
==== Front
Data Brief
Data Brief
Data in Brief
2352-3409
Elsevier

S2352-3409(24)00779-0
10.1016/j.dib.2024.110815
110815
Data Article
Dataset on MatK-based intra- and inter-specific genetic relationships among four Solanum L. species from Southwestern Nigeria
Oyelakin Abiodun Sunday oyelakinas@funaab.edu.ng
a
Popoola Jacob Olagbenro jacob.popoola@bowen.edu.ng
@jacob_popoola
b⁎
Babalola Favour Olanrewaju favourbabalola53@gmail.com
a
Obisesan Idowu Arinola idowu.obisesan@bowen.edu.ng
b
Omotayo Olumide Ekundayo olumide.omotayo@bowen.edu.ng
b
Oluwatuyi Victor Olamide olamidesco@gmail.com
a
Sobayo Alfuad alfuadsobayo@gmail.com
a
OlaOluwa Favour Daniel olaoluwa.favour@bowen.edu.ng
b
a Department of Pure and Applied Botany, Federal University of Agriculture, Abeokuta, P.M. B. 2240, Abeokuta, Ogun State, Nigeria
b Pure and Applied Biology Programme, College of Agriculture, Engineering and Science, Bowen University, Iwo, Osun State, Nigeria
⁎ Corresponding author. jacob.popoola@bowen.edu.ng@jacob_popoola
10 8 2024
10 2024
10 8 2024
56 1108153 4 2024
3 8 2024
5 8 2024
© 2024 The Author(s)
2024
https://creativecommons.org/licenses/by-nc/4.0/ This is an open access article under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/).
Globally, the eggplant clade (Solanum L.) (Solanaceae) is an economically important source of food, nutrition, income, and medicines. Members of the clade are distinctively known for their incompatibility and yet genetically related as a diploid hyper-diverse monophyletic group. The eggplant clade are underutilized, and there are concerns about genetic erosion in Nigeria, primarily attributed to a limited understanding of their genetic diversity. To improve the members of the clade, it is imperative to understand their intra- and inter-specific genetic diversity and relationships for sustainable cultivation, conservation, and genetic improvement. A total of twelve (12) eggplant accessions comprising four (4) accessions of Solanum aethiopicum, three (3) accessions each of S. macrocarpon and S. melongena, and two accessions of S. nigrum obtained from the National Centre for Genetic Resources and Biotechnology (NACGRAB) Ibadan, Oyo state, Nigeria were assessed for their intra- and inter-specific genetic diversity. Genomic DNA was extracted from four-week-old young leaves at the emergence of each accession, followed by Polymerase Chain Reaction (PCR) amplification of the maturase K (MatK) gene. The PCR amplicons were then sequenced using Sanger's technique and the results analysed. The dataset presents intra- and inter-specific diversity and population structure of the studied species. A relatively low level of intraspecific diversity and moderate to high level of interspecific diversity with varying degrees of nucleotide and haplotype diversities were recorded for the dataset. Quite elevated values of 693 total allele sites, 9 haplotypes, 0.96 gene diversity, 100 polymorphic sites, 16 parsimony information sites, and 101 total number of mutations were documented for the sequence dataset. Relatively high gene flow and genetic differentiation (Fst) were observed among the populations of S. aethiopicum and S. nigrum (0.939), S. macrocarpon and S. nigrum (0.833), whereas a moderate Fst was recorded for the populations of S. melongena and S. nigrum (0.254) and S. aethiopicum and S. melongena (0.047), while populations of S. aethiopicum and S. macrocarpon as well as S. macrocarpon and S. melongena showed a low Fst values of −0.129 and 0.014. Genetic distance and phylogenetic relationships showed a closely related taxa of four distinct cluster groups with three groups of mixed species and one unique cluster of S. nigrum. The dataset provides insights into the genetic diversity within and between Solanum species which could be used to inform commercial cultivation, conservation, and breeding efforts, as well as the evolutionary dynamics of the clade.

