In order to understand the evolution of the orchid plastome, we annotated and compared 124 complete plastomes of Orchidaceae representing all the major lineages in their structures, gene contents, gene rearrangements, and IR contractions/expansions. Fortytwo of these plastomes were generated from the corresponding author's laboratory, and 24 plastomes-including nine genera (Amitostigma, Bulbophyllum, Dactylorhiza, Dipodium, Galearis, Gymnadenia, Hetaeria, Oreorchis, and Sedirea)-are new in this study. All orchid plastomes, except Aphyllorchis montana, Epipogium aphyllum, and Gastrodia elata, have a quadripartite structure consisting of a large single copy (LSC), two inverted repeats (IRs), and a small single copy (SSC) region. The IR region was completely lost in the A. montana and G. elata plastomes. The SSC is lost in the E. aphyllum plastome. The smallest plastome size was 19,047 bp, in E. roseum, and the largest plastome size was 178,131 bp, in Cypripedium formosanum. The small plastome sizes are primarily the result of gene losses associated with mycoheterotrophic habitats, while the large plastome sizes are due to the expansion of noncoding regions. The minimal number of common genes among orchid plastomes to maintain minimal plastome activity was 15, including the three subunits of rpl (14, 16, and 36), seven subunits of rps (2, 3, 4, 7, 8, 11, and 14), three subunits of rrn (5, 16, and 23), trnC-GCA, and clpP genes. Three stages of gene loss were observed among the orchid plastomes. The first was ndh gene loss, which is widespread in Apostasioideae, Vanilloideae, Cypripedioideae, and Epidendroideae, but rare in the Orchidoideae. The second stage was the loss of photosynthetic genes (atp, pet, psa, and psb) and rpo gene subunits, which are restricted to Aphyllorchis, Hetaeria, Hexalectris, and some species of Corallorhiza and Neottia. The third stage was gene loss related to prokaryotic gene expression (rpl, rps, trn, and others), which was observed in Epipogium, Gastrodia, Lecanorchis, and Rhizanthella. In addition, an intermediate stage between the second and third stage was observed in Cyrtosia (Vanilloideae). The majority of intron losses are associated with the loss of their corresponding genes. In some orchid taxa, however, introns have been lost in rpl16, rps16, and clpP(2) without their corresponding gene being lost. A total of 104 gene rearrangements were counted when comparing 116 orchid plastomes. Among them, many were concentrated near the IRa/b-SSC junction area. The plastome phylogeny of

Cyrtosia septentrionalis is an achlorophyllous mycoheterotrophic orchid in the subfamily Vanilloideae (Orchidaceae). This article reports C. septentrionalis ’s complete plastome sequence and compare it with other orchid plastomes with a same mycoheterotrophic nutritional mode. The C. septentrionalis plastome has decreased to 96,859 bp in length, but it still maintains a quadripartite structure. The C. septentrionalis plastome contains 38 protein-coding genes, 25 tRNA genes, and four ribosomal RNA genes. Most genes related to photosynthesis have been lost, whereas the majority of housekeeping genes remain; this pattern corresponds to the end of stage 3 gene degradation. The inverted repeat regions of the C. septentrionalis plastome have decreased to 10,414 bp and mainly contain the gene ycf 2. A block consisting of four rrn genes and rps 7 and rps 12 has shifted to a small single-copy region. As a result, the small single-copy region was found to be expanded, despite the loss of all ndh genes in the region. Three inversion mutations are required to explain the C. septentrionalis plastome’s current gene order. The species is endangered, and these results have implications for its conservation.

No abstract

In the original article, there was a mistake in the legend for Figure 4 as published. The word "terrestrial" at the end of the legend for Figure 4A should be "epiphytic." The correct legend appears below. Figure 4. Relationships between plastome lengths and gene numbers. (A): Terrestrial orchids show a wider range of variation than epiphytic orchids. (B): Mycoheterotrophic orchids show a wider range of variation than photosynthetic orchids. (C,D): Plastome lengths are more strongly correlated with LSC lengths than IR lengths in both mycoheterotrophic and photosynthetic orchids.The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.

In this study, we report the first complete plastome sequence of Vitex rotundifolia (Lamiaceae) (MT937186). In addition, the plastome sequences of Phryma leptostachya subsp. asiatica (Phrymaceae) (153,324 bp; MT948145) and Mazus pumilus (Mazaceae) (152,847 bp; MT937187) are also included. The gene orders and structures of the three plastomes are collinear with those of the typical plastome of angiosperm. The plastome size of V. rotundifolia is 154,370 bp in length and consists of a large singlecopy region of 85,079 bp and a small single-copy region of 17,917 bp, which are separated by a pair of 25,687 bp-long inverted repeat regions. In addition, the plastome sizes of P. leptostachya subsp. asiatica and M. pumilus are 153,324 bp and 152,847 bp, respectively. The three plastomes contain 113 genes, including 79 protein-coding, 30 tRNA, and four rRNA genes. Sixteen genes contain one intron and two genes have two introns. A total of 41 simple sequence repeat loci was identified in the V. rotundifolia plastome. Phylogenetic analysis shows that Viticoideae is a sister group of the last of Lamiaceae except Nepetoideae. The Mazaceae are a sister group of Lamiaceae, while Phrymaceae form a sister group to the Paulowniaceae-Orobanchaceae clade.