XU Yiqing,BI Changwei,ZHANG Fuquan,et al.DNA Motif Prediction of Shrub Willow Based on Comparative Genetics[J].Northern Horticulture,2018,42(06):62-67.[doi:10.11937/bfyy.20172973]
基于比较基因组学的簸箕柳DNA模体预测
- Title:
- DNA Motif Prediction of Shrub Willow Based on Comparative Genetics
- Keywords:
- Salix suchowensis; DNA motif; comparative genetics
- 文献标志码:
- A
- 摘要:
- 以已完成全基因组测序及组装的模式生物拟南芥和具有很高研究价值的园艺植物柳树（Salix）的全基因组测序为数据源，采用基于位置的基因序列匹配方法，研究了新测序物种簸箕柳（Salix suchowensis）的DNA模体序列，以期为进一步了解柳树乃至林木的基因调控网络提供参考依据。结果表明：此次预测的结果与手工验证的部分簸箕柳的DNA模体一致，该研究发布的基于簸箕柳全基因组的DNA模体预测结果对于杨柳科植物的研究具有重要的意义。
- Abstract:
- Model species,Arabidopsis thaliana,and a high-valued horticultural plant shrub salix (Salix suchowensi) genome sequences were used as data origin,a new location-based alignment methodology was applied to study the DNA motif in this recent sequenced specie,in order to explore the regular network of salix and even other horticultural plants. The results showed that,the prediction was proofed by manual verification,and was meaningful for further research on Salicaceae plant.
参考文献/References:
[1]DJOMO S N,KASMIOUI O E,CEULEMANS R.Energy and greenhouse gas balance of bioenergy production from poplar and willow:A review[J].Global Change Biology Bioenergy,2011,3(3):181-197. [2]WANG Y,XU L.Research progress on Salix genetics[J].Chinese Bulletin of Botany,2008(2):240-247. [3]OKUMURA S,SAWADA M,PARK Y W,et al.Transformation of poplar (Populus alba) plastids and expression of foreign proteins in tree chloroplasts[J].Transgenic Research,2006,15(5):637-646. [4]BERLIN S,LAGERCRANTZ U,ARNOLD S,et al.High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus[J].BMC Genomics,2010,11(1):129. [5]HANLEY S J,MALLOTT M D,KARP A.Alignment of a Salix linkage map to the Populus genomic sequence reveals macrosynteny between willow and poplar genomes[J].Tree Genetics & Genomes,2006,3(1):35-48. [6]TUSKAN G.The genome of black cottonwood,Populus trichocarpa (Torr.&Gray)[J].Science,2006,313(5793):1596-1604. [7]DAI X,HU Q,CAI Q,et al.The willow genome and divergent evolution from poplar after the common genome duplication[J].Cell Research,2014,24(10):1274. [8]D′HAESELEER P.What are DNA sequence motifs?〖KG-*4〗[J].Nature Biotechnology,2006,24(4):423-425. [9]PRIBNOW D.Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter[J].Proceedings of the National Academy of Sciences of the United States of America,1975,72(3):784. [10]STORMO G D.DNA binding sites:Representation and discovery[J].Bioinformatics,2000,16(1):16-23. [11]BAILEY T L,GRIBSKOV M.Combining evidence using p-values:Application to sequence homology searches[J].Bioinformatics,1998,14(1):48. [12]MA Q,ZHANG H,MAO X,et al.DMINDA:An integrated web server for DNA motif identification and analyses[J].Nucleic Acids Research,2014,42(W1):12-19. [13]D′HAESELEER P.How does DNA sequence motif discovery work?[J].Nature Biotechnology,2006,24(8):959-961. [14]GRANT C E,BAILEY T L,NOBLE W S.FIMO:Scanning for occurrences of a given motif[J].Bioinformatics,2011,27(7):1017-1018. [15]TANAKA E,BAILEY T,GRANT C E,et al.Improved similarity scores for comparing motifs[J].Bioinformatics,2011,27(12):1603. [16]KAZAN H,MORRIS Q.RBPmotif:A web server for the discovery of sequence and structure preferences of RNA-binding proteins[J].Nucleic Acids Research,2013,41:180. [17]LEIBOVICH L,PAZ I,YAKHINI Z,et al.DRIMust:A web server for discovering rank imbalanced motifs using suffix trees[J].Nucleic Acids Research,2013,41:174-179. [18]BAILEY T L,BODEN M,BUSKE F A,et al.MEME SUITE:Tools for motif discovery and searching[J].Nucleic Acids Research,2009,37:202-208. [19]MATYS .V,FRICKE E,GEFFERS R,et al.TRANSFAC〖KG-*3〗:Transcriptional regulation,from patterns to profiles[J].Nucleic Acids Research,2003,31(1):374-378. [20]SANDELIN A,ALKEMA W,ENGSTRM P,et al.JASPAR:An open-access database for eukaryotic transcription factor binding profiles[J].Nucleic Acids Research,2004,32:91. [21]ROBERTSON G,BILENKY M,LIN K,et al.cisRED:A database system for genome-scale computational discovery of regulatory elements[J].Nucleic Acids Research,2006,34:68-73. [22]YANG L,ZHOU T,DROR I,et al.TFBSshape:A motif database for DNA shape features of transcription factor binding sites[J].Nucleic Acids Research,2013,42:148. [23]PALANISWAMY S K,JAMES S,SUN H,et al.AGRIS and AtRegNet:A platform to link cis-regulatory elements and transcription factors into regulatory networks[J].Plant Physiology,2006,140(3):818. [24]WITTKOPP P J,KALAY G.Cis-regulatory elements:Molecular mechanisms and evolutionary processes underlying divergence[J].Nature Reviews Genetics,2011,13(1):59-69. [25]BUTLER J E,KADONAGA J T.The RNA polymerase II core promoter:A key component in the regulation of gene expression[J].Genes & Development,2002,16(16):2583-2592. [26]BUHLER J D,LANCASTER J M,JACOB A C,et al.Mercury BLASTN:Faster DNA sequence comparison using a streaming hardware architecture[C].Proceedings of the reconfigurable systems summer institute,2008. [27]STEIN L D.Using GBrowse 2.0 to visualize and share next-generation sequence data[J].Briefings in Bioinformatics,2013,14(2):162.
备注/Memo
第一作者简介：徐逸卿（1981-），男，江苏南京人，博士研究生，讲师，研究方向为计算机应用与生物信息学。E-mail：yiqingxu@njfu.edu.cn.基金项目：国家重点基础研究发展计划资助项目（2012CB114505）；国家重点研发计划资助项目（2016YFD0600101）。收稿日期：2017-10-12