊植物类群空气凤梨对大气污染物甲醛的净化[J].环境工程学报,(04):1451-1458.
5.李小白,向林,罗洁,等.2013.转录组测序(RNA-seq)策略及其数据在分子标记开发上的应用[J].中国细胞生物学学报,(05):720-726.
6.李小白,金凤,金亮,等.2014a.利用建兰转录数据开发genie-SSR标记[J].农业生物技术学报,22(8):1046-1056.
7.李小白,向林,罗洁,等.2014b.建兰转录本的微卫星序列和单核苷酸多态性信息分析[J].浙江大学学报(农业与生命科学版),(04):463-472.
8.刘晓娜,俞禄生,沈永宝.2010.6种空气凤梨解剖学特征与耐旱性的关系[C].中国观赏园艺研究进展2010:470-474.
9.刘越,岳春江,王翊,等.2015.藏茵陈川西獐牙菜转录组SSR信息分析[J].中国中药杂志,(11):2068-2076.
10.王芳,谭俊杰,李秀伟.2013.松萝凤梨微观特性研究与植物窗帘构建[J].南京理工大学学报(自然科学版),37(2):325-330.
11.王洋洋,单文琪,徐文龙,等.2016.印度南瓜转录组SSR信息分析及其多态性研究[J].园艺学报,43(3):578-586.
12.鄢秀芹,鲁敏,安华明.2015.刺梨转录组SSR信息分析及其分子标记开发[J].园艺学报,(02):341-349.
13.俞禄生.神奇的无根花卉:空气凤梨[G].北京:中国农业出版社,2009.
14.郁永明,田丹青,潘晓韵,等.2015.基于红掌转录组序列的SSR标记分析与开发[J].分子植物育种,13(6):1349-1354.
15.张庆田,李晓艳,杨义明,等.2016.蓝靛果忍冬转录组SSR信息分析及其分子标记开发[J].园艺学报,43(3):557-563.
16.Figueiredo A M G,Nogueira C A,Saiki M,Milian F M,Domingos M.2007.Assessment of atmospheric metallic pollution in the metropolitan region of Sao Paulo,Brazil,employing Tillandsia usneoides L as biomonitor[J].Environmental Pollution,145(1):279-292.
17.Yue X,Liu G,Zong Y,Teng Y,Cai D.2014.Development of genie SSR markers from transcriptome sequencing of pear buds[J].Journal of Zhejiang University SCIENCE B,15(4):303-312.
18.Zheng G,Pemberton R,Li P.2016.Bioindicating potential of strontium contamination with Spanish moss Tillandsia usneoides[J].Journal of Environmental Radioactivity,152:23-27.
2.贾新平,孙晓波,邓衍明,等.2014.鸟巢蕨转录组高通量测序及分析[J].园艺学报,41(11):2329-2341.
3.巩檑,程永芳,甘晓燕,等.2015.马铃薯转录组ESTSSR挖掘及其多样性分析[J].分子植物育种,(07):1535-1544.
4.李俊霖,李鹏,王恒蓉,等.2013.特殊植物类群空气凤梨对大气污染物甲醛的净化[J].环境工程学报,(04):1451-1458.
5.李小白,向林,罗洁,等.2013.转录组测序(RNA-seq)策略及其数据在分子标记开发上的应用[J].中国细胞生物学学报,(05):720-726.
6.李小白,金凤,金亮,等.2014a.利用建兰转录数据开发genie-SSR标记[J].农业生物技术学报,22(8):1046-1056.
7.李小白,向林,罗洁,等.2014b.建兰转录本的微卫星序列和单核苷酸多态性信息分析[J].浙江大学学报(农业与生命科学版),(04):463-472.
8.刘晓娜,俞禄生,沈永宝.2010.6种空气凤梨解剖学特征与耐旱性的关系[C].中国观赏园艺研究进展2010:470-474.
9.刘越,岳春江,王翊,等.2015.藏茵陈川西獐牙菜转录组SSR信息分析[J].中国中药杂志,(11):2068-2076.
10.王芳,谭俊杰,李秀伟.2013.松萝凤梨微观特性研究与植物窗帘构建[J].南京理工大学学报(自然科学版),37(2):325-330.
11.王洋洋,单文琪,徐文龙,等.2016.印度南瓜转录组SSR信息分析及其多态性研究[J].园艺学报,43(3):578-586.
12.鄢秀芹,鲁敏,安华明.2015.刺梨转录组SSR信息分析及其分子标记开发[J].园艺学报,(02):341-349.
13.俞禄生.神奇的无根花卉:空气凤梨[G].北京:中国农业出版社,2009.
14.郁永明,田丹青,潘晓韵,等.2015.基于红掌转录组序列的SSR标记分析与开发[J].分子植物育种,13(6):1349-1354.
15.张庆田,李晓艳,杨义明,等.2016.蓝靛果忍冬转录组SSR信息分析及其分子标记开发[J].园艺学报,43(3):557-563.
16.Figueiredo A M G,Nogueira C A,Saiki M,Milian F M,Domingos M.2007.Assessment of atmospheric metallic pollution in the metropolitan region of Sao Paulo,Brazil,employing Tillandsia usneoides L as biomonitor[J].Environmental Pollution,145(1):279-292.
17.Yue X,Liu G,Zong Y,Teng Y,Cai D.2014.Development of genie SSR markers from transcriptome sequencing of pear buds[J].Journal of Zhejiang University SCIENCE B,15(4):303-312.
18.Zheng G,Pemberton R,Li P.2016.Bioindicating potential of strontium contamination with Spanish moss Tillandsia usneoides[J].Journal of Environmental Radioactivity,152:23-27.