Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri

Suryawanshi, Vasantika; Talke, Ina N.; Weber, Michael; Eils, Roland; Brors, Benedikt; Clemens, Stephan; Krämer, Ute

doi:10.1186/s12864-016-3319-5

Table 2 Genes identified to be altered in copy number in A. halleri through cross-species hybridization of gDNA onto A. thaliana microarrays

From: Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri

Affymetrix probeset ID	AGI locus ID	Short gene name^a	Gene description	A. halleri vs. A. thaliana		A. lyrata vs. A. thaliana
				L o g ₂ FC^b	P-value	L o g ₂ FC^b	P-value
(A)
Copy number expanded in A. halleri vs. A. thaliana(L o g ₂ F C> 1)
256055_at	At1g07030	Mfm1	Mitoferrin-related, mitochondrial solute carrier (MSC) family	1.23	0.01	-0.05	0.43
262832_s_at	At1g14870; At1g14880	PCR1; PCR2	Plant cadmium resistance 1/2	1.69	0.00	1.08	0.00
247824_at	At5g58460	CHX25	Member of Na⁺/H⁺ antiporter family	2.50	0.00	0.24	0.63
261448_at^c	At1g21140		Vacuolar iron transporter 1 (VIT1)-related	1.27	0.00	0.76	0.00
262958_at	At1g54410	ITP2	Ricinus iron transport protein 2-related	1.21	0.08	1.3	0.00
262936_at	At1g79400	CHX2	Cation/H⁺ exchanger 2	1.13	0.03	0.53	0.16
267304_at^d	At2g30080	ZIP6	ZRT-, IRT-like protein 6	1.12	0.08	0.46	0.55
263831_at	At2g40300	FER4	Ferritin 4	1.22	0.00	0.5	0.37
266718_at^c,d	At2g46800	MTP1	Metal transport/tolerance protein 1	2.5	0.00	0.24	0.63
259008_at	At3g09390	MT2a	Metallothionein 2a	1.22	0.00	0.57	0.00
252697_at	At3g43660		Vacuolar iron transporter 1 (VIT1)-related	1.16	0.08	0.78	0.02
251735_at	At3g56090	FER3	Ferritin 3	1.3	0.00	0.2	0.63
251733_at	At3g56240	CCH	Copper chaperone	1.12	0.00	0.44	0.19
255552_atd	At4g01850	SAMS2	S-adenosylmethionine synthetase 2	1.38	0.02	0.51	0.42
254604_at	At4g19070	AS8	Cadmium-induced protein AS8	1.13	0.00	0.49	0.05
253658_at^c,d	At4g30120	HMA3	Heavy metal ATPase 3	2	0.00	0.63	0.01
252864_at	At4g39740	HCC2	Homologue of yeast copper chaperone Sco1xx	1.06	0.01	0.34	0.66
250991_at	At5g02380	MT2b	Metallothionein 2b	1.32	0.05	0.43	0.34
248048_at^c	At5g56080	NAS2	Nicotianamine synthase 2	1.26	0.00	1.07	0.00
Putative copy number expanded in A. halleri vs. A. thaliana(L o g ₂ ≤ 1 and > 0.6)
249334_at	At5g41000	YSL4	Yellow stripe like transporter 4	0.99	0.43	0.00	0.08
266336_at	At2g32270	ZIP3	ZRT-, IRT-like^$ protein 3	0.97	0.28	0.09	0.58
260283_at	At1g80480	PTAC17	Plastid transcriptionally active 17, putative Zn metallochaperone	0.96	0.46	0.00	0.05
260551_at	At2g43510	TI1	Trypsin inhibitor 1, defensin-like protein family	0.95	0.24	0.00	0.74
250944_at^d	At5g03380	HIPP6	Putative metallochaperone-like protein	0.95	0.67	0.00	0.00
258745_at	At3g05920	HIPP43	Putative metallochaperone-like protein	0.93	0.45	0.00	0.06
253964_at	At4g26480	NAS-like	Protein with NAS domain and KH domain	0.93	0.37	0.01	0.14
247331_at	At5g63530	FP3	Farnesylated protein 3, metal-binding	0.92	0.45	0.00	0.09
266091_at	At2g37920	COPT4, EMB1513	Copper transporter 4, embryo defective 1513	0.92	0.68	0.01	0.01
259871_at^c	At1g76800		Vacuolar iron transporter 1 (VIT1)-related	0.91	0.18	0.02	0.85
256930_at^d	At3g22460	OASA2	O-acetylserine thiol lyase isoform A2	0.90	0.42	0.06	0.14
253413_at^c	At4g33020	ZIP9	ZRT-, IRT-like^$ protein 9	0.89	0.07	0.03	0.79
266115_at	At2g02140	PDF2.6	Plant defensin 2.6	0.86	0.46	0.00	0.01
258415_at	At3g17390	SAMS3/ MAT4*	S-adenosylmethionine synthetase 3	0.86	0.09	0.00	0.95
260489_at	At1g51610	MTP7	Metal transport protein 7	0.86	0.75	0.00	0.00
260913_at^d	At1g02500	SAMS1	S-adenosylmethionine synthetase 3	0.85	0.44	0.00	0.03
262324_at	At1g64170	CHX16	Cation/H⁺ exchanger, CPA2 family	0.84	0.38	0.07	0.36
257365_x_at^c,d	At2g26020	PDF1.2b	Plant defensin 1.2b	0.83	0.05	0.02	0.69
249255_at^c	At5g41610	CHX18	Cation/H⁺ exchanger, CPA2 family	0.77	0.63	0.00	0.01
263838_at^c,d	At2g36880	MAT3**	Methionine adenosyltransferase 3	0.74	0.45	0.00	0.01
247128_at	At5g66110	HIPP27	Putative metallochaperone-like protein	0.73	0.35	0.00	0.02
