Trait-directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus
Article first published online: 18 SEP 2013
© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust
Volume 201, Issue 1, pages 144–154, January 2014
How to Cite
Meharg, C., Khan, B., Norton, G., Deacon, C., Johnson, D., Reinhardt, R., Huettel, B. and Meharg, A. A. (2014), Trait-directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus. New Phytologist, 201: 144–154. doi: 10.1111/nph.12491
- Issue published online: 26 NOV 2013
- Article first published online: 18 SEP 2013
- Manuscript Accepted: 12 AUG 2013
- Manuscript Received: 1 JUL 2013
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Fig. S1 Alignment of Holcus lanatus translated isotig20112 against an Oryza sativa PSTOL1 (OsPupK46-2) reported as a newly identified tolerance gene for phosphorous deficiency in Gamuyao et al. (2012).
Fig. S2 Alignment of Holcus lanatus isotig16840 with an Oryza sativa putative auxin-binding protein 4 precursor and B. distachyon predicted auxin-binding protein 4-like.
Fig. S3 Alignment of Holcus lanatus translated isotig12721 with an Oryza sativa expansin precursor and B. distachyon expansin-B7-like protein.
Fig. S4 Alignment of Holcus lanatus translated isotig01092, isotig18981 and isotig09507 with an Oryza sativa putative high-affinity phosphate transporter (HAPT) (AAM49810.1), O. sativa putative phosphate transporters (LOC_Os08 g45000.1 and LOC_Os10 g30790.2) and Brachypodium distachyon phosphate transporter 1-4-like isoform 2 (XP_003558116.1).
Fig. S5 Alignment of Holcus lanatus translated isotig16690 with an Oryza sativa phosphate transporter, phosphate transporter 1-3 (PHO1-3) (Q651J5), and O. sativa putative phosphate transporter 1 (LOC_Os06 g29790.1).
Fig. S6 Alignment of Holcus lanatus translated isotig11028 with Oryza sativa integral membrane protein DUF6 containing protein, expressed Brachypodium distachyon predicted auxin-induced protein 5NG4-like.
Fig. S7 Alignment of Holcus lanatus translated isotig19077 against an H. lanatus CDC25-like tyrosine phosphatase reported by Bleeker et al. (2006).
Fig. S8 Alignment of Holcus lanatus translated isotig02053 with Arabidopsis thaliana ALFIN-LIKE 6 protein and Brachypodium distachyon PHD finger protein ALFIN-LIKE 2-like.
Fig. S9 Alignment of Holcus lanatus isotig09604 with LOC_Os03 g01700.1, an expressed Oryza sativa protein (arsB-like, putative arsenite transport protein/cation-related transport protein).
|nph12491-sup-0002-TableS1.xlsx||application/msexcel||14K||Table S1 Statistical overview of Holcus lanatus 454 and Illumina data|
|nph12491-sup-0003-TableS2.pdf||application/PDF||19097K||Table S2 Reference Holcus lanatus 454 transcriptome assembly with newbler 2.6|
|nph12491-sup-0004-TableS3.xlsx||application/msexcel||20181K||Table S3 Annotated expressed transcripts/isotigs, normalized counts, and differential expression results as identified in R with package DESeq for Holcus lanatus, comparing tolerant and nontolerant phenotypes and phosphate treatments|
|nph12491-sup-0005-TableS4.xlsx||application/msexcel||2880K||Table S4 Raw count data for all Holcus lanatus Illumina sequencing data|
|nph12491-sup-0006-TableS5.docx||Word document||125K||Table S5 Consistent SNPs identified in Holcus lanatus isotigs across all genotypes of either the nontolerant (N) or the tolerant (T) phenotype; six homozygous (close to 100%) and 30 heterozygous (close to 50%); plotted in Fig. 5|