Draft genome sequencing of the sugarcane hybrid SP80-3280

F1000Research

Volumn 6, Issue , 2017, Pages

  Riaño Pachón, Diego Mauricio ^a,b   Mattiello, Lucia ^a,c  

^a BRAZILIAN CENTER FOR RESEARCH IN ENERGY AND MATERIALS CNPEM   (Brazil)

^b UNIVERSITY OF SÃO PAULO   (Brazil)

^c UNIVERSITY OF CAMPINAS   (Brazil)

Author keywords

Genomics; Long reads; Polyploid; Sugarcane

Indexed keywords

GENOME; GENOMICS; NONHUMAN; POLYPLOIDY; SUGARCANE;

EID: 85024485223     PISSN: 20461402     EISSN: 1759796X     Source Type: Journal    
DOI: 10.12688/f1000research.11859.2     Document Type: Note

References (21)

1. Long SP Karp A Buckeridge MS: Feedstocks for Biofuels and Bioenergy. In Bioenergy & Sustainability: bridging the gaps. (eds. Souza GM, Victoria RL, Joly CA & Verdade LM), UNESCO.2015;302-347. Reference Source
2. Grivet L Arruda P: Sugarcane genomics: depicting the complex genome of an important tropical crop. Curr Opin Plant Biol. 2002;5(2):122-127. 11856607 10.1016/S1369-5266(02)00234-0
3. D'Hont A: Unraveling the genome structure of polyploids using FISH and GISH; examples of sugarcane and banana. Cytogenet Genome Res. 2005;109(1-3):27-33. 15753555 10.1159/000082378
4. Le Cunff L Garsmeur O Raboin LM: Diploid/polyploid syntenic shuttle mapping and haplotype-specific chromosome walking toward a rust resistance gene ( Bru1) in highly polyploid sugarcane (2 n approximately 12 x approximately 115). Genetics. 2008;180(1):649-660. 18757946 10.1534/genetics.108.091355 2535714
5. Miller JR Dilley KA Harkins DM: Initial genome sequencing of the sugarcane CP 96-1252 complex hybrid. F1000Res. 2017;6:688. 10.12688/f1000research.11629.1
6. Grativol C Regulski M Bertalan M: Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum. Plant J. 2014;79(1):162-172. 24773339 10.1111/tpj.12539 4458261
7. Okura VK de Souza RS de Siqueira Tada SF: BAC-Pool Sequencing and Assembly of 19 Mb of the Complex Sugarcane Genome. Front Plant Sci. 2016;7:342. 27047520 10.3389/fpls.2016.00342 4804495
8. de Setta N Monteiro-Vitorello CB Metcalfe CJ: Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genomics. 2014;15(1):540. 24984568 10.1186/1471-2164-15-540 4122759
9. Mattiello L Riaño-Pachón DM Martins MC: Physiological and transcriptional analyses of developmental stages along sugarcane leaf. BMC Plant Biol. 2015;15:300. 26714767 10.1186/s12870-015-0694-z 4696237
10. Hoang NV Furtado A Mason PJ: A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing. BMC Genomics. 2017;18(1):395. 28532419 10.1186/s12864-017-3757-8 5440902
11. Belesini AA Carvalho FMS Telles BR: De novo transcriptome assembly of sugarcane leaves submitted to prolonged water-deficit stress. Genet Mol Res. 2017;16(2). 28549198 10.4238/gmr16028845
12. Porebski S Bailey LG Baum BR: Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol Biol Rep. 1997;15(1):8-15. 10.1007/BF02772108
13. McCoy RC Taylor RW Blauwkamp TA: Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements. PLoS One. 2014;9(9): e106689. 25188499 10.1371/journal.pone.0106689 4154752
14. Altschul SF Gish W Miller W: Basic local alignment search tool. J Mol Biol. 1990;215(3): 403-410. 2231712 10.1016/S0022-2836(05)80360-2
15. Myers EW Sutton GG Delcher AL: A Whole-Genome Assembly of Drosophila. Science. 2000;287(5461):2196-2204. 10731133 10.1126/science.287.5461.2196
16. Fu L Niu B Zhu Z: CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28(23): 3150-3152. 23060610 10.1093/bioinformatics/bts565 3516142
17. Riaño-Pachón DM Mattiello L Cruz LP: Surveying the complex polyploid sugarcane genome sequence using synthetic long reads. Technical Memorandum Centro Nacional de Pesquisa em Energia e Materiais.2016. 10.13140/RG.2.1.3468.0565
18. Hoff KJ Lange S Lomsadze A: BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS. Bioinformatics. 2016;32(5):767-9. 26559507 10.1093/bioinformatics/btv661
19. Haas BJ Delcher AL Mount SM: Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 2003;31(19):5654-66. 14500829 10.1093/nar/gkg770 206470
20. Slater GS Birney E: Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 2005;6:31. 15713233 10.1186/1471-2105-6-31 553969
21. Haas BJ Salzberg SL Zhu W: Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 2008;9(1):R7. 18190707 10.1186/gb-2008-9-1-r7 2395244