Keywords

Breeding
Conservation
Hybridization
Improvement
==== Body
pmcSpecifications TableSubject	Biological Science	
Specific subject area	Botany; Agricultural; Genetic diversity; Plant breding; Hybridization	
Type of data	Tables, Figures, Raw, Analyzed	
Data collection	The seeds of twelve (12) accessions of Solanum nigrum (2), S. melongena (3), S. macrocarpon (3), and S. aethiopicum (4) were obtained from National Centre for Genetic Resources and Biotechnology (NACGRAB) Ibadan, Oyo state, Nigeria. The seeds were planted in the screen house of the Department of Pure and Applied Botany, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria for four weeks to initiate leaves. Young leaf samples were collected from each accession and had their genomic DNA extracted. The PCR amplification and Sanger Sequencing using the maturase K gene were performed on the samples. The partial MatK gene sequences were employed to evaluate intra- and inter-specific genetic diversity among the accessions of the four species. Genetic diversity indices such as total numbers of nucleotide sequences, total number of allele sites, number of polymorphic, number of haplotypes, gene diversity, number of InDel sites, InDel haplotype (gene) diversity, variance of haplotype diversity, nucleotide diversity (Pi), and number of nucleotide differences (k) were estimated using DnaSP 6.0. DNA sequence polymorphisms (SNPs), gene flow, and genetic differentiation among the populations were also estimated. The codon usage indices and the amino acid residues were estimated using CodonW. The phylogenetic tree to reveal the evolutionary relationship among the accessions was constructed using the UPGMA method.	
Data source location	Institution: National Centre for Genetic Resources and Biotechnology (NACGRAB)
City/Town/Region: Ibadan, Oyo state
Country: Nigeria	
Data accessibility	Repository name: NCBI (PopSet)
Data identification number: 2627419596
Direct URL to data:
https://www.ncbi.nlm.nih.gov/popset/?term=2627419596	

1 Value of the Data

• The dataset obtained from the matK gene sequence offers valuable information regarding the genetic variation and evolutionary relationships among twelve accessions of four Solanum species from Southwestern Nigeria. This information is based on the analysis of nucleotide polymorphisms, haplotype and gene diversities, total number of mutations, and codon usage.

• The dataset revealed the presence of 100 polymorphic sites (segregating sites) in nucleotide pairs, 101 total number of mutations along with 9 haplotypes, 115 total number of InDel sites, and 62 InDels events. These findings can be utilized to expand the genetic diversity of eggplants through mutation breeding.

• The dataset contains genetic information related to genome-based species recovery, conservation, and genetic improvement initiatives. These tactics include haplotype-assisted genomic selection and haplotype-based breeding, which could be used to enhance the natural breeding of Solanum species.

• Translating the MatK DNA sequences of the species into polypeptide sequences and amino acid profiles can assist researchers in predicting the protein structure and function of the gene. This data can enhance our comprehension of the molecular pathways that underlie their growth and development.

• The clustering pattern of S. melongena and S. macrocarpon as well as S. melongena and S. aethiopicum indicate that breeding efforts could be initiated to improve the desired qualities in the species.

• An analysis of the genetic diversity and phylogenetic relationship among Solanum nigrum, S. melongena, S. macrocarpon, and S. aethiopicum would be advantageous for breeders, researchers, and the scientific community working on crop utilization and improvement.

2 Background

Eggplants belong to the largest genus in the family Solanaceae (nightshade) known as Solanum and comprise about 1500 species [1]. Some of these species are found in the wild. They are rich in essential vitamins, particularly vitamin C, and minerals like potassium [2]. Their dietary fiber content supports digestive health and helps regulate blood sugar levels [2,3]. Additionally, these vegetables provide antioxidants, such as phenolic compounds, which have health benefits [2,3]. Solanum nigrum is a herbaceous annual or short-lived perennial plant that is recognized for its ecological adaptability and its historical use in traditional medicine and culinary practices [4]. It is native to Europe, Asia, and Africa, but is now naturalized in many other parts of the world. Solanum macrocarpon popularly known as African eggplant or garden egg is valuable for its cultural significance. This species is indigenous to West Africa but it has been naturalized into other parts of the world due to its culinary versatility and potential health benefits [[4], [5], [6]]. Solanum melongena is recognized for its culinary importance and its role as a dietary staple around the world [[6], [7], [8]]. Its adaptability to diverse climates and soil types has made it a valuable eggplant species contributing to food security in many regions [[8], [9], [10]]. Solanum aethiopicum commonly referred to as Ethiopian eggplant is very popular in East and West Africa because of its unique flavour and nutritional qualities [11]. It adapts well to local climates and thrives in both backyard gardens and larger agricultural settings. It is a source of vitamins, calcium, and iron and contains antioxidants and bioactive compounds that have been associated with potential health benefits [2,11]. Despite the eggplants' culinary and nutritional significance, maintaining genetic diversity within and among the species remains a challenge. Often, modern agriculture usually favored a limited number of commercially preferred cultivars, leading to genetic homogeneity [12]. Some of these highly nutraceutical and economically important species have not been properly domesticated and are still largely found in the wild. To harness their full potential, it is important to generate useful genetic data and information on their genetic diversity and relationships. Hence, this dataset aimed to assess the intra- and inter-specific genetic diversity and phylogenetic relationships among twelve accessions of Solanum species including S. nigrum, S. melongena, S. macrocarpon, and S. aethiopicum collected from NAGRAB, Nigeria using partial matK gene sequences.

