Inheritance of Solanum chloroplast genomic DNA in interspecific hybrids

Figures & data

Table 1. Comparison of chloroplast sequences of the seven samples.

Sample	Species	Total reads	Average organelle depth	Total length (bp)	GC content (%)	LSC length	IR length (bp)	SSC length (bp)
177	S. melongena	60,736,270	1521	155,581	37.71%	86,194	25,443	18,501
177 × y11	S. melongena×S. aethiopicum	42,488,436	1824	155,581	37.71%	86,194	25,443	18,501
177 ×torvum	S. melongena × S. torvum	43,425,370	1599	155,583	37.71%	86,196	25,443	18,501
53	S. aethiopicum	62,578,308	1288	155,598	37.70%	86,160	25,440	18,558
53 × y11	S. aethiopicum × S. aethiopicm	37,064,318	1722	155,598	37.70%	86,160	25,440	18,558
y11	S. aethiopicum	32,820,146	991	155,614	37.70%	86,168	25,441	18,564
y11 × 177	S. aethiopicum × S. melongena	34,130,550	764	155,606	37.70%	86,164	25,440	18,562

Figure 1. Chloroplast reference genome of seven Solanum species. Genes shown inside the outer circle are transcribed counter clockwise and those outside are transcribed clockwise. Genes belonging to different functional groups are color-coded. The gray area in the inner circle indicates the GC content (see Tables 2 and 3 for sample details).

Table 2. List of genes encoded in the chloroplast genome of the seven Solanum species.

Function	Gene group	Gene name
Photosynthesis pathways	Photosystem I	psa (A, B, C*,I, J)
	Photosystem I assembly	ycf (3, 4)
	Photosystem II	psb (A–F, H–L, N, T, Z)
	F-type ATP synthase	atp (A, B, E, F, H, I)
	NAD(P)H-dehydrogenase complex	ndh (A*, B#, C, D*, E*, F*, G*, H*, I*, J, K)
	Component of cytochrome b6/f complex	pet (A, B, D, L)
	Inner envelope membrane	cemA
	Cytochrome biogenesis protein	ccsA*
	Large subunit of Rubisco	rbcL
Structural RNAs	Transfer RNAs	trnH-GUG; trnK-UUU; trnQ-UUG; trnS-GCU; trnG-UCC; trnR-UCU; trnC-GCA; trnF-GAA; trnD-GUC; trnY-GUA; trnE-UUC; trnT-GGU; trnM-CAU; trnS-UGA; trnG-GCC; trnfM-CAU; trnS-GGA; trnT-UGU; trnL-UAA; trnV-UAC; trnW-CCA; trnP-UGG; trnP-GGG; trnI-GAU#; trnA-UGC#; trnN-GUU#; trnL-UAG; trnR-ACG#; trnV-GAC#; trnL-CAA#; trnI-CAU#
	Ribosomal RNAs	rrn (4.5#, 5#, 16#, 23#)
Genetic apparatus	Large subunit of ribosomal protein	rpl (2#, 14, 16, 20, 22, 23#, 32*, 33, 36)

Table 3. SNP types of the chloroplast genomes of the seven Solanum species.

Sample	Stop_Nonsynonymous	Synonymous	Nonsynonymous	Total_CDS_SNP	Intergenic	Total_SNP
177	1	1	7	9	30	39
177 × y11	1	1	7	9	30	39
177 ×torvum	1	1	7	9	30	39
53	1	59	40	100	239	339
53 × y11	1	59	40	100	239	339
y11	1	57	41	99	243	342
y11 × 177	1	58	41	100	244	344

Table 4. InDel types of the chloroplast genomes of the seven Solanum species.

Sample ID	I_gene_start	I_gene_middle	D_gene_middle	Total_CDS_InDel	Intergenic	Insertion	Deletion	Total
177	0	6	2	8	46	46	8	54
177 × y11	0	6	2	8	46	46	8	54
177 ×torvum	0	6	2	8	46	46	8	54
53	0	4	3	6	86	58	34	92
53 × y11	0	4	3	6	86	58	34	92
y11	1	4	3	7	81	56	32	88
y11 × 177	1	4	3	7	83	57	33	90

Figure 2. Phylogenetic analysis of the seven Solanum species.

Table 5. Basic information of the seven Solanum plants.

Sample ID	Code	Genome accession number	The original data accession number
NN2	53	MN218077	SAMN16746488
NN4	Y11	MN218079	SAMN16746490
NN5	177	MN218080	SAMN16746491
NN10	177 × y11	MN218085	SAMN16746496
NN17	y11 × 177	MN218092	SAMN16746503
NN16	53 × y11	MN218091	SAMN16746502
NN18	177 × torvum	MN218093	SAMN16746504

Data availability statement

The raw data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov, reference numbers: SAMN16746488, SAMN16746490, SAMN16746491, SAMN16746496, SAMN16746503, SAMN16746502, and SAMN16746504.