Table 4 |
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|
Summary of the high-throughput sequencing data available for sugarcane, Sorghum and Miscanthus |
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|
Platform |
Record GEO/NCBI, SRA |
No. of samples |
Sample description |
Variety |
Reference |
|
|
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|
Illumina Genome Analyzer IIx |
GPL16316 |
8 |
sRNA and non-coding RNAs of sugarcane in response to drought stress |
Saccharum hybrid (mixed) |
[92] |
|
Illumina Genome Analyzer IIx |
GPL15137 |
3 |
Examination of small RNAs in the sugarcane leaves that match to sugarcane LTR-RTs |
Saccharum hybrid cv. SP80-3280 |
[93] |
|
Identification of small RNAs associated with auxiliary bud outgrowth |
Saccharum hybrid cv. SP80-3280 |
[121] |
|||
|
Illumina Genome Analyzer IIx |
GPL16317 |
6 |
Screening of small RNA transcriptome of sugarcane plants infected with Acidovorax avenae subsp. avenae after 7 days |
Saccharum hybrid cv. SP70-1143 |
[92] |
|
Identification of sugarcane microRNAs after exposure to pathogens and microorganisms |
Saccharum hybrid cv. SP70-1143 |
||||
|
SOLEXA technology |
Not available |
8 |
Identification of microRNA differentially expressed under drought stress, correlation between two cultivars with different drought tolerance |
Saccharum hybrid cv. RB867515, RB855536 |
[90] |
|
SOLEXA technology |
Not available |
2 |
Increase the understanding of the role of microRNAs in the complex regulation of drought stress in field-grown sugarcane |
Saccharum hybrid cv. RB867515, RB855536 |
[91] |
|
Illumina Genome Analyzer II |
GPL13779 |
24 |
RNA-Seq of Sorghum bicolor 9-day seedlings in response to osmotic stress and abscisic acid |
Sorghum bicolor |
[75] |
|
Illumina Genome Analyzer IIx |
GPL14633 |
3 |
Comparative sequence analysis of plant small RNAs |
S. bicolor |
GEO |
|
Comparative sequence analysis of plant small RNAs from leaves, flowers and panicle tissues |
S. bicolor |
GEO |
|||
|
Illumina Genome Analyzer II |
GPL9983 |
3 |
Develop sequence resources of small RNAs from different Miscanthus × giganteus tissues (including leaves, flowers and rhizomes) |
Miscanthus × giganteus |
[94] |
|
Illumina Genome Analyzer II |
SRX131848/SRX131845 |
1 |
RNAseq from two Miscanthus sinensis to define single nucleotide variants and find simple sequence repeat markers for understanding genomic responses to tetraploidy and chromosome fusion |
Miscanthus sinensis |
[96] |
|
|
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|
Data were catalogued based on MIAME compliant public repositories such as Gene Expression Omnibus/Center for Information Biology Gene (GEO/NCBI) Expression Database (CIBEX), Microarray Gene Expression Data Society (MGED) and ArrayExpress. LTR-RT, long terminal repeat retrotransposon. |
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|
de Siqueira Ferreira et al. Genome Biology 2013 14:210 doi:10.1186/gb-2013-14-6-210 |
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