3 Data Description

Partial sequences derived from Sanger's sequencing of the MatK gene were used to assess the genetic relatedness of the 12 eggplants accessions. Pictures of the four species are shown in Fig. 1. The species name, collection number, area of collection, and Genbank accession numbers are presented in Table 1. The deposited sequences, Genbank accession numbers, matched organism, and sequence length are shown in Table 2. Fig. 2 presents the sequence length,% GC, and nucleotide contents of the species while Fig. 3 shows the sequence alignment of the species studied. Data in Table 3 shows the estimate of the genetic diversity of the species/accessions based on the matK sequence analyses. The single nucleotide polymorphism (SNPs) among the species is presented in Table 4. Multidomain analysis of within-population diversity among the species of Solanum studied is shown in Table 5. Genetic distance between the species, gene flow, and genetic differentiation among the four species of the Solanum studied are presented in Table 6, Table 7. The codon bias usage information and the frequency of codons used to encode particular amino acids are shown in Table 8 whereas codon usage indices are shown in Table 9. The amino acids composition of the 12 accessions of Solanum studied is shown in Table 10. Fig. 5 shows the phylogenetic relationships among the Solanum species with four cluster groups.Fig. 1 Phenotypic images of the Solanum species displaying floral and fruit traits. A. Solanum nigrum. B. Solanum macrocarpon. C. Solanum aethiopicum. D. Solanum melongena.

Fig. 1:

Table 1 Species name, collection number, area of collection, and Genbank accession number of Solanum species studied.

Table 1:Species name	Collection No.	Area of collection	Accession No	
Solanum nigrum	NaSn001	NACGRAB	OR855783.1	
Solanum nigrum	NaSn002	NACGRAB	OR855784.1	
Solanum macrocarpon	NaSma001	NACGRAB	OR855777.1	
Solanum macrocarpon	NaSma002	NACGRAB	OR855778.1	
Solanum macrocarpon	NaSma003	NACGRAB	OR855779.1	
Solanum melongena	NaSm001	NACGRAB	OR855780.1	
Solanum melongena	NaSm002	NACGRAB	OR855781.1	
Solanum melongena	NaSm003	NACGRAB	OR855782.1	
Solanum aethiopicum	NaSa001	NACGRAB	OR855773.1	
Solanum aethiopicum	NaSa002	NACGRAB	OR855774.1	
Solanum aethiopicum	NaSa003	NACGRAB	OR855775.1	
Solanum aethiopicum	NaSa004	NACGRAB	OR855776.1	
NACGRAB - National Centre for Genetic Resources and Biotechnology (NACGRAB) Ibadan, Oyo state, Nigeria.

Table 2 Summary of the deposited sequences, Genbank accession numbers, matched organism, and sequence length.

Table 2:Sequence name	GenBank Accession No	Matched Organism	% Identity	SL(bp)	
Solanum nigrum isolate NaSn001 maturase K gene, partial cds; chloroplast	OR855783.1	Solanum nigrum	100 %	883	
Solanum nigrum isolate NaSn002 maturase K gene, partial cds; chloroplast
Solanum macrocarpon isolate NaSma001 maturase K gene, partial cds; chloroplast
Solanum macrocarpon isolate NaSma002 maturase K gene, partial cds; chloroplast	OR855784.1
OR855777.1
OR855778.1	Solanum nigrum
Solanum macrocarpon
Solanum macrocarpon	100 %
100 %
100 %	883
894
893	
Solanum macrocarpon isolate NaSma003 maturase K gene, partial cds; chloroplast
Solanum aethiopicum isolate NaSa001 maturase K gene, partial cds; chloroplast	OR855779.1
OR855773.1	Solanum macrocarpon
Solanum aethiopicum	100 %
100 %	891
890	
Solanum aethiopicum isolate NaSa002 maturase K gene, partial cds; chloroplast
Solanum aethiopicum isolate NaSa003 maturase K gene, partial cds; chloroplast
Solanum aethiopicum isolate NaSa004 maturase K gene, partial cds; chloroplast
Solanum melongena isolate NaSm001 maturase K gene, partial cds; chloroplast	OR855774.1
OR855775.1
OR855776.1
OR855780.1	Solanum aethiopicum
Solanum aethiopicum
Solanum aethiopicum
Solanum melongena	100 %
100 %
100 %
100 %	898
894
891
892	
Solanum melongena isolate NaSm002 maturase K gene, partial cds; chloroplast	OR855781.1	Solanum melongena	100 %	892	
Solanum melongena isolate NaSm003 maturase K gene, partial cds; chloroplast	OR855782.1	Solanum melongena	100 %	892	

Fig. 2 Sequence length, percentage nucleotide content of the matK gene of accessions of Solanum species.% = Percentage, G = Guanine, C = Cytosine, T = Thyamine, U = Uracil, A = Adenine.

Fig. 2:

Fig. 3 Sequence alignment of the 12 sequences of Solanum species studied (MatK OR855773 was used as the reference sequence).

Fig. 3:

Table 3 Genetic diversity among twelve (12) accessions of Solanum species.

