Chimeras in Merlot grapevine revealed by phased assembly

Sichel, V.; Sarah, G.; Girollet, N.; Laucou, V.; Roux, C.; Roques, M.; Mournet, P.; Cunff, L. Le; Bert, P.F.; This, P.; Lacombe, T.

doi:10.1186/s12864-023-09453-8

BMC Genomics

Table 11 Description of the periclinal chimeras on Merlot-Hap-CF located in a gene

From: Chimeras in Merlot grapevine revealed by phased assembly

Chr	Position on Merlot Root Hap CF	Cell layer	Coding region	Gene orientation	REF Codon	REF Amino Acid	ALT Codon	ALT Amino Acid	Gene name	LOC	NAME
chr 01	10,384,263	L1	gene						Vitvi01g00875	LOC100263854	disease resistance protein TAO1
chr 02	7,380,049	L1	CDS	reverse	AAC	N	AGC	S	Vitvi02g00607.CDS16	LOC100260794	uncharacterized
chr 04	23,822,006	L1	gene						Vitvi04g02171.t01	LOC104879118	protein FREE1
chr 05	22,934,305	L1	gene						Vitvi05g01344.t01	LOC100248036	eukaryotic translation initiation factor 3 subunit H
chr 07	8,599,845	L1	gene						Vitvi07g00711	LOC100251541	WD repeat-containing protein 26
chr 08	20,988,006	L1	CDS	reverse	AAG	K	AAA	K	Vitvi08g01573.CDS1	LOC100259003	caffeic acid 3-O-methyltransferase
chr 10	8,445,101	L2	gene						Vitvi10g01813.t01	LOC104880497	uncharacterized
chr 10	16,298,623	L1	gene						Vitvi10g01120.t01	LOC100252938	lysine-specific demethylase JMJ18
chr 11	7,012,825	L1	gene						Vitvi19g00471.t01
chr 11	9,424,215	L2	gene						Vitvi11g00777.t01	LOC100267388	autophagy-related protein 11
chr 12	8,907,103	L1	CDS	forward	CTC	L	CTA	L	Vitvi12g02494.CDS1	LOC100251126	myelin transcription factor 1-like protein
chr 12	16,700,578	L1	gene						Vitvi12g01666.t01	LOC100245109	protein FAM135B
chr 12	22,268,147	L2	CDS	reverse	TAG	STOP	AAG	K	Vitvi12g02051.CDS3	LOC104881
chr 13	23,444,751	L1	gene						Vitvi13g01459.t01	LOC100263567	lowering time control protein FY [ Vitis vinifera
chr 14	8,620,581	L1	gene						Vitvi14g00503	LOC100250122	phosphoribosylaminoimidazole carboxylase, chloroplastic
chr 15	13,526,354	L2	CDS	forward	AAC	N	AGC	S	Vitvi15g00455.CDS2
chr 15	19,297,087	L1	CDS	forward	TCC	S	TTC	F	Vitvi15g00839.CDS9	LOC100260889	homeobox-leucine zipper protein ANTHOCYANINLESS 2
chr 15	20,162,161	L1	CDS	reverse	ACC	T	ACT	T	Vitvi15g00907.CDS5	LOC100245390	rho GTPase-activating protein 5 [ Vitis vinifera
chr 15	20,298,163	L1	gene						Vitvi00g01964.t01
chr 17	3,559,600	L2	gene						Vitvi17g00302.t01	LOC100267388	autophagy-related protein 11
chr 17	7,610,259	L2	gene						Vitvi17g01488.t01	LOC100251937	zinc finger protein 346
chr 17	9,516,464	L1	gene						Vitvi17g00813.t01	LOC100250198	serine/threonine-protein kinase ATM
chr 17	12,223,344	L1	gene						Vitvi17g01006.t01	LOC100255285	callose synthase 10
chr 18	4,105,052	L1	gene						Vitvi18g00368.t01	LOC100247288	acetyl-CoA carboxylase 1
chr 18	5,367,698	L1	gene						Vitvi18g00496	LOC100255806	WD and tetratricopeptide repeats protein 1
chr 18	11,379,480	L1	gene						Vitvi18g02778.t01	LOC100247127	purple acid phosphatase 2
chr 19	468,364	L2	CDS	reverse	GCG	A	GAG	E	Vitvi19g01801.CDS6	LOC100255520	probable leucine-rich repeat receptor-like serine/threonine-protein kinase At3g14840
chr 19	6,420,354	L1	CDS	reverse	GTG	V	GTA	V	Vitvi19g00471.CDS1

All chimeras included in a gene are shown in this table. Their exact location on Merlot-Root-Hap-CF and the cell layer are given. If the chimera is located in a coding region it is marked “CDS” otherwise it is “gene”. When the position is in a coding region, the gene orientation either reversed or forward is given with the reference codon and amino acid, the nucleotide carrying the mutation is written in bold. The alternative sections show the impact of the mutation on the codon and the amino acid. Three last columns allow gene identification through gene name, LOC code and name.

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ISSN: 1471-2164

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