Gender-specific selection on codon usage in plant genomes

Whittle, Carrie-Ann; Malik, Meghna R; Krochko, Joan E

doi:10.1186/1471-2164-8-169

BMC Genomics

Table 3 Difference in the relative synonymous codon usage (RSCU) for short genes (less than or equal to 200 amino acids in the homologous Arabidopsis thaliana protein), medium length genes (more than 200 amino acids and less than or equal to 400) and long genes (more 400 amino acids) as determined from concatenated EST sequences of female- and male-specific sequences in Zea mays and Triticum aestivum and male-specific and flower-specific sequences in Brassica napus.

From: Gender-specific selection on codon usage in plant genomes

Amino acid	Codon	Difference in RSCU (Female-specific genes minus male-specific genes)^a								Difference in RSCU (Male-specific genes minus flower-specific genes)^b
		Zea mays ^c				Triticum aestivum ^c				Brassica napus ^c
		Short	Medium	Long	Codon(s) previously identified as preferred^d	Short	Medium	Long	Codon(s) previously identified as preferred^d	Short	Medium	Long
Phe	UUU	-0.15	-0.19	-0.23		-0.06	-0.12	-0.24		+0.05	-0.01	-0.21
	UUC	+0.15	+0.19	+0.23	*	+0.06	+0.12	+0.24	*	-0.05	+0.01	+0.21
Leu	UUA	-0.07	-0.15	-0.19		-0.06	-0.09	-0.14		-0.03	-0.01	-0.28
	UUG	-0.22	-0.20	-0.16	*	-0.01	-0.13	-0.15		+0.13	-0.05	-0.02
	CUU	-0.22	-0.10	-0.18		-0.17	-0.20	-0.30		+0.09	-0.09	-0.06
	CUC	+0.50	+0.34	+0.27	*	+0.24	+0.24	+0.32	*	-0.18	-0.05	+0.59
	CUA	-0.06	-0.10	-0.07		-0.03	-0.04	-0.10		-0.06	+0.02	-0.17
	CUG	+0.07	+0.23	+0.32	*	+0.04	+0.23	+0.37		+0.05	+0.18	-0.04
Ile	AUU	-0.14	-0.21	-0.18		-0.16	-0.14	-0.22		+0.08	+0.06	-0.08
	AUC	+0.24	+0.33	+0.35	*	+0.12	+0.25	+0.33	*	-0.09	-0.07	+0.46
	AUA	-0.09	-0.13	-0.17		+0.03	-0.12	-0.11		0	+0.01	-0.38
Val	GUU	-0.32	-0.22	-0.30		-0.20	-0.14	-0.30		+0.06	-0.07	-0.05
	GUC	+0.25	+0.22	+0.08	*	+0.06	+0.13	+0.15	*	-0.13	+0.01	+0.20
	GUA	-0.17	-0.08	-0.09		-0.04	-0.06	-0.10		-0.02	+0.03	-0.20
	GUG	+0.23	+0.08	+0.31	*	+0.18	+0.07	+0.25	*	+0.08	+0.03	+0.05
Ser	UCU	-0.19	-0.14	-0.28		-0.13	-0.17	-0.32		-0.01	-0.06	-0.01
	UCC	+0.19	+0.11	+0.22	*	+0.19	+0.19	+0.13	*	-0.06	+0.02	+0.30
	UCA	-0.33	-0.38	-0.25		-0.09	-0.28	-0.15		+0.04	+0.05	-0.34
	UCG	+0.11	+0.10	+0.15	*	+0.13	+0.23	+0.25		+0.02	-0.02	+0.15
	AGU	-0.19	-0.18	-0.20		-0.14	-0.13	-0.17		+0.09	-0.02	-0.21
	AGC	+0.41	+0.47	+0.36	*	+0.04	+0.16	+0.25	*	-0.09	+0.03	+0.10
Pro	CCU	-0.28	-0.19	-0.14		-0.10	-0.14	-0.24		+0.15	+0.03	+0.05
	CCC	+0.29	+0.26	+0.18	*	+0.22	+0.19	+0.13	*	-0.01	+0.05	+0.10
	CCA	-0.25	-0.23	-0.33		-0.22	-0.24	-0.21		-0.03	+0.03	-0.25
	CCG	+0.23	+0.17	+0.28	*	+0.10	+0.19	+0.31	*	-0.10	-0.12	+0.10
Thr	ACU	-0.21	-0.18	-0.21		-0.01	-0.26	-0.25		+0.09	+0.01	-0.01
	ACC	+0.29	+0.33	+0.31	*	+0.13	+0.25	+0.28	*	-0.10	-0.06	+0.37
	ACA	-0.17	-0.30	-0.30		-0.11	-0.19	-0.29		+0.01	+0.04	-0.43
	ACG	+0.10	+0.14	+0.20	*	-0.01	+0.19	+0.27	*	0	+0.01	+0.07
Ala	GCU	-0.11	-0.21	-0.22		-0.19	-0.27	-0.28		+0.18	0	+0.02
	GCC	+0.18	+0.19	+0.25	*	+0.22	+0.27	+0.22	*	-0.15	0	+0.16
	GCA	-0.10	-0.19	-0.19		-0.11	-0.18	-0.23		-0.04	+0.01	-0.33
	GCG	+0.03	+0.19	+0.17	*	+0.08	+0.18	+0.29		+0.02	-0.01	+0.15
Tyr	UAU	-0.13	-0.28	-0.19		-0.11	-0.08	-0.21		+0.06	+0.07	-0.24
	UAC	+0.13	+0.28	+0.19	*	+0.11	+0.08	+0.21	*	-0.06	-0.07	+0.24
His	CAU	-0.27	-0.22	-0.16		-0.03	-0.13	-0.20		+0.04	-0.01	-0.21
	CAC	+0.27	+0.22	+0.16	*	+0.03	+0.13	+0.20	*	-0.04	+0.01	+0.21
Gln	CAA	-0.11	-0.10	-0.15		-0.10	-0.10	-0.14		-0.09	-0.03	-0.17
	CAG	+0.11	+0.10	+0.15	*	+0.10	+0.10	+0.14	*	+0.09	+0.03	+0.17
Asn	AAU	-0.32	-0.32	-0.21		-0.01	-0.11	-0.19		+0.05	+0.06	-0.15
	AAC	+0.32	+0.32	+0.21	*	+0.01	+0.11	+0.19	*	-0.05	-0.06	+0.15
Lys	AAA	-0.14	-0.17	-0.20		-0.03	-0.10	-0.12		-0.09	-0.08	-0.27
	AAG	+0.14	+0.17	+0.20	*	+0.03	+0.10	+0.12	*	+0.09	+0.08	+0.27
Asp	GAU	-0.06	-0.21	-0.24		-0.09	-0.13	-0.20		+0.04	-0.01	-0.10
	GAC	+0.06	+0.21	+0.24	*	+0.09	+0.13	+0.20	*	-0.04	+0.01	+0.10
Glu	GAA	-0.08	-0.20	-0.20		-0.05	-0.07	-0.13		-0.08	-0.02	-0.16
	GAG	+0.08	+0.20	+0.20	*	+0.05	+0.07	+0.13	*	+0.08	+0.02	+0.16
Cys	UGU	-0.08	-0.14	-0.20		-0.10	-0.18	-0.17		+0.04	+0.02	-0.14
	UGC	+0.08	+0.14	+0.20	*	+0.10	+0.18	+0.17	*	-0.04	-0.02	+0.14
Arg	CGU	-0.01	-0.16	-0.07		-0.14	-0.12	-0.07		+0.12	-0.05	+0.22
	CGC	+0.14	+0.17	+0.14	*	+0.06	+0.33	+0.20	*	+0.02	-0.01	+0.22
	CGA	+0.01	-0.18	-0.12		-0.03	-0.08	-0.12		-0.11	+0.03	-0.03
	CGG	+0.03	+0.08	+0.18		+0.18	+0.10	+0.18		-0.05	-0.01	-0.10
	AGA	-0.21	-0.18	-0.26		-0.03	-0.15	-0.27		+0.04	+0.03	-0.57
	AGG	+0.04	+0.28	+0.12	*	-0.05	-0.07	+0.07	*	-0.02	-0.01	+0.20
Gly	GGU	-0.11	-0.11	-0.21		-0.16	-0.11	-0.23		+0.08	+0.05	+0.03
	GGC	+0.34	+0.16	+0.31	*	+0.20	+0.29	+0.29	*	-0.15	+0.01	+0.12
	GGA	-0.22	-0.08	-0.16		-0.07	-0.19	-0.18		-0.04	-0.06	-0.06
	GGG	0	+0.04	+0.07		+0.04	+0.01	+0.12		+0.11	0	-0.09