Table 3:Index	Value	
Number of nucleotides	12	
Total number of sites (excluding sites with gaps / missing data	793	
Sites with alignment gaps or missing data	115	
Invariable (monomorphic) sites	693	
Number of polymorphic (segregating sites)	100	
Parsimony informative sites	16	
Total number of mutations (Eta)	101	
Number of haplotypes (h)	9	
Haplotype (gene) diversity (Hd)	0.955	
Variance of Haplotype diversity + SD	0.00218 ± 0.047	
Nucleotide diversity (Pi)	0.02497 (low)	
Average number of nucleotide differences (k)	19.803	
Total number of InDel sites: 115	115	
Total number of (InDel and non-InDel) sites analyzed	793 + 88 = 881	
Total number of InDels events	62	
Number of InDel Haplotypes	7	

Table 4 Single nucleotide polymorphisms of the Solanum species studied.

Table 4:Coding/Non Coding	?	?	?	A	r	G	A	l	a	?	?	?	*	*	*	?	M	E	T	T	*	*	I	l	e	T	y	r	*	*	T	
OR855784	–	–	G	C	G	G	G	c	G	T	C	–	T	a	A	–	A	T	G	T	A	G	A	T	A	T	A	C	T	A	T	
OR855783	–	–	–	–	–	–	T	.	A	.	.	–	.	.	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	
OR855782	–	–	–	–	–	–	–	t	C	A	T	–	C	t	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	
OR855781	–	–	–	–	–	–	C	.	A	.	.	–	.	.	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	
OR855780	–	G	C	T	.	A	.	.	A	.	.	–	.	.	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	
OR855779	–	–	–	–	–	–	.	.	A	.	.	C	.	.	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	
OR855778	–	–	–	.	.	A	A	.	.	C	T	–	C	t	g	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	
OR855777	–	–	C	.	C	A	C	t	.	A	T	–	C	t	c	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	
OR855776	–	–	–	–	–	–	.	.	A	.	.	–	.	.	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	
OR855775	–	–	C	.	A	T	A	.	C	A	T	–	C	t	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	
OR855774	–	A	T	T	.	T	.	.	A	.	.	–	–	t	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	
OR855773	A	G	C	.	C	A	C	t	–	–	–	–	C	t	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	
Note: Arg = Arginine, Ala = Alanine, Met = Methionine, Ile = Ileusine, Try = Trypsin, A – Adenine, T – Thymine, G – Guanine, C – Cytosine, ? – Unknown.

Table 5 Multidomain analysis of within-population diversity among the species of Solanum studied.

Table 5:Solanum spp	Pop	N	S	Eta	Hap	Hd	VarHd	Pi	ThetaNu	TajimaD	FuLiD*	SigD	FuLiF*	FuFs	G+Cn	G+Ctot	
S. aethiopicum	Pop 1	4	7	8	4	1	0.031	0.005	0.0049	−0.4464	−0.4976	0	−0.498	−0.769	0.3318	0.3318	
S. macrocarpon	Pop 2	3	13	16	3	1	0.07407	0.011	0.0120	n.d	n.d	n.d	n.d	1.103	0.3326	0.3326	
S. melongena	Pop 3	3	92	92	3	1	0.07407	0.076	0.0763	n.d	n.d	n.d	n.d	3.007	0.3275	0.3275	
S. nigrum	Pop 4	2	3	3	2	1	0.25	0.003	0.0034	n.d.	n.d.	n.d.	n.d.	1.099	0.3422	0.3422	
All Sequence	Total	12	100	101	9	0.96	0.00218	0.025	0.0422	−1.902	−2.2047	*	−2.1999	1.359	0.3283	0.3283	
N: Number of sequences per population; S: Total number of Polymorphic sites; Eta: Total number of mutations; Hap: Haplotype number; Hd: Haplotype diversity; VarHd: Haplotype diversity variance; ThetaNu: mutation rate per population/sequences; Pi (π): Nucleotide diversity; D, D*, F, and F* statistics test various predictions of the neutral theory of molecular evolution and their significance: *p < 0.1, G + C, G + C content; tot, -total.

Table 6 Genetic distance among the species of Solanum studied.

Table 6:S/N	Species/Accessions	1	2	3	4	5	6	7	8	9	10	11	12	
1	OR855784 - S. nigrum													
2	OR855783 - S. nigrum	0.003												
3	OR855782 - S. melongena	0.026	0.027											
4	OR855781 - S. melongena	0.021	0.020	0.007										
5	OR855780 - S. melongena	0.134	0.134	0.128	0.121									
6	OR855779 - S. macrocarpon	0.021	0.021	0.014	0.006	0.121								
7	OR855778 - S. macrocarpon	0.025	0.029	0.008	0.012	0.128	0.012							
8	OR855777 - S. macrocarpon	0.029	0.028	0.003	0.009	0.133	0.014	0.009						
9	OR855776 - S. aethiopicum	0.021	0.024	0.014	0.007	0.118	0.001	0.014	0.015					
10	OR855775 - S. aethiopicum	0.029	0.030	0.007	0.014	0.131	0.011	0.010	0.014	0.009				
11	OR855774 - S. aethiopicum	0.023	0.022	0.009	0.006	0.125	0.003	0.010	0.014	0.005	0.012			
12	OR855773 - S. aethiopicum	0.025	0.023	0.003	0.007	0.129	0.008	0.007	0.003	0.011	0.011	0.009		
1–12 – Species/Accessions.

