Table 1. List of Recently Duplicated Arabidopsis Gene Pairs Encoding Plastid Preproteins in Which Only One of the Isoforms (the One at Top) Possesses Extra Twin-Positive Motifs.

No.	Gene	Transit Peptide Sequence (First 60 Amino Acids of the N Terminus)	Root Protein (Log2)a	Association	Root RNA	Leaf RNA
1	AT2G30950.1	MAASSACLVGNGLSVNTTTKQRLSKHFSGRQTSFSSVIRTSKVNVVKASLDGKKKQEGRR———–	−2.14	Yes	82.30	1632.73
	AT1G06430.1	MAASSACLLGNGLSVYTT-KQRFQK–LG——-LDRTSKVTVVKASLD-EKKHEGRRGFFKLLLGNAA	–		6.95	150.96
2	AT1G17050.1	MMMSCRNIDLGTSVLDHSCSSSSTSRRFLFGNSSKTVCMIGGRS-CVGNLVFLRRDLATCR—–	−1.41	Yes	50.76	151.48
	AT1G78510.1	MMTSCRNIDLGTMMMACGCG—–RR-QFPSLAKTVCKFTSSNRSYGGLVGSCKAVPTKSKEISL	−3.32		17.70	53.73
3	AT1G55490.1	MASTFTATSSIGSMVAPNGHKSDKKLISKLSSSSFGRRQSVCPRPRRSSSAIVCAAKELH—-	−2.76	Yes	187.73	2437.78
	AT3G13470.1	MASTFTATSSLGSLLAPNAIKLSS–ATSISSSSFGRRHNVCV–RRSRPAIVCAAKELHFNKD	−3.72		360.90	1454.63
4	AT2G47400.1	MTTIAAAGLNVATPRVVVRPVAR—VLGPVRLNYPWKFGS—–MKRMVVVKATSEGEISEKVEKS	−1.37	Yes	128.19	2174.71
	AT3G62410.1	MATIAT-GLNIATQRVFVTSENRPVCLAGPVHLNNSWNLGSRTTNRMMKLQPIKAAPEGGI——-	–		6.68	496.4
5	AT3G22890.1	MASMAAVLSK-TPFLSQPLTKSSPNSDLPFAAVSFPSKSLRR–RVGSIRAGLIAPDGGKLVE	0.33	Yes	434.31	957.01
	AT4G14680.1	MASMSTVFPKPTSFISQPLTKS-HKSDSVTTSISFPSNSKTRSLRTISVRAGLIEPDGGKL–	–		78.73	216.16
6	AT5G24650.1	–MGKDGEGDKKR—ETMAVMSLMKDQQNPIQQFQVKFKEIETGFKSWLSKQKLPVEAAVVTAM	0.74	Yes	170.20	364.01
	AT3G49560.1	MVVGGGGEGDQKRSSGEMMAMASLFNDQQNPIQQFQVKFKEVETNFKTWLSKQSIPVEAA—–	−0.37		128.60	453.28
7	AT3G05020.1	MATQFSASVSLQTSCLATT-RISFQKPALISNHGKTN-LSFNLRRSIPSRRLSVSCAAKQET	0.98	Yes	371.42	129.6
	AT5G27200.1	MATSFCSSISMQAPFSATTTRFCLNKQATIFNNEKTNNLSFSLRRLMPAR-LAVSCAVKQE-	–		21.75	8.18
8	AT3G11630.1	–MASVASS–TTLISSPSSRVFPAKSSLSSPSVSFLRTLSSPSASAS-LRSGFARRSSLSSTSRR	1.47	Yes	548.53	2728.13
	AT5G06290.1	MSMASIASSSSTTLLSS-SRVLLPSKSSLLSPTVSFPRIIPSSSASSSSLCSGFSSLGSLTT—-	−1.61		95.41	1446.05
9	AT3G02730.1	MPLSLRLSPSPTAL–SPTT—-GGFGPSRKQCRIPYSGVPTTKIGFCS—–LDSRKRGDSSVVRCSL-	−2.17	Yes	20.68	925.86
	AT5G16400.1	MPLSLRLAPSPTSFRYSPITSTGAGGFSPVKQHCRIPNSGVAT-KIGFCSGGGGVLDSGRR	−2.27		17.33	485.15
10	AT2G45440.1	MAALKGYGLCSMDSALQFPCPKLFNSYKRRSSKWVSPKAAVVPNFHLPMRSLEVKNRTNT-	−1.83	Yes	148.71	254.88
	AT3G60880.1	MSALKNYGLISIDSALHFPRSNQLQSYKR-NAKWVSPIAAVVPNFHLPMRSLEDKNRTNTD	–		110.91	101.45
11	AT3G29200.1	MEASLLMRSSCCSSAIGGFFDHRRELSTSTPISTLLPLPSTKSSFSVRCSLPQPSKPRSG-	−0.83	Yes	82.15	144.48
	AT1G69370.1	MEAKLLKPAFYNSPNLN-LTNSSRLISRLSIWNDKSKVGLSSGSLFLRLSAASPIRYSRGL	−2.69		88.73	162.94
12	AT3G47060.1	MTTTFEFLQPRIHG—FATCCSSNSLLYSKASRFFNDRCRVYRQNPNRFVSN-SITLPLQKKQ	−4.01	Yes	49.98	74.64
	AT5G58870.1	MTS-IELLSPLIHDKFRFSTCCSTSSLLYLHASSFFRDRSFGFRQNPNRFVSNSSIQLPQS—	–		142.86	456.78
