Table 2.

Protein-coding gene annotation of S. grahami genome.

Method	Software or Species	Gene number	Average
			Transcript Length (bp)	CDS Length (bp)	Exons per Gene	Exon Length (bp)	Intron Length (bp)
de novo	Augustus	47,723	20,378	1,148	7.6	150.9	2,911
Homolog	Danio rerio	64,268	36,029	1,523	11.4	134.1	3,333
	Oryzias latipes	29,532	29,701	1,637	12.5	131.2	2,445
	Sinocyclocheilus anshuiensis	55,080	19,982	1,644	12.6	130.3	1,579
	Sinocyclocheilus rhinocerous	57,118	21,844	1,631	12.5	130.6	1,760
	Sinocyclocheilus grahami	49,556	29,535	1,507	11.1	135.5	2,768
Transcriptome		31,114	9,515	1,628	7.6	214.7	1,198
Consensus	MAKER	42,806	18,370	1,331	8.9	148.2	1,984

Note: In homolog annotation, we used the genome and gene set of S. grahami, which were assembled using Illumina data [46].