scholarly journals The Challenge of Analyzing the Sugarcane Genome

2018 ◽  
Vol 9 ◽  
Author(s):  
Prathima P. Thirugnanasambandam ◽  
Nam V. Hoang ◽  
Robert J. Henry
Keyword(s):  
Sugarcane Genome

scholarly journals De novo assembly and characterizing of the culm-derived meta-transcriptome from the polyploid sugarcane genome based on coding transcripts

Heliyon ◽  
2018 ◽  
Vol 4 (3) ◽  
pp. e00583 ◽  
Author(s):  
Nam V. Hoang ◽  
Agnelo Furtado ◽  
Prathima P. Thirugnanasambandam ◽  
Frederik C. Botha ◽  
Robert J. Henry
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Sugarcane Genome

scholarly journals Diversification of hAT transposase paralogues in the sugarcane genome

2012 ◽  
Vol 287 (3) ◽  
pp. 205-219 ◽  
Author(s):  
Erika M. de Jesus ◽  
Edgar A. Ochoa Cruz ◽  
Guilherme M. Q. Cruz ◽  
Marie-Anne Van Sluys
Keyword(s):  
Sugarcane Genome

scholarly journals Gene Duplication in the Sugarcane Genome: A Case Study of Allele Interactions and Evolutionary Patterns in Two Genic Regions

2019 ◽  
Vol 10 ◽  
Author(s):  
Danilo Augusto Sforça ◽  
Sonia Vautrin ◽  
Claudio Benicio Cardoso-Silva ◽  
Melina Cristina Mancini ◽  
María Victoria Romero-da Cruz ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Evolutionary Patterns ◽  
Sugarcane Genome

The Sugarcane Genome Challenge: Strategies for Sequencing a Highly Complex Genome

2011 ◽  
Vol 4 (3-4) ◽  
pp. 145-156 ◽  
Author(s):  
Glaucia Mendes Souza ◽  
Helene Berges ◽  
Stephanie Bocs ◽  
Rosanne Casu ◽  
Angelique D’Hont ◽  
...  
Keyword(s):  
Sugarcane Genome ◽  
Complex Genome

scholarly journals Mutator System Derivatives Isolated from Sugarcane Genome Sequence

2012 ◽  
Vol 5 (3) ◽  
pp. 233-243 ◽  
Author(s):  
M. E. Manetti ◽  
M. Rossi ◽  
G. M. Q. Cruz ◽  
N. L. Saccaro ◽  
M. Nakabashi ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Sugarcane Genome

scholarly journals Building the sugarcane genome for biotechnology and identifying evolutionary trends

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
Author(s):  
Nathalia de Setta ◽  
Cláudia Barros Monteiro-Vitorello ◽  
Cushla Jane Metcalfe ◽  
Guilherme Marcelo Queiroga Cruz ◽  
Luiz Eduardo Del Bem ◽  
...  
Keyword(s):  
Evolutionary Trends ◽  
Sugarcane Genome

scholarly journals 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 ◽  
Vol 18 (1) ◽  
Author(s):  
Nam V. Hoang ◽  
Agnelo Furtado ◽  
Patrick J. Mason ◽  
Annelie Marquardt ◽  
Lakshmi Kasirajan ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Full Length ◽  
Short Read ◽  
Short Read Sequencing ◽  
Sugarcane Genome

scholarly journals A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6080
Author(s):  
Clicia Grativol ◽  
Flavia Thiebaut ◽  
Sara Sangi ◽  
Patricia Montessoro ◽  
Walaci da Silva Santos ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Small Rna ◽  
Genome Assembly ◽  
Inverted Repeat ◽  
Small Rnas ◽  
Distribution Patterns ◽  
Plant Genomes ◽  
Sugarcane Genome

Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses.

scholarly journals Molecular chaperone genes in the sugarcane expressed sequence database (SUCEST)

