Supporting Information Legends
Supplementary_file_1 as PDF
Supplementary file 1: Figure S1. Transcription directions of peRNA-seq-assembled transcripts were
supported by ssRNA-seq reads. A. Distribution of reads-mapping ratio (log2 of S/A) of rice genes. B. Distribution
of reads-mapping ratio (log2 of S/A) of maize genes. Reads-mapping ratio was calculated by dividing the total reads
mapped to the same strand of an annotated genes by the total reads mapped to the antisense strand of an annotated
genes. C. Transcription directions of peRNA-seq assemblies in rice. ND, not determined. D. Determined
transcription directions of peRNA-seq assemblies in maize. ND, not determined. E. Transcription directions of rice
lincRNA genes and neighboring protein-coding genes. ND, not determined. F. Transcription directions of maize
lincRNA genes and neighboring protein-coding genes. ND, not determined. G. Rice transcripts assembled from nondirectional paired-end RNA-seq and directional single-end RNA-seq experiments. H. Maize transcripts assembled
from non-directional paired-end RNA-seq and directional single-end RNA-seq experiments.
Figure S2. Genomic features of lincRNAs in rice and maize. A&B. Distribution of lincRNA lengths (blue color)
and the distance of their genes to flanking genes (yellow color) in rice and maize. Y-axis gives the log10 value of
length or distance (bp). C&D. Gene density of the 50-kb genomic region flanking lincRNA loci and protein-coding
genes in rice and maize. Blue, protein-coding gene; red, lincRNA gene.
Figure S3. Distribution of three kinds of histone marks on the up-stream, transcribed and down-stream
regions of lincRNA genes and the correlation with expression levels. A. Distribution of histone marks on rice
lincRNA genes. B. Distribution of histone marks on maize lincRNA genes. C. Expression levels of rice lincRNA
genes associated with different groups of histone marks in leaves. D. Expression levels of maize lincRNA genes
associated with different groups of histone marks in shoots.
Figure S4. Genomic features of NATs in rice and maize. A. Classification of NAT pairs. B. Proportion of each
group of NAT pairs in rice and maize.
Figure S5. Temporal-spatial expression of lincRNAs and mRNAs in maize. Heat maps of differentially
expressed lincRNAs (leaf panel) and mRNAs (right panel) in maize.
Figure S6. K-means clustering of rice lincRNAs. Y-axis gives the log2 value of FPKM. The total number of
lincRNAs in each group is given. S1, milk grains. S2, mature seeds. R1, roots sampled before flowering. L1, leaves
sampled before flowering. F1, flower buds. R2, roots sampled after flowering. L2, leaves sampled after flowering.
F2, flowers.
Figure S7. Validation of differentially expressed lincRNAs by qRT-PCR. A. Expression levels of rice lincRNAs.
Y-axis gives the relative expression levels. Error bars represent standard errors (n = 3). B. FPKM values of rice
lincRNAs. C. Expression levels of maize lincRNAs. Y-axis gives the relative expression levels. Error bars represent
standard errors (n = 3). D. FPKM values of maize lincRNAs.
Figure S8. Expression correlation of selected rice lincRNAs and their nearest genes. X-axis gives the fold
change of lincRNA expression between organs (log2 value) and Y-axis gives the fold change of flanking gene
expression between organs (log2 value). Blue dots present positively correlated lincRNA loci and flanking gene
(Pearson's product-moment correlation = 0.80) and red dots present negatively correlated lincRNA loci and flanking
gene (Pearson's product-moment correlation = 0.78).
Figure S9. Numbers of positively-correlated and negatively-correlated NAT pairs in rice and maize
Venn diagrams present numbers of positively-correlated and negatively-correlated NAT pairs in rice and maize.
Figure S10. Sequence and positional conservation of maize lincRNAs. A. Sequence conservation of maize
lincRNAs based on results of whole genome alignment. B. Positional conservation of maize lincRNA genomic loci
based on analysis of synteny blocks.
Figure S11. Function enrichment analysis of sense genes involved in positionally conserved NAT pairs. A.
Function enrichment analysis of sense genes involved in positionally conserved NAT pairs in rice. B. Function
enrichment analysis of sense genes involved in positionally conserved NAT pairs in maize.
Supplementary_file_2 as XLS
Supplementary file 2:
Table S1. Primers used in qRT-PCR experiments.
Table S2. Rice lincRNAs.
Table S3. Rice NATs.
Table S4. Maize lincRNAs.
Table S5. Maize NATs.
Table S6. Original genomic positions of trait-associated SNPs (TAS-SNPs) and their associated lincRNAs.
Table S7. RNA-seq dataset.
Table S8. Histone marks association with lincRNA genes, protein-coding genes and transposon elements.
Table S9. GO enrichment analysis of sense genes involved in NAT pairs.
Table S10. GO enrichment analysis of genes surrounding conserved lincRNA genes.