13	AT1G31230.1	MPVVSLAKVVTSPAVAG-DLAVRVPFIYGKRLVSNRVSFGKLRRRSCIG-QCVRSELQSPRV	0.49	Yes	136.48	196.58
	AT4G19710.2	MATLKPSFTVSPPNSNPIRFGSFPPQCFLRVPKPRRLILPRFRKTTGGGGGLIRCEL–PDF	−1.34		102.78	215.33
14	AT1G15500.1	MEGLIQTRGILSLPAKPIGVRRLLQPSHGLKQRLFTT—NLPALSLSSNGHKKFQAFQQIPL	−0.12	Yes	159.78b	354.58b
	AT1G80300.1	MEAVIQTRGLLSLPTKPIGVRSQLQPSHGLKQRLFAAKPRNLHGLSLSFNGHKKFQTFEP—	−0.19		159.78b	354.58b
15	AT1G14410.1	MSQLLSTPLMAVN———SNPRFLSSSSVLVTGGFAVKRHGFALKPTTKTVKLFSVKSRQTDYFE	−1.03	Noc	89.60	261.13
	AT2G02740.1	MSQLLSSPPMAVFSKTFINHKFSDARFLSSHSILTSGGFAGK–IIPLKPTAR-LKL-TVKSRQ—–	−0.83		25.81	103.56
16	AT2G37400.1	MESLGKLQLHQQPNHLSFTHFSSS-FPKKPSSFSLRSLPRSTSSFKCISIKASSSKSQDSK—	–	Noc	68.85	95.36
	AT3G53560.1	MESLGKLQLHHQPFHLSFTHTSSSTFPKN—-LFKSSIQPISSLKSASIKASSSKFQNSITPL	−3.01		59.13	479.76
17	AT1G77060.1	MSMLMAVKTTSLCCSSLNLTASPTFRRNPRAARLVNPTARIQTRFHRLIEEQGIVLMPGC–	–	No	22.30	210.06
	AT1G21440.1	MSMLMAAKSTSLFSS–NPTISAKIGQNPRGVRSVYPTVRMQSRVHRLIEEQGAVLIPGVYD	1.24		524.05	326.13
18	AT3G25740.1	—–MLQKISQS–ISLCN—GDQFKPLIYLAGAPTNFISSPLSGKKKSSSLRIKRIQQLQSTLEDRI	–	No	19.34	26.80
	AT1G13270.1	MASSVFLSSFSSSSSLQLCSSFHGEYLAPSRCFLGAPVTSSSLSLSGKKNSYSPRQFHVS———-	−3.01		33.33	478.56
19	AT3G23790.1	M-ASTSLGASILVSHCSSAPEFQVSGMRLVFGYKAFGCRTSRRGFR-VRCESKIQEKELRRCS	–	No	20.90	28.86
	AT4G14070.1	MQIRLKPDYSFFIASSSTMASTSSLGPSTLLSYGSPSRQFPDFGFRLISGHESVRIPSFRR–	−3.98		21.10	115.58
20	AT5G47110.1	MSISMALFSPPISSS-LQNPNLIPKISTSLLSTKRFSLISVPRASSDNGTTSP—-VVEIPKPA	–		20.63	840.26
	AT4G17600.1	—-MALFSPPISSSSLQNPNFIPKFSFSLLSSNRFSLLSVTRASSDSGSTSPTAAVSVEAPEP-	–		4.16	1218.96
21	AT4G39030.1	MLIKSQRLTLFSPLLSKTRRIPVNSHQTLVA-ESVITRRTLGAITATPSFHKNPVVIRRRI	–		146.83	52.11
	AT2G21340.1	MQIQCKTLTFTVSSIPCNPKLPFPSSLTLRSWNPSFPSFRSSAVSGPKSSLKLNRFLRNC-	–		49.80	224.11
22	AT1G18170.1	MANLFTATAP-FLSLSKP–FTKTASYHQCYASS-SNPPEPESSSPPPPPPPPQPLASQQKRKK	–		12.83	98.83
	AT1G73655.1	MATLFTATVPSHHRFVSPSQHPKQSLLSQSLSVTFTENPQPTAVVTLQEQQLTDWITSPV—-	–		61.78	542.31

Twin-positive motifs are denoted with boldface underlined letters. The root and leaf RNA (fluorescence intensity, arbitrary units) and the root protein data were downloaded from the Arabidopsis eFP Browser (Winter et al., 2007) and AtProteome (Baerenfaller et al., 2008) databases, respectively. “Yes” in the Association column indicates that the isoform with extra twin-positive motifs also has higher root protein abundance. Blank cells in the Association column indicate no data. The sequence alignment was produced using ClustalW with default parameters and refined manually.

^aDashes in this column indicate not detected.

^bThe same probe set was used for the two genes.

^cThe isoform with extra twin-positive motifs also has higher leucoplast import, as shown in Supplemental Figure 6.