Table 7 Gene flow and genetic differentiation among 4 populations of the 12 accessions of the Solanum species.

Table 7:POPULATION 1	POPULATION 2	Hs	Ks	Kxy	Gst	DeltaSt	GammaSt	Nst	Fst	Dxy	Da	
Pop1_S_aethiopicum	Pop_2_S_macrocarpon	0.89	2.71	2.58	0.003	0.000	0.131	−0.130	−0.129	0.003	0.000	
Pop1_S_aethiopicum	Pop_3_S_melongena	0.89	26.00	31.58	0.046	0.007	0.244	0.043	0.047	0.040	0.002	
Pop1_S_aethiopicum	Pop_4_S_nigrum_	0.83	1.00	12.25	0.328	0.007	0.874	0.939	0.939	0.015	0.015	
Pop_2_S_macrocarpon	Pop_3_S_melongena	1.00	31.50	31.89	0.000	0.007	0.206	0.011	0.012	0.040	0.000	
Pop_2_S_macrocarpon	Pop_4_S_nigrum_	1.00	2.60	13.00	0.290	0.007	0.762	0.835	0.833	0.016	0.014	
Pop_3_S_melongena	Pop_4_S_nigrum_	1.00	35.20	39.33	0.290	0.012	0.288	0.247	0.254	0.050	0.013	
Hs = haplotype-based statistics; Ks = statistics based on nucleotide sequences, Kxy = average proportion of nucleotide difference between populations; Gst = genetic differentiation index based on the frequency of haplotypes; GammaSt = genetic differentiation coefficient; Fst = genetic differentiation; Dxy = average number of nucleotide substitutions per site between populations; Da = net nucleotide substitutions per site between populations.

Table 8 Codon usage bias: Relative Synonymous Codon Usage (RSCU) and count for Solanum species nucleotides.

Table 8:Codon	Count	RSCU	Codon	Count	RSCU	Codon	Count	RSCU	Codon	Count	RSCU	
UUU(F)	17	1	UCU(S)	12	2	UAU(Y)	11	1	UGU(C)	7	1	
UUC(F)	12	1	UCC(S)	6	1	UAC(Y)	5	1	UGC(C)	3	1	
UUA(L)	9	2	UCA(S)	9	2	UAA(*)	8	1	UGA(*)	6	1	
UUG(L)	5	1	UCG(S)	2	0	UAG(*)	5	1	UGG(W)	4	1	
CUU(L)	13	2	CCU(P)	4	1	CAU(H)	2	1	CGU(R)	3	1	
CUC(L)	2	0	CCC(P)	1	0	CAC(H)	1	1	CGC(R)	0	0	
CUA(L)	4	1	CCA(P)	4	1	CAA(Q)	5	2	CGA(R)	7	2	
CUG(L)	0	0	CCG(P)	2	1	CAG(Q)	1	0	CGG(R)	2	1	
AUU(I)	12	1	ACU(T)	3	1	AAU(N)	10	2	AGU(S)	1	0	
AUC(I)	9	1	ACC(T)	2	1	AAC(N)	2	0	AGC(S)	3	1	
AUA(I)	6	1	ACA(T)	3	1	AAA(K)	15	2	AGA(R)	5	1	
AUG(M)	5	1	ACG(T)	6	2	AAG(K)	3	0	AGG(R)	4	1	
GUU(V)	3	2	GCU(A)	0	0	GAU(D)	4	2	GGU(G)	5	2	
GUC(V)	1	1	GCC(A)	1	1	GAC(D)	1	0	GGC(G)	1	0	
GUA(V)	2	1	GCA(A)	3	2	GAA(E)	7	2	GGA(G)	3	1	
GUG(V)	0	0	GCG(A)	2	1	GAG(E)	0	0	GGG(G)	1	0	

Table 9 Codon usage Indices of 12 accessions of Solanum species.

