2.1 Plant materials and sequencing
For genome sequencing, one adult plant ofS. tetraptera was collected
from Xining, Qinghai Province, China (N37°15′8, E101°22′18). Fresh
leaves were collected and snap-frozen
in liquid nitrogen for DNA isolation. The modified CTAB method (Doyle &
Doyle, 1987) was used to extract the genomic DNA. A Nanopore library was
constructed following the Nanopore library construction protocol. A
total of 152.6 Gb long reads were generated using the PromethION
sequence platform (Oxford Nanopore Technologies, [ONT]) (Table S1).
A paired-end library with 350 bp insert fragments was constructed and
then 51.8 Gb of raw data were produced using the Illumina HiSeq 2000
platform (Table S1). We also built a Hi-C library from young leaves as
described previously (Y. Yang et al., 2020) and obtained 121.31 Gb Hi-C
reads using the Illumina HiSeq 2000 platform (Table S1).
In addition, seven tissues (roots, stems, cCH [closed chasmogamous]
flowers, bCH [blooming chasmogamous] flowers, CL [cleistogamous]
flowers, and leaves from the branch of CH [termed ’CH leaf’] and CL
[CL leaf] flowers, respectively) from the same plant were collected
and immediately frozen in liquid nitrogen. For each tissue, three
samples were collected as biological replicates for RNA-sequencing
(RNA-seq) and metabolome analysis. The total RNA was extracted using a
QIAGEN RNeasy plant mini kit for each sample. The RNA-seq libraries were
then constructed with a TruSeq RNA library preparation kit (Illumina). A
total of 96.24Gb RNA-seq reads for all 21 libraries were obtained from
the HiSeq 2000 platform (Table S1).