An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps

作者: Prashant S. Hosmani , Mirella Flores-Gonzalez , Henri van de Geest , Florian Maumus , Linda V. Bakker

DOI: 10.1101/767764

关键词: FosmidGenomeSequence assemblyBiologyAnnotationGenome browserReference genomeGeneRetrotransposonComputational biology

摘要: … We present here the latest tomato reference … or lncRNA are relatively newly described class of RNAs and thought to be involved in the regulation of many biological processes. LncRNA …

参考文章(51)
Anthony Schilmiller, Feng Shi, Jeongwoon Kim, Amanda L. Charbonneau, Daniel Holmes, A. Daniel Jones, Robert L. Last, Mass spectrometry screening reveals widespread diversity in trichome specialized metabolites of tomato chromosomal substitution lines Plant Journal. ,vol. 62, pp. 391- 403 ,(2010) , 10.1111/J.1365-313X.2010.04154.X
Florian Jupe, Kamil Witek, Walter Verweij, Jadwiga Śliwka, Leighton Pritchard, Graham J. Etherington, Dan Maclean, Peter J. Cock, Richard M. Leggett, Glenn J. Bryan, Linda Cardle, Ingo Hein, Jonathan D.G. Jones, Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. Plant Journal. ,vol. 76, pp. 530- 544 ,(2013) , 10.1111/TPJ.12307
Adam C. English, Stephen Richards, Yi Han, Min Wang, Vanesa Vee, Jiaxin Qu, Xiang Qin, Donna M. Muzny, Jeffrey G. Reid, Kim C. Worley, Richard A. Gibbs, Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLOS ONE. ,vol. 7, ,(2012) , 10.1371/JOURNAL.PONE.0047768
André Gilles, Emese Meglécz, Nicolas Pech, Stéphanie Ferreira, Thibaut Malausa, Jean-François Martin, None, Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing BMC Genomics. ,vol. 12, pp. 245- 245 ,(2011) , 10.1186/1471-2164-12-245
ID Sormacheva, AG Blinov, None, LTR Retrotransposons in Plants Russian Journal of Genetics: Applied Research. ,vol. 1, pp. 540- 564 ,(2011) , 10.1134/S2079059711060098
Bruce J. Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A. Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K. Young, Ashlee M. Earl, Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement PLoS ONE. ,vol. 9, pp. e112963- ,(2014) , 10.1371/JOURNAL.PONE.0112963
Silin Zhong, Zhangjun Fei, Yun-Ru Chen, Yi Zheng, Mingyun Huang, Julia Vrebalov, Ryan McQuinn, Nigel Gapper, Bao Liu, Jenny Xiang, Ying Shao, James J Giovannoni, Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening Nature Biotechnology. ,vol. 31, pp. 154- 159 ,(2013) , 10.1038/NBT.2462
Evgeni M Zdobnov, Rolf Apweiler, None, InterProScan--an integration platform for the signature-recognition methods in InterPro. Bioinformatics. ,vol. 17, pp. 847- 848 ,(2001) , 10.1093/BIOINFORMATICS/17.9.847
Hernan G. Rosli, Gregory B. Martin, Functional genomics of tomato for the study of plant immunity. Briefings in Functional Genomics. ,vol. 14, pp. 291- 301 ,(2015) , 10.1093/BFGP/ELV007