玉米Glyco-hydro-16糖苷酶家族全基因组的鉴定及其遗传分化

doi:10.3864/j.issn.0578-1752.2016.11.001

摘要/Abstract

摘要： 【目的】全基因组水平鉴定玉米Glyco-hydro-16家族，分析该家族基因在不同组织中的表达模式以及在不同玉米杂种优势群中的遗传分化。【方法】根据Glyco-hydro-16家族相对保守的序列及结构域，构建Glyco-hydro-16家族的隐马尔科夫模型文件（Glyco-hydro-16.hmm），利用hmmersearch程序在玉米全基因组中进行比对，获得玉米中含有该家族保守结构域的所有序列。通过Blast2GO进行功能注释，利用蛋白质序列构建该家族的系统发育进化树。使用玉米自交系B73不同组织及不同发育时期的RNA-seq数据库分析该家族基因的表达模式。根据该家族基因在染色体上的位置筛选SNP标记，计算其在不同玉米杂种优势群间的群间遗传分化系数（genetic differentiation coefficient，Fst），分析其遗传分化。【结果】根据该家族相对保守的序列及结构域，在全基因组水平共鉴定出34个玉米Glyco-hydro-16家族成员，注释表明所有基因都是木葡聚糖转移酶/水解酶基因，3个保守性较高的Motif区段存在于该家族所有成员中。通过系统发育关系和序列相似性将该家族分为8个亚家族，每个亚家族有2—8个基因，分布在除第3和第6染色体外的其他8条染色体上，在第2、第5及第10染色体上成簇分布。该家族在禾本科作物中同源性较高，与拟南芥分属不同的分支，但只有3个玉米成员（AC210669.3、GRMZM2G413006和GRMZM2G166944）被划分到禾本科分支中，其他玉米成员被划分到单独的分支中。通过表达谱分析表明该家族成员在玉米中均有表达，但在不同组织中的表达水平有差异。为解析该家族基因在不同玉米种质资源中等位基因的变异，根据玉米Glyco-hydro-16家族基因在染色体上的位置筛选SNP标记，计算其在玉米杂种优势群SS及NSS间的群间遗传分化系数。结果显示，共有10个该家族基因所处位点的Fst值高于阈值0.15，达到高度分化水平，分别位于第1、第2、第4、第5、第7以及第9染色体上。其中，位于第2染色体上的GRMZM2G091118相应位点的Fst值为0.52，表明该位点在SS群和NSS群间的群间遗传分化度极大。【结论】通过全基因组扫描在玉米中鉴定出34个Glyco-hydro-16家族成员，均为木葡聚糖转移酶/水解酶基因，在不同组织中，其表达模式不同，可能参与不同生理发育过程。部分该家族成员所处位点在玉米杂种优势群SS和NSS间的等位基因分化极大。

关键词: 玉米, Glyco-hydro-16, 基因家族, 杂种优势群, RNA-seq

Abstract: 【Objective】Genome-wide identification was carried out for Glycoside hydrolase family 16 in maize, and their expression profile across tissues and differentiation between heterotic groups were analyzed. 【Method】Based on the maize V3 sequences, genome-wide survey of Glycoside hydrolase family 16 was conducted according to conserved sequences and domains through hmmersearch program. Blast2GO was used for gene annotation and phylogenetic relationships were analyzed through protein sequences. Expression profiles were examined within the whole transcriptome context at different tissues across development stages in B73. In line with the chromosome locations of the family genes, the authors screened the SNP markers and analyzed their genetic differentiation in different heterotic groups. 【Result】Totally 34 genes were identified in maize throughout genome-wide survey and annotated as xyloglucan endotransglucosylase with 3 conserved motifs discovered in all members. According to the phylogenetic relationships and sequence similarity they were divided into 8 subgroups. Glycoside hydrolase family 16 members were conserved in Gramineae, however, most maize members were not closely related with other Gramineae plants except only 3 members (AC210669.3, GRMZM2G413006, and GRMZM2G166944). The family genes in maize distributed on almost all chromosomes except on chromosomes 3 and 6 with several genes clustered on chromosomes 2, 5 and 10. Different expression profiles across tissues indicated their diversity functions. According to their chromosome location, the authors screened the SNP markers and calculated the genetic differentiation coefficient between the heterotic groups SS and NSS. Ten genes in Glycoside hydrolase family 16 differentiated significantly between the two heterotic groups, distributing on chromosomes 1, 2, 4, 5, 7 and 9. The one on chromosome 2 corresponding to GRMZM2G091118 got the highest Fst 0.52, indicating possible role contribute to heterosis. 【Conclusion】Based on the V3 sequences of maize, 34 genes were identified for Glycoside hydrolase family 16 and annotated as xyloglucan endotransglycosylase. Their expression profiles were different across tissues implying diversity functions. Some family members differentiated significantly between heterotic groups SS and NSS.