Table 9:Sequence Name	T3s	C3s	A3s	G3s	CAI	CBI	Fop	Nc	GC3s	GC	Lsym	Laa	Gravy	Aromo	
OR855773.1	0.45	0.22	0.42	0.17	0.17	−0.08	0.37	51.01	0.30	0.34	270	279	0.12	0.18	
OR855774.1	0.43	0.27	0.36	0.24	0.17	−0.06	0.37	58.47	0.37	0.34	271	283	0.52	0.18	
OR855775.1	0.42	0.25	0.37	0.25	0.16	−0.08	0.35	56.87	0.37	0.34	271	284	0.48	0.18	
OR855776.1	0.45	0.23	0.42	0.16	0.18	−0.05	0.39	50.72	0.30	0.34	268	277	0.09	0.18	
OR855777.1	0.47	0.27	0.32	0.21	0.18	−0.03	0.40	53.86	0.36	0.35	264	278	0.17	0.19	
OR855778.1	0.44	0.22	0.42	0.19	0.17	−0.07	0.37	51.91	0.31	0.36	270	279	0.11	0.18	
OR855779.1	0.42	0.25	0.36	0.25	0.16	−0.08	0.35	57.26	0.37	0.34	270	282	0.50	0.17	
OR855780.1	0.46	0.26	0.41	0.17	0.18	−0.07	0.37	53.07	0.32	0.35	249	260	0.32	0.19	
OR855781.1	0.45	0.22	0.42	0.18	0.18	−0.06	0.38	52.27	0.30	0.34	268	277	0.09	0.18	
OR855782.1	0.49	0.19	0.47	0.14	0.16	−0.14	0.33	49.67	0.25	0.33	285	296	−0.07	0.17	
OR855783.1	0.44	0.22	0.41	0.19	0.17	−0.06	0.38	54.30	0.32	0.35	270	278	0.10	0.17	
OR855784.1	0.44	0.22	0.40	0.19	0.17	−0.06	0.38	53.91	0.32	0.36	268	276	0.13	0.17	
CAI - Codon Adaptation Index, CBI - Codon Bias Index, Aromo - Aromaticity, FoP - frequency of optimal codons, GRAVY - The general average hydropathicity or the grand average of hydropathicity.

Table 10 Amino acids composition of 12 accessions of Solanum species.

Table 10:Amino Acids	
Accession No	Ala	Cys	Asp	Glu	Phe	Gly	His	Ile	Lys	Leu	Met	Asn	Pro	Gln	Arg	Ser	Thr	Val	Trp	Tyr	
OR855784.1	2	3	1	2	9	4	1	9	6	13	1	5	5	2	8	12	5	3	1	5	
OR855783.1	2	4	1	2	9	4	2	9	7	13	1	5	5	2	8	12	5	3	1	5	
OR855782.1	2	3	2	3	11	4	1	10	7	12	2	4	4	2	7	12	5	2	1	5	
OR855781.1	2	4	2	3	10	4	1	10	7	12	2	4	4	2	7	12	5	2	1	5	
OR855780.1	2	3	2	2	13	5	2	8	5	14	2	6	5	3	7	10	4	2	2	4	
OR855779.1	2	4	2	3	10	4	1	10	7	12	2	4	4	2	8	12	5	2	1	6	
OR855778.1	3	3	2	3	10	4	1	10	6	12	2	5	4	2	8	12	5	2	1	6	
OR855777.1	2	3	2	3	10	4	1	10	7	12	2	4	4	2	7	12	5	2	1	5	
OR855776.1	2	3	2	3	10	4	1	10	7	12	2	4	4	2	8	12	5	2	1	6	
OR855775.1	2	3	2	3	10	4	1	10	6	12	2	4	4	2	8	12	5	3	1	6	
OR855774.1	2	4	2	3	10	4	1	10	6	12	2	4	4	2	8	12	5	3	2	6	
OR855773.1	2	4	2	3	10	4	1	10	7	12	2	4	4	2	8	12	5	2	1	6	
Avg.	2	3	2	2	10	4	1	10	7	12	2	5	4	2	8	12	5	2	1	6	
The values represent the frequency at which each amino acid appears in the sequence per accession/species. The range of frequencies observed was from 1 (for Trp) to 14 (for Leu in accession OR855779.1). The average values per amino acid are displayed in bold font.

4 Experimental Design, Materials and Methods

The seeds of twelve (12) accessions of Solanum nigrum (2), S. melongena (3), S. macrocarpon (3), and S. aethiopicum (4) were obtained from the National Centre for Genetic Resources and Biotechnology (NACGRAB) Ibadan, Oyo state, Nigeria. The seeds were sown in the screenhouse of the Department of Pure and Applied Botany, at the Federal University of Agriculture, Abeokuta, Nigeria. They were planted in perforated 5-liter buckets filled with topsoil to facilitate germination into seedlings. After four weeks, young leaves were harvested from the seedlings of each accession for DNA extraction. The experiment was conducted using a randomised block design. The freshly picked leaves were dried using silica gel and then sent to the laboratory of Inqaba Biotec West Africa Ltd in Ibadan, Nigeria for molecular analysis.

4.1 Genomic DNA extraction

The genomic DNA was extracted from the four weeks-old young leaves using Zymo Research Quick- DNA Plant/Seed Miniprep Kit (Catalogue No D6020) and the manufacturer's instructions were adhered to. ThermoFischer®Nanodrop spectrophotometer ND-80 0 0-GL was used to determine the quality and quantity of the DNA.