264644_at	At1g08960	CAX11	Ca2⁺/H⁺ exchanger 11	0.67	0.60	0.00	0.00
252694_at^c	At3g43630		Vacuolar iron transporter 1 (VIT1)-related	0.67	0.60	0.02	0.00
261135_at	At1g19610	PDF1.4	Plant defensin 1.4	0.67	0.42	0.00	0.01
260601_at	At1g55910	ZIP11	ZRT-, IRT-like^$ protein 11	0.65	0.02	0.02	0.57
257054_at	At3g15353	MT3	Metallothionein 3	0.62	0.30	0.01	0.12
258987_at^d	At3g08950	HCC1	Homologue of yeast copper chaperone Sco1^∞	0.61	0.23	0.00	0.25
(B)
Affymetrix probeset ID	AGI locus ID	Short gene name	Gene description	A. halleri vs. A. thaliana		A. lyrata vs. A. thaliana
				L o g ₂ FC^b	P-value	L o g ₂ FC^b	P-value
264097_s_at	At1g16700; At1g79010	—; TYKY	Complex I & 23 kDa subunit; α-helical ferredoxin	2.18	0.00	1.11	0.00
261489_at	At1g14450	B12-1	Complex I & B12 subunit	1.84	0.00	1.19	0.00
254120_at	At4g24570	DIC2	Dicarboxylate carrier 2	1.80	0.00	1.11	0.00
245715_s_at	At5g08670; At5g08690		ATP synthase β-subunit	1.78	0.00	0.64	0.01
266512_at	At2g47690		Complex I & 14 kDa subunit; Fe-S subunit 5	1.73	0.00	1.24	0.00
258847_at	At3g03100	B17.2	Complex I & 17.2 kDa subunit	1.69	0.06	1.17	0.07
260767_s_at	At1g49140; At3g18410	PDSW; —	Complex I & 12 kDa subunit NDUFS6; PDSW subunit	1.34	0.00	0.76	0.00
256679_at	At3g52300	ATPQ	ATP synthase D chain	1.26	0.00	0.03	0.66
262397_at	At1g49380		Cytochrome c biogenesis protein family	1.21	0.01	0.48	0.21
249627_at^d	At5g37510	EMB1467	Complex I & subunit of the 400 kDa subcomplex; Embryo defective 1467	1.18	0.00	0.76	0.00
246309_at	At3g51790	CCME	Orthologue of E. coli CcmE heme chaperone in cytochrome c maturation	1.10	0.01	0.60	0.06
252864_at	At4g39740	HCC2	Homologue of yeast copper chaperone Sco1^∞	1.06	0.01	0.34	0.66
263375_s_at	At2g20530; At4g28510	PHB6; PHB1	Complex I & Prohibitin 6; Prohibitin 1	1.02	0.00	0.36	0.04
256267_at	At3g12260	B14	Complex I & LYR family of Fe/S cluster biogenesis protein	1.02	0.01	0.31	0.32
(C)
Affymetrix probeset ID	AGI locus ID	Short gene name^a	Gene description	A. halleri vs. A. thaliana		A. lyrata vs. A. thaliana
				L o g ₂ FC^b	P-value	L o g ₂ FC^b	P-value
245219_at	At1g58807; At1g59124		Disease resistance protein (CC-NBS-LRR^# class) family	–1.50	0.00	–1.30	0.00
248851_s_at	At5g46260; At5g46490		Disease resistance protein (TIR-NBS-LRR^# class) family	–1.37	0.00	–1.26	0.00
262374_s_at	At1g72910; At1g72930		TIR domain-containing protein	–1.20	0.00	–0.70	0.00
255060_at	At4g09430		TIR-NBS-LRR^# class	–1.20	0.00	–0.84	0.00
250069_at	At5g17970		TIR-NBS-LRR^# class	–1.20	0.00	–0.70	0.00
250771_at	At5g05400		LRR and NB-ARC⁺ domains-containing disease resistance protein	–1.17	0.00	–0.59	0.00
262362_at	At1g72840		TIR-NBS-LRR^# class	–1.12	0.00	–0.76	0.00
245454_at	At4g16920		TIR-NBS-LRR^# class	–1.12	0.00	–0.59	0.00
257099_s_at	At3g24982; At3g25020	RLP40; RLP42	Receptor like protein 40/42	–1.11	0.00	–0.77	0.00
252648_at	At3g44630		TIR-NBS-LRR^# class	–1.11	0.00	–0.59	0.00
250039_at	At5g18370		TIR-NBS-LRR^# class	–1.11	0.00	–0.74	0.00
251438_s_at	At3g59930; At5g33355		Defensin-like (DEFL) family	–1.10	0.00	–0.54	0.00
252489_at	At3g46710		NB-ARC⁺ domain-containing disease resistance protein	–1.10	0.00	–0.70	0.00
262363_at	At1g72850		TIR-NBS^# class	–1.09	0.00	–0.67	0.00
248973_at	At5g45050	TTR1; WRKY16	Tolerant to tobacco ringspot nepovirus	–1.09	0.00	–0.24	0.01
256431_s_at	At3g11010; At5g27060	RLP34; RLP53	Receptor like protein 34/53	–1.06	0.00	–0.60	0.00
245674_at	At1g56680		Chitinase family protein	–1.06	0.00	–0.83	0.00
249320_at	At5g40910		TIR-NBS-LRR^# class	–1.06	0.00	–0.37	0.00
262364_at	At1g72860		TIR-NBS-LRR^# class	–1.05	0.00	–0.64	0.00
255059_at	At4g09420		TIR-NBS-LRR^# class	–1.04	0.00	–0.62	0.00
265723_at	At2g32140		TIR domain transmembrane protein	–1.03	0.00	–0.74	0.00
252684_at	At3g44400		TIR-NBS-LRR^# class	–1.03	0.00	–0.66	0.00
263572_at	At2g17060		TIR-NBS-LRR^# class	–1.02	0.00	0.00	0.33
245457_s_at	At4g16940; At4g16960		TIR-NBS-LRR^# class	–1.01	0.00	–0.68	0.00

