New insights into the evolutionary characteristic between the New World and Old World Lupinus species using complete chloroplast genomes

Figures & data

Table 1. Features of six Lupinus species with L. westianus as the reference.

Features of species	L. westianus**	L. albus^*,**	L. atlanticus*	L. luteus*	L. micranthus*	L. princei*
Total cpDNA size (bp)	154,270	154,140	152,272	151,894	151,808	152,243
LSC size (bp)	82,438	82,266	82,674	82,327	82,145	82,663
SSC size (bp)	15,854	15,764	17,894	17,847	17,857	17,876
IRs size (bp)	27,989	28,055	25,852	25,860	25,903	25,852
Number of different Genes	111	111	111	111	111	111
Number of different Protein coding genes	77	77	77	77	77	77
Number of different tRNA genes	30	30	30	30	30	30
Number of different rRNA genes	4	4	4	4	4	4
Number of genes with introns	22	22	24	24	24	24
Genome GC (%)	36.47	36.55	36.61	36.61	36.62	36.65
Protein coding GC (%)	37.25	37.05	37.27	37.25	37.27	37.30
tRNA GC (%)	53.39	53.36	53.36	53.29	53.29	53.36
rRNA GC (%)	55.33	55.31	55.33	55.36	55.33	55.33
Intergenic GC (%)	30.47	30.62	30.32	30.35	30.38	30.43
Gene losses	Ψ ycf1

cpDNA: chloroplast DNA; LSC: large single-copy region; SSC: small single-copy region; IR: inverted repeat; * The presence of pseudogenes in the complete genome of L. albus (ycf1), L. atlanticus (ycf1), L. luteus (ycf1), L. micranthus (ycf1) and L. princei (ycf1); ** Introns losses: two intron missing in rps12 (L. westianus and L. albus).

Figure 1. Analysis of simple sequence repeats (SSRs) in the chloroplast genome of six Lupinus species. (a) The types and numbers of SSRs identified in six Lupinus species; (b) The frequency of SSRs motifs in six Lupinus species.

Figure 2. Analysis of repeat types and numbers in six Lupinus speices.

Figure 3. Comparisons of borders between neighboring genes and junctions of the LSC, SSC and IR regions among the six Lupinus species. Boxes above or below the main line indicate genes adjacent to borders. The figure is not to scale with regard to sequence length and shows only relative changes at or near (inverted repeats/single copy) IR/SC borders. Number above the gene features means the distance between the ends of genes and the borders sites.

Figure 4. Comparison of chloroplast genome sequences of six Lupinus species. The outer ring show the coding sequences, tRNA genes, rRNA genes and other genes in the forward and reverse strands. The next six rings show the blast results between the chloroplast genomes of L. westianus and other 5 Old World Lupinus species based on BlastN. The following ring is GC skew curve for the L. westianus chloroplast genome. GC skew+ (green) indicates G > C, GC skew − (purple) indicates G < C. The innermost black ring is the GC content curve for the L. westianus chloroplast genome.

Figure 5. Genomic rearrangement of six Lupinus species. The blue frame represents a 20kb inversion region (ndhF-ycf1).

Figure 6. Comparative analysis of nucleotide variability (Pi) values among the chloroplast genome sequences of six Lupinus species.(a) Analysis of the homologous protein-coding genes; (b) Analysis of the intron regions; (c) Analysis of the IGS regions.

Figure 7. The Ka/Ks ratios of homologous protein-coding genes in six Lupinus species, with L. westianus as the reference.

Table 2. Parameter estimates and log-likelihood values for different models in selectivepressure analysis.

Gene	Model	df	LnL/ω	LRTs	Putative Sites under Positive Selection
rpoA	M0(one ratio)	10	ω=0.9725
	M1(neutral)	11	−1444.3872	M1 vs. M2	1(145 L)
	M2(selection)	13	−1443.5617	1.6510
	M7(beta)	11	−1444.5014	M7 vs. M8
	M8(beta&ω)	13	−1443.7158	1.5712
matK	M0(one ratio)	10	ω=0.7211
	M1(neutral)	11	−2234.0735	M1 vs. M2	2(402 D,490 L)
	M2(selection)	13	−2232.1969	3.7533
	M7(beta)	11	−2234.1531	M7 vs. M8
	M8(beta&ω)	13	−2232.1972	3.9118
accD	M0(one ratio)	10	ω=0.6321
	M1(neutral)	11	−2574.8125	M1 vs. M2	10(21 R,24 W,25 G,39 T,41 V,42 S, 50 D,51 P,169 R,465 A)
	M2(selection)	13	−2555.9764	37.6721**
	M7(beta)	11	−2575.2924	M7 vs. M8
	M8(beta&ω)	13	−2556.5373	37.5101**
rpoC2	M0(one ratio)	10	ω=0.5828
	M1(neutral)	11	−6330.4636	M1 vs. M2	16(366 L,454 D,460 K,594 R,641 I, 940 K,1001 Y,1003 F,1004 Y,1006 L,1007 I,1008 T,1009 H,1010 N,1011 Q,1013 S)
	M2(selection)	13	−6307.7611	45.4050
	M7(beta)	11	−6330.819	M7 vs. M8
	M8(beta&ω)	13	−6311.0321	39.5756
ycf1	M0(one ratio)	10	ω=0.5026
	M1(neutral)	11	−9229.0063	M1 vs. M2	10(199 L,375 T,412 F,480 C,914 L,963 V,978 R,1210 Y,1232 M,1258 Q)
	M2(selection)	13	−9221.3009	15.4106
	M7(beta)	11	−9229.0740	M7 vs. M8
	M8(beta&ω)	13	−9221.3011	15.5459*

* p < 0.05, ** p < 0.01; df: degree of freedom; LRT(Likelihood ratio test) = |df(M2/M8) − df(M1/M7)| × |lnL(M2/M8) −lnL(M1/M7)|; Putative Sites under Positive Selection: the selective sites under the Bayes empirical Bayes (BEB) model.

Figure 8. Phylogenetic relationships based on the chloroplast genomes of six Lupinus species and two Sophera species with the ML and NJ method. (a) ML tree; (b) NJ tree. Sophera species was selected as the outgroup. Numbers on the left side at the branches represent bootstrap values.

Data availability statement

The data that support the findings of this study are openly available in National Center of Biotechnology Information at https://www.ncbi.nlm.nih.gov/, accession number are MG252262, KJ468099, KU726827, NC023090, KU726828, KU726829, NC045070, NC0-42688.