2.4 Genome size estimation
The short-reads from the BGI platform were quality filtered by HTQC v 1.92.310 (Yang. et al.,2013) using the following method. Firstly, the adapters were removed from the sequencing reads. Second, read pairs were excluded if any one end had an average quality lower than 20. Third, the ends of reads were trimmed if the average quality was lower than 20 in the sliding window size of 5 bp. Finally, read pairs with any end shorter than 50 bp were removed. Then, the quality filtered reads were used for genome size estimation. We estimated the genome size of theC. sonnerati genome by using the k-mer analysis, which was performed with GCE (Liu et al., 2013).