Start and termination codons and the single codon for tryptophan have been excluded. Preferred codon data is not available for B napus. Data for codons previously identified as having codon biases (bold in Table 2) are in bold. [See Additional data file 1 (Tables 1 to 3) for the full data].
^a +, higher RSCU in female-specific genes; -, higher RSCU in male-specific genes.
^b +, higher RSCU in male-specific genes; -, higher RSCU in flower-specific genes.
^c The total number of short genes and the average gene length (± Standard error), respectively, used to estimate RSCU: Z. mays sperm 149, 137.9 (± 3.2), Z. mays egg 204, 135.3 (± 2.9), T. aestivum anther 340, 142.3 (± 2.0), T. aestivum ovary 309, 138.8 (± 2.3), B. napus microspore 485, 144.8 (± 1.5), B. napus flower 598, 140.6 (± 1.6). The total number of medium length genes and the average gene length, respectively, used to estimate RSCU: Z. mays sperm 330, 295.2 (± 3.1), Z. mays egg 352, 296.2 (± 3.2), T. aestivum anther 893, 309.0 (± 1.9), T. aestivum ovary 520, 298.4 (± 2.6), B. napus microspore 608, 294.3 (± 2.4), B. napus flower 1127, 297.5 (± 1.7). The total number of long genes and the average gene length, respectively, used to estimate RSCU: Z. mays sperm 476, 741.6 (± 20.7), Z. mays egg 390, 655.4 (± 18.9), T. aestivum anther 2093, 753.4 (± 8.3), T. aestivum ovary 660, 661.7 (± 13.0), B. napus microspore 582, 639.5 (± 12.6), B. napus flower 1456, 676.1 (± 8.6).
^d Previously described as preferred codons in Z. mays and T. aestivum as indicated by their frequencies in high-versus low-biased genes by Kawabe and Miyashita (2003) [42]. Asterisk (*) indicates a preferred codon. No values available for B. napus.

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