(A) Transition metal homeostasis. (B) Mitochondrial electron transport/ATP synthesis. (C) biotic stress MapMan functional classes
^aShort names of genes previously reported to be copy-number expanded in A. halleri based on other experimental approaches are given in bold type (see also Additional file 5)
^b L o g ₂ fold-change (FC) is underlined for genes that are concordantly copy number expanded/reduced in both A. halleri and A. lyrata
^cHigher transcript abundance in roots of A. halleri vs. A. thaliana (Supplemental Table 1 of ref. Talke et al. 2006)
^dHigher transcript abundance in shoots of A. halleri vs. A. thaliana (Supplemental Table 2 of Talke et al. 2006)
^∞Synthesis of cytochrome c oxidase;
^$Zinc-regulated transporter, iron-regulated transporter-like; *At3g17390 was annotated as SAMS4 in ref. Talke et al. 2006; **At2g36880 was annotated as SAMS3 in Talke et al. 2006; ^&NADH-ubiquinone oxidoreductase, mitochondrial respiratory chain complex I;^#Coiled Coil (CC) or Toll-Interleukin Receptor (TIR)-Nucleotide Binding Site (NBS)-Leucine Rich Repeat (LRR);⁺nucleotide-binding (NB) motif-containing domain shared by human APAF-1, certain plant R gene products, and Caenorhabditis elegans CED-4 (ARC)

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com

BMC Genomics

Contact us