Key words: maize, Glyco-hydro-16, gene family, heterotic groups, RNA-seq

林峰，葛敏，周玲，赵涵. 玉米Glyco-hydro-16糖苷酶家族全基因组的鉴定及其遗传分化[J]. 中国农业科学, 2016, 49(11): 2039-2048.

LIN Feng, GE Min, ZHOU Ling, ZHAO Han. Genome-Wide Identification of Glyco-hydro-16 Family in Maize and Differentiation Analysis[J]. Scientia Agricultura Sinica, 2016, 49(11): 2039-2048.

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参考文献

[1] Minic Z. Physiological roles of plant glycoside hydrolases. Planta, 2008, 227(4): 723-740.

[2] Henrissat B, Callebaut I, Fabrega S, Lehn P, Mornon J P, Davies G. Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases. Proceedings of the National Academy of Sciences of the USA,1995, 92(15): 7090-7094.

[3] Davies G, Henrissat B. Structures and mechanisms of glycosyl hydrolases. Structure, 1995, 3(9): 853-859.

[4] Fry S, Smith R C, Renwick K F, Martin D J, Hodge S, Matthews K J. Xyloglucan endotransglycosylase, a new wall- loosening enzyme activity from plants. Biochemical Journal, 1992, 282(3): 821-828.

[5] Kurasawa K, Matsui A, Yokoyama R, Kuriyama T, Yoshizumi T, Matsui M, Suwabe K, Watanabe M, Nishitani K. The AtXTH28 gene, a xyloglucan endotransglucosylase/ hydrolase, is involved in automatic self-pollination in Arabidopsis thaliana. Plant and Cell Physiology, 2009, 50(2): 413-422.

[6] Strohmeier M, Hrmova M, Fischer M, Harvey A J, Fincher G B, Pleiss J. Molecular modeling of family GH16 glycoside hydrolases: Potential roles for xyloglucan transglucosylases/ hydrolases in cell wall modification in the poaceae. Protein Science,2004, 13(12): 3200-3213.

[7] 张黎, 牛向丽, 张惠莹, 刘永胜. 水稻木葡聚糖内糖基转移酶基因OsXTH11过表达的作用分析. 中国农业科学, 2012, 45(16): 3231-3239.

ZHANG L, NIU X L, ZHANG H Y, LIU Y S. Functional analysis via overexpressing Xyloglucan endotransglycosylase gene OsXTH11 in rice. Scientia Agricultura Sinica, 2012, 45(16): 3231-3239. (in Chinese)

[8] Linton S M, Cameron M S, Gray M, Donald J A, Saborowski R, von Bergen M, Tomm J M, Allardyce B J. A glycosyl hydrolase family 16 gene is responsible for the endogenous production of β-1, 3-glucanases within decapod crustaceans. Gene,2015, 569(2): 203-217.

