Comparative Analysis of the Complete Plastomes of Apostasia wallichii and Neuwiedia singapureana (Apostasioideae) Reveals Different Evolutionary Dynamics of IR/SSC Boundary among Photosynthetic Orchids

Abstract

Apostasioideae, consists of only two genera, Apostasia and Neuwiedia, which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of Apostasia wallichii and Neuwiedia singapureana were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids. Unlike many orchid plastomes (e.g., Paphiopedilum and Vanilla), the plastomes of Apostasioideae contain a full set of 11 functional NADH dehydrogenase (ndh) genes. The distribution of repeat sequences and simple sequence repeat elements enhanced the view that the mutation rate of non-coding regions was higher than that of coding regions. The 10 loci-ndhA intron, matK-5'trnK, clpP-psbB, rps8-rpl14, trnT-trnL, 3'trnK-matK, clpP intron, psbK-trnK, trnS-psbC, and ndhF-rpl32-that had the highest degrees of sequence variability were identified as mutational hotspots for the Apostasia plastome. Furthermore, our results revealed that plastid genes exhibited a variable evolution rate within and among different orchid genus. Considering the diversified evolution of both coding and non-coding regions, we suggested that the plastome-wide evolution of orchid species was disproportional. Additionally, the sequences flanking the inverted repeat/small single copy (IR/SSC) junctions of photosynthetic orchid plastomes were categorized into three types according to the presence/absence of ndh genes. Different evolutionary dynamics for each of the three IR/SSC types of photosynthetic orchid plastomes were also proposed.

Keywords: Apostasioideae; IR expansion/contraction; hotspots; plastome; substitution rates.

FIGURE 1

Plastome map of Neuwiedia singapureana. The plastome of Apostasia wallichii has an identical structure to that of N. singapureana, except for an inversion from trnS-GCU to trnS-GGA. The genes outside and inside the circle are transcribed clockwise and counterclockwise, respectively.

FIGURE 2

Analysis of repeat sequences and SSR elements in the plastomes of Apostasia wallichii and Neuwiedia singapureana. (A) Number of repeat sequences identified by REPuter. (B) Number of SSR elements determined by GMATo.

FIGURE 3

Top 10 syntenic intergenic and intronic loci with the highest sequence variability (%) in Apostasia plastomes.

FIGURE 4

Comparison of non-synonymous (dn) and synonymous (ds) substitution rates among the five orchid subfamilies (Epidendroideae, Orchidoideae, Cypripedioideae, Vanilloideae, and Apostasioideae). The substitutions rates were calculated for the whole plastome by using Lilium longiflorum as the reference. Each subfamily is color coded. Of note, the plastomes of Epidendroideae, Orchidoideae, Cypripedioideae, and Apostasioideae showed diversified substitution rates in their plastomic protein-coding sequences.

FIGURE 5

The mean non-synonymous (dn) and synonymous (ds) substitution ratios among 10 genera of orchids. The mean value was calculate from 11 species for Cymbidium, two species for Masdevallia, three species for Phalaenopsis, four species for Dendrobium, two species for Bletilla, three species for Goodyera, two species for Cypripedium, two species for Paphiopedilum, two species for Vanilla, and two species for Apostasia. The SD bars for each genus are not indicated. (A) Non-synonymous (dn) substitution rates for 66 plastomic protein-coding genes are depicted for 10 genera of orchids. (B) Synonymous (ds) substitution rates.

FIGURE 6

Comparison of IR/SSC boundaries among photosynthetic orchid plastomes. The pseudogenes are denoted by “Ψ.” J_SA and J_Sb were stand for the junctions between IR_A/SSC and IR_B/SSC. The variable length of the 5′ end of ycf1 to J_SA and the intergenic spacer regions adjacent to J_SA and J_Sb are indicated. The most variable plastomes of Cymbidium tracyanum and Cymbidium mannii were used to represent the genus Cymbidium.