Genome of extreme halophyte Puccinellia tenuiflora

BMC Genomics

Table 5 General statistics for feature of predicted protein-coding genes of P. tenuiflora genome. Protein-coding genes were predicted through the annotation strategy of de novo prediction and evidence based on homology and transcriptome data. The gene model was integrated with EVM and corrected by PASA to obtain the final set of protein-coding genes

Gene set		Number	Average gene length (bp)	Average CDS length (bp)	Average exons per gene	Average exon length (bp)	Average intron length (bp)
De novo^a	Augustus	59,267	1866.04	873.71	3.04	287.43	486.52
	GlimmerHMM	195,821	4538.43	540.7	2.16	250.76	3457.37
	SNAP	115,465	3464.46	615.94	2.8	220.02	1582.94
	Geneid	122,152	2958.40	684.27	3.08	222.01	1092.23
	Genscan	92,436	5507.46	609.14	2.96	205.68	2497.19
Homolog^b	Zea mays	40,162	1988.08	978.69	3.32	294.72	434.93
	Sorghum bicolor	73,561	2000.94	1121.24	2.57	436.89	561.61
	Brachypodium distachyon	67,858	2097.32	1124.66	2.8	401.87	540.8
	Setaria italica	62,339	1568.92	826.04	2.68	308.16	442.05
	Arabidopsis thaliana.	43,096	1629.35	839.3	2.77	302.45	445.1
	Oryza sativa	76,835	1550.38	915.3	2.35	389.23	469.88
RNA-seq	Cufflinks^c	62,560	5041.52	1845.64	5.54	333.32	704.38
RNA-seq	PASA	63,952	2292.77	934.6	3.9	239.86	468.9
EVM		66,649	2149.27	869.1	3.23	268.94	573.67
PASA-update		66,482	2122.71	871.22	3.22	270.77	564.36
Final set ^c		39,725	2818.49	1081.99	4.15	260.54	550.76

^aStatistics calculated from the gene set predicted from each method.
^bStatistics calculated from the gene set predicted by homolog proteins from each species.
^cFinal results of P. tenuiflora genome

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