Genetic Diversity and Phylogenetic Analyses of Laurus nobilis L. (Lauraceae) Populations Revealed Chloroplast (cpDNA) trnL Intron and trnL-F Region

Figures & data

Figure 1. trnL intron and trnL-F regions (Amirahmadi et al., 2010)

Figure 2. Location of Aegean region. The maps were obtained from Google Maps (maps.google.com)

Table 1. Cycles and conditions of cpDNA trnL intron and trnL-F region PCR reactions

Pre-heating	94°C	5 min	1 cycle
1. step	94°C	30 s
2. step	50°C	30 s
3. step	72°C	90 s	35 cycles
4. step	72°C	8 min	1 cycle
5. step	4°C	20 min

Table 2. Length and A + T and G + C contents of trnL intron sequences of Laurus nobilis populations

Populations	trnL intron (bp)	A (%) content	T (%) content	G (%) content	C (%) content	A + T (%) content	G + C(%) content
Seferihisar population	519,0	26,4	36,4	17,0	20,2	62.8	37.2
Salihli population	526,0	26,2	36,7	16,9	20,2	62.9	37.1
Çigli population	523,0	26,2	36,5	17,0	20,3	62.7	37.3
Denizli population	523,0	26,4	36,7	16,6	20,3	63.1	36.9
Aydın population	523,0	26,4	36,3	16,8	20,5	62.7	37.3
Yesilyurt population	523,0	26,4	36,5	16,8	20,3	62.9	37.1
Kuşadası population	526,0	26,6	35,9	17,3	20,2	62.5	37.5
Muğla population	528,0	26,3	36,6	17,0	20,1	62.9	37.1
Average	523,9	26,4	36,5	16,9	20,2	62.9	37.1

Table 3. Pairwise sequence distances among Laurus nobilis populations taxa for trnL intron data using MEGA 6.0 software distance matrix

Populations	1	2	3	4	5	6	7	8
Seferihisar population
Salihli population	0,000
Çigli population	0,000	0,000
Denizli population	0,002	0,002	0,002
Aydın population	0,000	0,000	0,000	0,002
Yesilyurt population	0,000	0,000	0,000	0,002	0,000
Kuşadası population	0,002	0,002	0,002	0,004	0,002	0,002
Muğla population	0,000	0,000	0,000	0,002	0,000	0,000	0,002	-

Table 4. Tajima’s Neutrality Test Values based on trnL intron of eight date Laurus nobilis populations MEGA6

No. of sequences “m”	No. of segregating sites “S”	Ps = S/n	Θ = ps/a1	nucleotide diversity ‘’ π ‘’	Tajima test statistic ‘’D”
8	2	0.004016	0.001549	0.0001004	−1.310092

Table 5. Maximum likelihood estimate of substitution matrix

	A	T/U	C	G
A	-	9.48	5.11	0.00
T/U	6.8	-	17.05	4.27
C	6.8	31.66	-	4.27
G	0.00	9.48	5.11	-

Table 6. Length and A + T and G + C contents of cpDNA trnL-F sequences of Laurus nobilis populations

Populations	trnL-F(bp)	A (%) content	T (%) content	G (%) content	C (%) content	A + T (%) content	G + C(%) content
Muğla population	373	32,4	31,1	22,5	13,9	63,5	36,4
Aydın population	373	31,9	30,6	21,4	16,1	62,5	37,5
Çiğili population	375	31,7	30,7	21,3	16,3	62,4	37,6
Denizli population	373	31,9	30,6	21,4	16,1	62,5	37,5
Kuşadası population	373	31,6	30,8	21,4	16,1	62,4	37,5
Salihli population	372	32,0	30,4	21,5	16,1	62,4	37,6
Seferihisar population	373	31,9	30,6	21,4	16,1	62,5	37,5
Yeşilyurt population	376	31,6	30,9	21,3	16,2	62,5	37,5
Average	373,5	31,9	30,7	21,6	15,9	62,6	37,5

Table 7. Pairwise sequence distances among some Laurus nobilis populations for cpDNA trnL-F data using MEGA 6.0 software distance matrix

Populations	1	2	3	4	5	6	7	8
Muğla population	-	-	-	-	-	-	-	-
Aydın population	0,000	-	-	-	-	-	-	-
Çiğili population	0,000	0,000	-	-	-	-	-	-
Denizli population	0,000	0,000	0,000	-	-	-	-	-
Kuşadası population	0,000	0,000	0,000	0,000	-	-	-	-
Salihli population	0,000	0,000	0,000	0,000	0,000	-	-	-
Seferihisar population	0,000	0,000	0,000	0,000	0,000	0,000	-	-
Yeşilyurt population	0,000	0,000	0,000	0,000	0,000	0,000	0,000	-

Table 8. Tajima’s Neutrality Test Values based on trnL-F of eight date Laurus nobilis populations MEGA6

No. of sequences “m”	No. of segregating sites “S”	Ps = S/n	Θ = ps/a1	nucleotide diversity ‘’ π ‘’	Tajima test statistic ‘’D”
8	0	0.000000	0.00000E+000	0.000000	n/c

Table 9. Maximum likelihood estimate of substitution matrix

	A	T/U	C	G
A	-	10.11	4.86	7.28
T/U	11.08	-	4.86	7.29
C	11.08	10.10	-	7.29
G	11.07	10.11	4.86	-

Figure 3. Phylogenetic tree of Laurus nobilis populations trnL intron sequences constructed using maximum likelihood method with MEGA 6.0

Figure 4. Phylogenetic tree of Laurus nobilis populations trnL intron sequences constructed using neighbor joining method with MEGA 6.0

Figure 5. Phylogenetic tree of Laurus nobilis populations trnL-F sequences constructed using maximum likelihood method with MEGA 6.0

Figure 6. Phylogenetic tree of Laurus nobilis populations trnL-F sequences constructed using neighbor joining method with MEGA 6.0

Amirahmadi, S., S. Kazempour Osaloo, and A.A. Maassoumi. 2010. Loss of chloroplast trnLUAA intron in two species of Hedysarum (Fabaceae): Evolutionary implications. Iran J. Biotechnol. 8(3):150–155.

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