1.2 DNA extraction and sequencing
The plant genomic DNA extraction kit (TIANGEN) was used to extract the
total DNA of the samples. After the quality of the total DNA samples was
confirmed by Shanghai Hanyu Biotechnology Co., Ltd., the samples were
subjected to bidirectional sequencing using an Illumina HiSeq 2500, and
the raw data obtained were converted into raw reads by CASAVA
base-calling analysis. The clean data obtained after removing the
adaptor-containing, low-quality sequences were taken for subsequent
analysis. Data processing was performed by Trimmomatic v0.32 (Bolger et
al., 2014) with the following steps: (1) removal of sequences containing
N bases; (2) removal of adaptor sequences in the reads; (3) removal of
low-quality bases (Q value < 20) from the reads in the 3′ to
5′ direction; (4) removal of low-quality bases (Q value < 20)
from the reads in the 5′ to 3′ direction; (5) removal of four bases with
an average base quality of less than 20; and (6) removal of the reads
and their pairs with a length less than 50 nt. Velvet v1.2.03 (Zerbino
& Birney, 2008) was used to assemble the clean data.