Solyntus, the New Highly Contiguous Reference Genome for Potato ( Solanum tuberosum)
作者： Natascha van Lieshout , Ate van der Burgt , Michiel E. de Vries , Menno ter Maat , David Eickholt
关键词:
摘要: With the rapid expansion of application genomics and sequencing in plant breeding, there is a constant drive for better reference genomes. In potato (Solanum tuberosum), third largest food crop world, related species S. phureja, designated “DM”, has been used as most popular genome last 10 years. Here, we introduce de novo sequenced Solyntus next standard studies. A true Solanum tuberosum made up 116 contigs that also highly homozygous, diploid, vigorous self-compatible, provides more direct contiguous then ever before available. It was constructed by with state-of-the-art long short read technology assembled Canu. The were into scaffolds to form each pseudochromosome, three 17 per chromosome. This assembly contains 93.7% single-copy gene orthologs from Solanaceae set an N50 63.7 Mbp. files can be found at https://www.plantbreeding.wur.nl/Solyntus/. release this research line its draft anticipate many exciting developments (diploid) research.
g3journal.org
oup.com参考文章(40)
Umesh R. Rosyara, Walter S. De Jong, David S. Douches, Jeffrey B. Endelman, Software for Genome-Wide Association Studies in Autopolyploids and Its Application to Potato. The Plant Genome. ,vol. 9, ,(2016) , 10.3835/PLANTGENOME2015.08.0073
Jiahan Li, Kiranmoy Das, Jingyuan Liu, Guifang Fu, Yao Li, Christian Tobias, Rongling Wu, Statistical models for genetic mapping in polyploids: challenges and opportunities. Methods of Molecular Biology. ,vol. 871, pp. 245- 261 ,(2012) , 10.1007/978-1-61779-785-9_13
Anthony T. Slater, Noel O.I. Cogan, John W. Forster, Benjamin J. Hayes, Hans D. Daetwyler, Improving Genetic Gain with Genomic Selection in Autotetraploid Potato The Plant Genome. ,vol. 9, ,(2016) , 10.3835/PLANTGENOME2016.02.0021
Elsa Sverrisdóttir, Stephen Byrne, Ea Høegh Riis Sundmark, Heidi Øllegaard Johnsen, Hanne Grethe Kirk, Torben Asp, Luc Janss, Kåre L. Nielsen, Genomic prediction of starch content and chipping quality in tetraploid potato using genotyping-by-sequencing Theoretical and Applied Genetics. ,vol. 130, pp. 2091- 2108 ,(2017) , 10.1007/S00122-017-2944-Y
Jens Keilwagen, Frank Hartung, Michael Paulini, Sven O. Twardziok, Jan Grau, Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi BMC Bioinformatics. ,vol. 19, pp. 189- 189 ,(2018) , 10.1186/S12859-018-2203-5
Floréal Cabanettes, Christophe Klopp, D-GENIES: dot plot large genomes in an interactive, efficient and simple way. PeerJ. ,vol. 6, ,(2018) , 10.7717/PEERJ.4958
Heng Li, Minimap2: pairwise alignment for nucleotide sequences Bioinformatics. ,vol. 34, pp. 3094- 3100 ,(2018) , 10.1093/BIOINFORMATICS/BTY191
Courtney P. Leisner, John P. Hamilton, Emily Crisovan, Norma C. Manrique‐Carpintero, Alexandre P. Marand, Linsey Newton, Gina M. Pham, Jiming Jiang, David S. Douches, Shelley H. Jansky, C. Robin Buell, Genome sequence of M6, a diploid inbred clone of the high-glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity. Plant Journal. ,vol. 94, pp. 562- 570 ,(2018) , 10.1111/TPJ.13857
R Lanfear, M Schalamun, D Kainer, W Wang, B Schwessinger, MinIONQC: fast and simple quality control for MinION sequencing data. Bioinformatics. ,vol. 35, pp. 523- 525 ,(2019) , 10.1093/BIOINFORMATICS/BTY654
Shan Wu, Biyao Zhang, Neda Keyhaninejad, Gustavo R. Rodríguez, Hyun Jung Kim, Manohar Chakrabarti, Eudald Illa-Berenguer, Nathan K. Taitano, M. J Gonzalo, Aurora Díaz, Yupeng Pan, Courtney P. Leisner, Dennis Halterman, C. Robin Buell, Yiqun Weng, Shelley H. Jansky, Herman van Eck, Johan Willemsen, Antonio J. Monforte, Tea Meulia, Esther van der Knaap, A common genetic mechanism underlies morphological diversity in fruits and other plant organs Nature Communications. ,vol. 9, pp. 4734- ,(2018) , 10.1038/S41467-018-07216-8