2001 ◽  
Vol 24 (1-4) ◽  
pp. 85-92 ◽  
Author(s):  
Júlio C. Borges ◽  
Maria C. Peroto ◽  
Carlos H.I. Ramos
Keyword(s):  
Molecular Chaperone ◽  
Molecular Chaperones ◽  
Expressed Sequence Tag ◽  
Protein Sequences ◽  
Genome Project ◽  
Related Protein ◽  
Sequence Database ◽  
Bioinformatic Tools ◽  
Expressed Sequence ◽  
Sugarcane Genome

Some newly synthesized proteins require the assistance of molecular chaperones for their correct folding. Chaperones are also involved in the dissolution of protein aggregates making their study significant for both biotechnology and medicine and the identification of chaperones and stress-related protein sequences in different organisms is an important task. We used bioinformatic tools to investigate the information generated by the Sugarcane Expressed Sequence Tag (SUCEST) genome project in order to identify and annotate molecular chaperones. We considered that the SUCEST sequences belonged to this category of proteins when their E-values were lower than 1.0e-05. Our annotation shows that 4,164 of the 5’ expressed sequence tag (EST) sequences were homologous to molecular chaperones, nearly 1.8% of all the 5’ ESTs sequenced during the SUCEST project. About 43% of the chaperones which we found were Hsp70 chaperones and its co-chaperones, 10% were Hsp90 chaperones and 13% were peptidyl-prolyl cis, trans isomerase. Based on the annotation results we predicted 156 different chaperone gene subclasses in the sugarcane genome. Taken together, our results indicate that genes which encode chaperones were diverse and abundantly expressed in sugarcane cells, which emphasizes their biological importance.

scholarly journals Development of Transgenic Sugarcane Resistant to Stem Borer by Transforming cry1Ab-cry1Ac Fusion Gene through Agrobacterium tumefaciens Transformation Method

2021 ◽  
Vol 17 (1) ◽  
pp. 11
Author(s):  
Deden Sukmadjaja ◽  
Sri Koerniati ◽  
Auliya Lukman
Keyword(s):  
Agrobacterium Tumefaciens ◽  
Molecular Analysis ◽  
Transformation Efficiency ◽  
Insect Pests ◽  
Fusion Gene ◽  
Stem Borer ◽  
Transformation Method ◽  
High Yield ◽  
Research Activities ◽  
Sugarcane Genome

<p>Bulu Lawang (BL) is a sugarcane variety preferred by farmers in Indonesia due to its high yield, but this cultivar is susceptible to shoot and stem borer insect pests. Genetic engineering using cry1Ab and cry1Ac fusion gene is an effort to generate BL varieties resistant to the insect pests. This study aimed to 1) transform T-DNA containing cry1Ab-cry1Ac fusion gene into sugarcane genome by using Agrobacterium tumefaciens method, 2) obtain selection media composition of callus transformants, and 3) obtain transformation efficiency comparison of A. tumefaciens strains EHA105 and GV3101. The research was conducted at the Laboratory of Cell and Tissue Biology, the Laboratory of Molecular Biology, and the greenhouse of the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor from March to August 2019. Research activities consisted of four parts namely 1) callus induction and Agrobacterium culture preparation containing pCambia5300-cry1Ab-cry1Ac ///// pCambia-5300_OaRbcS-prom-cTP-cry1Ab-cry1Ac plasmid, 2) callus incubation in cocultivation and resting media, 3) selection and differentiation of shoots on regeneration media, and 4) molecular analysis using PCR method. Results showed that the composition of media, both for selection and regeneration processes of putative plant transformants, was the key to the success of this experiment. A. tumefaciens strain EHA105 resulted in higher transformation efficiency (11.1%) compared to that of strain GV3101 (9.0%). Molecular analysis showed that cryIAb-cryIAc fusion gene was successfully inserted into the sugarcane genome suggesting that the transgenic plant containing cry1Ab-cry1Ac fusion gene was obtained. The putative transgenic plants need further assay through bioassay tests to verify its resistance phenotype to the insect pests.</p>

Sign in / Sign up

Export Citation Format

Share Document