4.2 PCR amplification, purification and visualization

PCR amplification for the MatK regions was performed using a final volume of 25 µL comprising 12.5 µL of NEB OneTaq 2X Master Mix with Standard Buffer (Catalogue No M0482S), 2 µL of genomic DNA (10–30 ng/µl), 0.5 µL MatK390_F (5-CGATCTATTCATTCAATATTTC-3 (Tm = 50 °C), MatK132_R (5- TCTAGCACACGAAAGTCGAAGT-3 (Tm = 50 °C) (10 µM), and 9.5 µL of nuclease-free water. The PCR reaction conditions, and the purity of the PCR samples adhered to established protocols [13,14]. The PCR products detection and analysis were executed on agarose gel electrophoresis using 1 % agarose with 1 kbp DNA ladder and were visible as shown in Fig. 4.Fig. 4 PCR products amplified using MatK_390F and MatK_132R primers and resolved on 1 % agarose gel with 1 kbp DNA ladder.

Fig. 4:

Fig. 5 Phylogenetic relationships among Solanum species based on matK gene sequence depicting four cluster groups (I–IV).

Fig. 5:

4.3 Post-PCR purification and sequencing analysis

The PCR products underwent enzymatic purification using ExoSAP, while the PCR amplicons were sequenced at Inqaba biotechnical Industries (Pty) Ltd, South Africa. The sequencing was performed using the Nimagen, Brilliant Dye™ Terminator Cycle Sequencing Kit V3.1, BRD3-100/1000, following the instructions provided by the manufacturer.

4.4 Data analysis

The Sanger sequences of the Solanum species were edited and aligned using ClustalW on BioEdit (ver. 7.2.5) [15] and MEGA (11.0.13) [16]. Sequences were submitted to the NCBI Gen-Bank and sequence accession numbers were provided as presented in Table 2. Genetic diversity and population structure parameters such as the number of nucleotides, total number of sites, total number of Polymorphic sites, total number of mutations number – Eta, the number of haplotypes, gene diversity, the number of InDel sites, InDel haplotype (gene) diversity, the variance of haplotype diversity (Varhp), nucleotide diversity (Pi), the number of nucleotide differences (k), the average proportion of nucleotide difference between populations (Kxy), genetic differentiation index based on the frequency of haplotypes (Gst), genetic differentiation coefficient (GammaSt), genetic differentiation (Fst), average number of nucleotide substitutions per site between populations (Dxy), net nucleotide substitutions per site between populations (Da) were estimated using DnaSP 6.0 [17]. The codon usage indices and amino acid residues were estimated using CodonW [18]. The phylogenetic tree to reveal the evolutionary relationship among the accessions/species was constructed using the UPGMA method [19].

Limitations

Presently, the seed bank of the National Centre for Genetic Resources and Biotechnology (NACGRAB) in Ibadan, Oyo state, Nigeria, contains a mere four species of eggplants. Consequently, the dataset was limited to only four species. The small size of the accessions used for this analysis can be attributed to the genetic erosion resulting from a limited or non-existent genetic variation within and among the Solanum species of the Eggplant clade. Maintaining genetic diversity within and among the species of the clade remains a concern, using a large size might complicate the outcome. Furthermore, the assessment is primarily focused on the MatK (saturate K) gene marker, suggesting that a low number of accessions is suitable for evaluating the genetic diversity and evolutionary relationships of the species. Utilizing a high quantity of accessions may potentially complicate the investigation, resulting in less robust conclusions. The MatK gene utilized in this investigation has effectively revealed the genetic variability both among and within the studied Solanum species. Furthermore, the utilization of simple sequence repeat marker (SSR) might be employed to examine the genetic variability across and within the Solanum species using a substantial sample size.

Ethics Statement

The samples used as shown in Table 1 were obtained from the National Centre for Genetic Resources and Biotechnology (NACGRAB) Ibadan, Oyo state, Nigeria. No data or any parts were obtained from any Social Media platform.

CRediT Author Statement

Abiodun Sunday Oyelakin: Conceptualization, Supervision, Validation, Original draft writing; Jacob Olagbenro Popoola: Software, Formal analysis, Data curation; Data interpretation; Validation, Visualization, Review manuscript and submission of manuscript; Favour Olanrewaju Babalola: Accession collection; Formal analysis, Methodology, Submission of Sequences on GenBank; Idowu Arinola Obisesan: Review manuscript; Olumide Ekundayo Omotayo: Review manuscript; Victor Olamide Oluwatuyi: Accession collection, Experimentation; Alfuad Sobayo: Accession collection, Experimentation, Methodology; Favour Daniel OlaOluwa: Review manuscript.

Data Availability

Solanum maturase K gene, partial cds; chloroplast. (Original data) (NCBI).