[9] 陈姣荣, 方彦, 孙万仓, 令利军, 姜海杨. 芸芥木葡聚糖内糖基转移酶/水解酶基因 EsXTH1的cDNA克隆和生物信息学分析. 中国油料作物学报,2013, 35(2): 131-136.

CHEN J R, FANG Y, SUN W c, LING L J, JIANG H Y. Cloning and bioinformatics of xyloglucan endotrans glycosylase and hydrolase EsXTH1 gene in Eruca sativa. Chinese Journal of Oil Crop Sciences, 2013, 35(2): 131-136. (in Chinese)

[10] Lin H J, Gao J, Zhang Z M, Shen Y O, Lan H, Liu L, Xiang K, Zhao M, Zhou S, Zhang Y Z. Transcriptional responses of maize seedling root to phosphorus starvation. Molecular Biology Reports,2013, 40(9): 5359-5379.

[11] Conesa A, Götz S, García-Gómez J M, Terol J, Talón M, Robles M. Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 2005, 21(18): 3674-3676.

[12] Bailey T L, Boden M, Buske F A, Frith M, Grant C E, Clementi L, Ren J, Li W W, Noble W S. MEME SUITE: Tools for motif discovery and searching. Nucleic Acids Research,2009, 37(Suppl. 2): w202-w208.

[13] Thompson J D, Gibson T J, Plewniak F, Jeanmougin F, Higgins D G. The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 1997, 25(24): 4876-4882.

[14] Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution,1987, 4(4): 406-425.

[15] Cox M P, Peterson D A, Biggs P J. SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics,2010, 11(1): 485.

[16] Langmead B, Trapnell C, Pop M, Salzberg S L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology,2009, 10(3): R25.

[17] Trapnell C, Williams B A, Pertea G, Mortazavi A, Kwan G, van Baren M J, Salzberg S L, Wold B J, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology,2010, 28(5): 511-515.

[18] Tracy W, Chandler M. The historical and biological basis of the concept of heterotic patterns in corn belt dent maize//Plant Breeding: The Arnel R Hallauer International Symposium.2006: 219-233.

[19] Mikel M A, Dudley J W. Evolution of North American dent corn from public to proprietary germplasm. Crop Science,2006, 46(3): 1193-1205.

[20] Romay M C, Millard M J, Glaubitz J C, Peiffer J A, Swarts K L, Casstevens T M, Elshire R J, Acharya C B, Mitchell S E, Flint-Garcia S A. Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biology,2013, 14(6): R55.

[21] van Heerwaarden J, Hufford M B, Ross-Ibarra J. Historical genomics of North American maize. Proceedings of the National Academy of Sciences of the USA, 2012, 109(31): 12420-12425.

[22] Wright S. Evolution and the genetics of populations: Experimental results and evolutionary deductions: Vol. 3. Chicago, IL: University of Chicago Press, 1977.

[23] Harada T, Torii Y, Morita S, Onodera R, Hara Y, Yokoyama R, Nishitani K, Satoh S. Cloning, characterization, and expression of xyloglucan endotransglucosylase/hydrolase and expansin genes associated with petal growth and development during carnation flower opening. Journal of Experimental Botany, 2011, 62(2): 815-823.

[24] Xie W, Wang G, Yuan M, Yao W, Lyu K, Zhao H, Yang M, Li P, Zhang X, Yuan J. Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection. Proceedings of the National Academy of Sciences of the USA,2015, 112(39): 5411-5419.

[25] Huang X, Yang S, Gong J, Zhao Y, Feng Q, Gong H, Li W, Zhan Q, Cheng B, Xia J. Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis. Nature Communications, 2015, 6: 6258.

[26] Guo M, Rupe M A, Wei J, Winkler C, Goncalves- Butruille M, Weers B P, Cerwick S F, Dieter J A, Duncan K E, Howard R J. Maize ARGOS1 (ZAR1) transgenic alleles increase hybrid maize yield. Journal of Experimental Botany,2014, 65(1): 249-260.