Leaf variegation caused by plastome structural variation: an example from Dianella tasmanica

Abstract

Variegated plants often exhibit plastomic heteroplasmy due to single-nucleotide mutations or small insertions/deletions in their albino sectors. Here, however, we identified a plastome structural variation in albino sectors of the variegated plant Dianella tasmanica (Asphodelaceae), a perennial herbaceous plant widely cultivated as an ornamental in tropical Asia. This structural variation, caused by intermolecular recombination mediated by an 11-bp inverted repeat flanking a 92-bp segment in the large single-copy region (LSC), generates a giant plastome (228 878 bp) with the largest inverted repeat of 105 226 bp and the smallest LSC of 92 bp known in land plants. It also generates an ~7-kb deletion on the boundary of the LSC, which eliminates three protein coding genes (psbA, matK, and rps16) and one tRNA gene (trnK). Albino sectors exhibit dramatic changes in expression of many plastid genes, including negligible expression of psbA, matK, and rps16, reduced expression of photosynthesis-related genes, and increased expression of genes related to the translational apparatus. Microscopic and ultrastructure observations showed that albino tissues were present in both green and albino sectors of the variegated individuals, and chloroplasts were poorly developed in the mesophyll cells of the albino tissues of the variegated individuals. These poorly developed chloroplasts likely carry the large and rearranged plastome, which is likely responsible for the loss of photosynthesis and albinism in the leaf margins. Considering that short repeats are relatively common in plant plastomes and that photosynthesis is not necessary for albino sectors, structural variation of this kind may not be rare in the plastomes of variegated plants.

Figure 1

Photographs of green and variegated plants of D. tasmanica. a Green plant. b Variegated plant. c Adaxial leaf surface of a green plant. d Abaxial leaf surface of a green plant. e Adaxial leaf surface of a variegated plant. f Abaxial leaf surface of a variegated plant.

Figure 2

Gene map of the plastome of the green plant of D. tasmanica. Genes shown outside the outer circle are transcribed counterclockwise, whereas those inside the outer circle are transcribed clockwise. The dark and light shading inside the inner circle indicates GC and AT content, respectively. Asterisks (^*) indicate genes containing intron(s). Areas A, B, and C, which are defined in the Results section, are shown between the inner and outer circles.

Figure 3

Structural difference between G- and A-type plastomes in D. tasmanica. Plastid sequences are shown as light yellow blocks, with sequence identity and their sizes shown on the top. The quadripartite structure and connections among the LSC, IRs, and SSC of G- and A-type plastomes are indicated by arrows and dashed lines. Like those of most other angiosperms, the G-type plastome is composed of the LSC, SSC, and two copies of the IR (shown in the middle of this figure). In the A-type plastome, area A is moved to the IR, resulting in a greatly expanded IR (26 990 + 78 236 bp) and a greatly contracted LSC (only 92 bp), and area C is deleted, while the SSC is unchanged relative to the G-type plastome (shown in the lower of this figure). Here the 92-bp area is enlarged for a clear view. See the Results section for definitions of G- and A-type plastomes and areas A, B, and C.

Figure 4

Schematic diagram showing the formation of the A-type plastome in D. tasmanica through intermolecular recombination of the G-type plastome. The first recombination mediated by the 11-bp IRs merges two G-type plastomes into a recombined intermediate product. The second recombination mediated by the large IRs splits the recombined intermediate product into an A-type plastome and a rearranged plastome (not detected). Solid lines and gridded lines represent sequences from two copies of the G-type plastome. Dotted lines and boxes indicate the positions of recombination. The recombination positions are magnified to show how the recombination proceeds.

Figure 5

A volcano plot showing expressional difference in plastid genes between albino leaf sectors of the variegated plants and leaves of the green plants of D. tasmanica. Genes with significantly reduced and increased expression in the albino sectors are plotted in blue and red dots, respectively. The horizontal dashed line marks Q = 0.05.

Figure 6

Leaf transverse sections of a variegated individual of D. tasmanica showing the distribution of albino mesophyll tissue (a–d) and transmission electron micrographs showing chloroplast ultrastructure in green and albino mesophyll cells (e, f). a Adaxial part of transverse section through the albino sector. b Abaxial part of transverse section through the albino sector. c Adaxial part of transverse section through the green sector, with one albino cell layer beneath the upper leaf epidermis. d Abaxial part of transverse section through the green sector, with one albino cell layer beneath the lower leaf epidermis. e A chloroplast in a green mesophyll cell of the green sector, with well-developed grana lamellae (GL). f A chloroplast in a mesophyll cell of the albino sector, without GL. UE, upper epidermis; LE, lower epidermis; P1, first layer of palisade mesophyll; P2, second layer of palisade mesophyll; S1, first layer of spongy mesophyll (first layer beneath the lower epidermis); S2, second layer of spongy mesophyll; St, stoma; PG, plastoglobule.