Genome-wide analysis of small RNAs responsive to cold stress inB. rapa
To study the cold response of B. rapa , the degree of cold
tolerance was estimated by evaluating morphological traits under cold
stress. After 7 days of cold treatment (4 °C), the plants stopped
growing and their leaves drooped (Figure 1A). Therefore, to identify
genome-wide cold-responsive miRNAs, we performed cold treatment for 7
days (B_V7) on 3-week-old seedlings of B. rapa in a growth
chamber, and plants grown at 22 °C (B_V0) was used as control for small
RNA sequencing.
Totally, 17.96 million (B_V0) and 17.17 million (B_V7) raw reads were
obtained from these two samples (Figure 1B). Among them, most of reads
were shared between the two libraries, while 2.82 million reads were
B_V0-specific, and 2.23 million reads were B_V7-specific (Figure 1B).
Small RNA length distribution analysis showed that 24-nt small RNAs were
most abundant, and 21-nt small RNAs were second most abundant (Figure
1C).
To learn the genomic loci that produced these small RNAs, 11.46 million
(B_V0) and 11.36 million (B_V7) clean reads were mapped to theB. rapa reference genome (http://brassicadb.cn/#/). We found
that the small RNAs were generated from exons, introns, miRNAs, rRNAs,
snRNAs, snoRNAs, tRNAs, and repeat regions (Table S1). Notably, focusing
on small RNAs from no-coding gene regions, most abundant small RNAs were
produced from ribosomal RNAs (rRNAs) (B_V0, 44.67% and B_V7,
48.10%), followed by unknown RNAs (B_V0, 27.65% and B_V7, 25.22%),
and miRNA precursors (B_V0, 8.50% and B_V7, 8.71%) (Figure S1).