High contiguity de novo genome sequence assembly of Trifoliate yam (Dioscorea dumetorum) using long read sequencing

作者: Christian Siadjeu , Boas Pucker , Prisca Viehöver , Dirk C. Albach , Bernd Weisshaar

DOI: 10.1101/2020.01.31.928630

关键词:

摘要: Trifoliate yam (Dioscorea dumetorum) is one example of an orphan crop, not traded internationally. Post-harvest hardening of the tubers of this species starts within 24 h after harvesting and renders the tubers inedible. Genomic resources are required for D. dumetorum to improve breeding for non-hardening varieties as well as for other traits. We sequenced the D. dumetorum genome and generated the corresponding annotation. The two haplophases of this highly heterozygous genome were separated to a large extent. The …

参考文章(49)
Hodeba D Mignouna, Mathew M Abang, Robert Asiedu, None, Genomics of Yams, a Common Source of Food and Medicine in the Tropics Genomics of Tropical Crop Plants. pp. 549- 570 ,(2008) , 10.1007/978-0-387-71219-2_23
Samuel Sefa-Dedeh, Emmanuel Ohene Afoakwa, Biochemical and textural changes in trifoliate yam Dioscorea dumetorum tubers after harvest Food Chemistry. ,vol. 79, pp. 27- 40 ,(2002) , 10.1016/S0308-8146(02)00172-3
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
Mario G. Rosso, Yong Li, Nicolai Strizhov, Bernd Reiss, Koen Dekker, Bernd Weisshaar, An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics. Plant Molecular Biology. ,vol. 53, pp. 247- 259 ,(2003) , 10.1023/B:PLAN.0000009297.37235.4A
M. Iwu, C. Okunji, G. Ohiaeri, P. Akah, D. Corley, M. Tempesta, Hypoglycaemic activity of dioscoretine from tubers of Dioscorea dumetorum in normal and alloxan diabetic rabbits. Planta Medica. ,vol. 56, pp. 264- 267 ,(1990) , 10.1055/S-2006-960952
Guillaume Marçais, Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers Bioinformatics. ,vol. 27, pp. 764- 770 ,(2011) , 10.1093/BIOINFORMATICS/BTR011
P. Jones, D. Binns, H.-Y. Chang, M. Fraser, W. Li, C. McAnulla, H. McWilliam, J. Maslen, A. Mitchell, G. Nuka, S. Pesseat, A. F. Quinn, A. Sangrador-Vegas, M. Scheremetjew, S.-Y. Yong, R. Lopez, S. Hunter, InterProScan 5: genome-scale protein function classification Bioinformatics. ,vol. 30, pp. 1236- 1240 ,(2014) , 10.1093/BIOINFORMATICS/BTU031
Y. Alozie, M.I. Akpanabiat, E.U. Eyong, I.B. Umoh, G. Alozie, Amino acid composition of Dioscorea dumetorum varieties. Pakistan Journal of Nutrition. ,vol. 8, pp. 103- 105 ,(2009) , 10.3923/PJN.2009.103.105
E. P. Nawrocki, S. R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches Bioinformatics. ,vol. 29, pp. 2933- 2935 ,(2013) , 10.1093/BIOINFORMATICS/BTT509