Exploring the systematic positions of two infraspecific taxa of <i>Dioscorea bulbifera</i> based on next-generation sequencing technology, morphology and cytology

Figures (6) Tables (2)

Figure 1.
(a), (d), (g), (j) Morphological comparison of D. bulbifera var. bulbifera; (b), (e), (h), (k) D. bulbifera var. kacheo; and (c), (f), (i), (l) D. bulbifera f. domestica. (a)–(c) Female inflorescences; (d)–(f) female flowers; (g)–(i) leaves; (j)–(l) stems.
Figure 2.
Morphological comparison of (a), (d) D. bulbifera var. bulbifera; (b), (e) D. bulbifera var. kacheo; and (c), (f) D. bulbifera f. domestica. (a)–(c) Bulbils. (d)–(f) Tubers. Scale bar = 5 cm.
Figure 3.
Chromosome spreads of D. bulbifera var. bulbifera, D. bulbifera var. kacheo and D. bulbifera f. domestica. (a) D. bulbifera var. bulbifera (HNLS, 2n = 40); (b) D. bulbifera var. bulbifera (HNHK, 2n = 60); (c) D. bulbifera var. bulbifera (ZJLS, 2n = 80); (d) D. bulbifera var. kacheo (JCHD1, 2n = 80); (e) D. bulbifera f. domestica (YZ1, 2n = 60). Scale bar = 2 μm.
Figure 4.
Plastome map of D. bulbifera. Genes on the outer circle are transcribed clockwise, and those on the inner circle are transcribed counterclockwise. Functional categories are indicated by color-coded genes. The dark grey and the light grey plots in the inner circle correspond to the GC content and AT content, respectively.
Figure 5.
Phylogenetic relationships and cytonuclear discordance in D. bulbifera. (a) Maximum likelihood (ML) tree based on complete plastome sequences; node labels show SH-aLRT/UFBoot/PP (SH-aLRT support [%], ultrafast bootstrap support [%], and Bayesian posterior probabilities). (b) ML tree based on genome-wide nuclear SNPs; node labels show SH-aLRT/UFBoot support (%), with * indicating SH-aLRT/UFBoot = 100/100. All trees were rooted with D. zingiberensis.
Figure 6.
Population genomic analyses of three D. bulbifera infraspecific taxa: HD (D. bulbifera var. bulbifera), JC (D. bulbifera var. kacheo), and YZ (D. bulbifera f. domestica). (a) PCA based on genome-wide SNPs; PC1 and PC2 explain 16.91% and 13.39% of genetic variation. Orange, purple, and blue denote HD (n = 13), JC (n = 2), and YZ (n = 2), respectively. (b) ADMIXTURE analysis (K = 1–8) showing ancestry proportions of each sample. (c) Network of (π) nucleotide diversity and (F_ST) population differentiation; values inside circles indicate π, and lines show pairwise F_ST (white to red indicates increasing differentiation). (d) TreeMix analysis (m = 1) showing population divergence and gene flow; the yellow arrow indicates migration from YZ to JC (weight = 0.183).

Organ	Character	D. bulbifera var. bulbifera	D. bulbifera var. kacheo	D. bulbifera f. domestica
Leaf	Shape	Broadly ovate-cordate or ovate-cordate	Broadly ovate-cordate or ovate-cordate	Broadly cordate, length nearly equal to width
Leaf	Length/width ratio	1.20−1.60	1.17−1.38	1.02−1.07
Stem	Shape	Terete	Ridged	Terete
	Epidermal color	Often dark red, or green with red stripes	Pale green	Usually emerald green
	Epidermal features	Longitudinally striate	With membranous wings along the ridges	Subglabrous, sometimes longitudinally striate
Bulbil	Shape	Subglobose	Subglobose to broadly ellipsoid	Highly variable in shape, ridged
	Epidermal features	Irregularly arranged depressions	Regularly arranged protuberances	Irregularly arranged protuberances of various sizes
	Diameter (cm)	2.9−4.7	2.8−6.5	2.0−8.5
Tuber	Diameter (cm)	8.0−13.0	4.0−5.0	1.0−1.5
Data were collected from mature field specimens (n ≥ 5 per taxon). Diameters of bulbils and tubers were measured at the widest transverse position.

Table 1.

Morphological traits of three taxa in Dioscorea bulbifera.

	Sample name	Internal reference	Reference fluorescence intensity	Target fluorescence intensity	Ratio	Estimated genome size (Gb)
D. bulbifera var. bulbifera	ZJLS	Zea mays	105.51	60.01	0.57	1.31
	HNHK	Zea mays	44.22	19.62	0.44	1.02
	HNLS	Zea mays	50.97	14.69	0.29	0.66

D. bulbifera var. kacheo	JCHD1	Solanum lycopersicum	22.58	35.53	1.57	1.38

D. bulbifera f. domestica	YZ1	Zea mays	44.46	22.14	0.5	1.15

Table 2.

Estimated genome size of Dioscorea bulbifera accessions determined by flow cytometry.