Acknowledgments

The authors thank the National Centre for Genetic Resources and Biotechnology (NACGRAB), Ibadan, Oyo state, Nigeria for providing the seeds used for this research. This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Declaration of Competing Interest

The authors declare that there are no competing financial or personal interests that could have influenced the report of this research.
==== Refs
References

1 Gbile Z.O. Adesina S.K. Nigerian Solanum species of economic importance Ann. Missouri Bot. Garden 75 1988 862 10.2307/2399374
2 Faraone I. Lela L. Ponticelli M. Gorgoglione D. De Biasio F. Valentão P. Andrade P.B. Vassallo A. Caddeo C. Falabella R. Ostuni A. Milella L. New insight on the bioactivity of Solanum aethiopicum Linn. Growing in Basilicata Region (Italy): phytochemical characterization, liposomal incorporation, and antioxidant effects Pharmaceutics 14 2022 1168 10.3390/pharmaceutics14061168 35745745
3 Oboh G. Ekperigin M.M. Kazeem M.I. Nutritional and haemolytic properties of eggplants (Solanum macrocarpon) leaves J. Food Compos. Anal. 18 2005 153 160 10.1016/j.jfca.2003.12.013
4 Chen X. Dai X. Liu Y. Yang Y. Yuan L. He X. Gong G. Solanum nigrum Linn.: an insight into current research on traditional uses Phytochem. Pharmacol., Front. Pharmacol. 13 2022 918071 10.3389/fphar.2022.918071
5 Kauma C.M. Anywar G. Serunjogi D. Katuura E. Namaganda M. Dataset on the geographical distribution of species of the genus Solanum, subgenus Leptostemonum in Uganda Data Br. 53 2024 110159 10.1016/j.dib.2024.110159
6 Morris W.L. Taylor M.A. The Solanaceous vegetable crops: potato, tomato, pepper, and eggplant Encyclopedia of Applied Plant Sciences 2017 Elsevier 55 58 10.1016/B978-0-12-394807-6.00129-5
7 Taher D. Solberg S.Ø. Prohens J. Chou Y. Rakha M. Wu T. World vegetable center eggplant collection: origin, composition, seed dissemination and utilization in breeding Front. Plant Sci. 8 2017 1484 10.3389/fpls.2017.01484 28970840
8 Saini D.K. Kaushik P. Visiting eggplant from a biotechnological perspective: a review Sci. Hortic. 253 2019 327 340 10.1016/j.scienta.2019.04.042
9 Roy S.K. Chakrabarti A.K. Vegetables of tropical climates | commercial and dietary importance Encyclopedia of Food Sciences and Nutrition 2003 Elsevier 5956 5961 10.1016/B0-12-227055-X/01242-6
10 Behera T.K. Sharma P. Singh B.K. Kumar G. Kumar R. Mohapatra T. Singh N.K. Assessment of genetic diversity and species relationships in eggplant (Solanum melongena L.) using STMS markers Sci. Hortic. 107 2006 352 357 10.1016/j.scienta.2005.11.004
11 Nwanna E.E. Adebayo A.A. Ademosun A.O. Oboh G. Phenolic distribution, antioxidant activity, and enzyme inhibitory properties of eggplant (Solanum aethiopicum) cultivated in two different locations within Nigeria J. Food Biochem. 43 2019 e12797 10.1111/jfbc.12797 31353619
12 Breseghello F. Coelho A.S.G. Traditional and modern plant breeding methods with examples in rice (Oryza sativa L.) J. Agric. Food Chem. 61 2013 8277 8286 10.1021/jf305531j 23551250
13 Kadri K. Polymerase chain reaction (PCR): principle and applications Nagpal M.L. Boldura O.-M. Baltă C. Enany S. Synthetic Biology - New Interdisciplinary Science 2020 IntechOpen 10.5772/intechopen.86491
14 Popoola J.O. Igwe D.O. Iwu V. Adegbite A.E. Omonhinmin C.A. Genetic diversity, clustering pattern and breeding implications of 40 Moringa oleifera accessions using AFLP markers JARDCS 12 2020 659 670 10.5373/JARDCS/V12SP8/20202568
15 Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucl. Acids. Symp. Ser. 41 1999 95 98
16 Tamura K. Stecher G. Kumar S. MEGA11: molecular evolutionary genetics analysis Version 11 Mol. Biol. Evol. 38 2021 3022 3027 10.1093/molbev/msab120 33892491
17 Rozas J. DNA sequence polymorphism analysis using DnaSP Posada D. Bioinformatics for DNA Sequence Analysis 2009 Humana Press Totowa, NJ 337 350 10.1007/978-1-59745-251-9_17
18 F. Mareuil, O. Doppelt-Azeroual, H. Ménager, A public Galaxy platform at Pasteur used as an execution engine for web services, (2017). 10.7490/F1000RESEARCH.1114334.1.
19 Kumar S. Stecher G. Li M. Knyaz C. Tamura K. MEGA X. Molecular evolutionary genetics analysis across computing platforms Mol. Biol. Evol. 35 2018 1547 1549 10.1093/molbev/msy096 29722887
