Ancient Horizontal Gene Transfers from Plastome to Mitogenome of a Nonphotosynthetic Orchid, Gastrodia pubilabiata (Epidendroideae, Orchidaceae).

Gastrodia pubilabiata is a nonphotosynthetic and mycoheterotrophic orchid belonging to subfamily Epidendroideae. Compared to other typical angiosperm species, the plastome of G. pubilabiata is dramatically reduced in size to only 30,698 base pairs (bp). This reduction has led to the loss of most photosynthesis-related genes and some housekeeping genes in the plastome, which now only contains 19 protein coding genes, three tRNAs, and three rRNAs. In contrast, the typical orchid species contains 79 protein coding genes, 30 tRNAs, and four rRNAs. This study decoded the entire mitogenome of G. pubilabiata, which consisted of 44 contigs with a total length of 867,349 bp. Its mitogenome contained 38 protein coding genes, nine tRNAs, and three rRNAs. The gene content of G. pubilabiata mitogenome is similar to the typical plant mitogenomes even though the mitogenome size is twice as large as the typical ones. To determine possible gene transfer events between the plastome and the mitogenome individual BLASTN searches were conducted, using all available orchid plastome sequences and flowering plant mitogenome sequences. Plastid rRNA fragments were found at a high frequency in the mitogenome. Seven plastid protein coding gene fragments (ndhC, ndhJ, ndhK, psaA, psbF, rpoB, and rps4) were also identified in the mitogenome of G. pubilabiata. Phylogenetic trees using these seven plastid protein coding gene fragments suggested that horizontal gene transfer (HGT) from plastome to mitogenome occurred before losses of photosynthesis related genes, leading to the lineage of G. pubilabiata. Compared to species phylogeny of the lineage of orchid, it was estimated that HGT might have occurred approximately 30 million years ago.

Evolutionary Patterns of the Chloroplast Genome in Vanilloid Orchids (Vanilloideae, Orchidaceae).

The Vanilloideae (vanilloids) is one of five subfamilies of Orchidaceae and is composed of fourteen genera and approximately 245 species. In this study, the six new chloroplast genomes (plastomes) of vanilloids (two Lecanorchis, two Pogonia, and two Vanilla species) were decoded, and then the evolutionary patterns of plastomes were compared to all available vanilloid plastomes. Pogonia japonica has the longest plastome, with 158,200 bp in genome size. In contrast, Lecanorchis japonica has the shortest plastome with 70,498 bp in genome size. The vanilloid plastomes have regular quadripartite structures, but the small single copy (SSC) region was drastically reduced. Two different tribes of Vanilloideae (Pogonieae and Vanilleae) showed different levels of SSC reductions. In addition, various gene losses were observed among the vanilloid plastomes. The photosynthetic vanilloids (Pogonia and Vanilla) showed signs of stage 1 degradation and had lost most of their ndh genes. The other three species (one Cyrotsia and two Lecanorchis), however, had stage 3 or stage 4 degradation and had lost almost all the genes in their plastomes, except for some housekeeping genes. The Vanilloideae were located between the Apostasioideae and Cypripedioideae in the maximum likelihood tree. A total of ten rearrangements were found among ten Vanilloideae plastomes when compared to the basal Apostasioideae plastomes. The four sub-regions of the single copy (SC) region shifted into an inverted repeat (IR) region, and the other four sub-regions of the IR region shifted into the SC regions. Both the synonymous (dS) and nonsynonymous (dN) substitution rates of IR in-cooperated SC sub-regions were decelerated, while the substitution rates of SC in-cooperated IR sub-regions were accelerated. A total of 20 protein-coding genes remained in mycoheterotrophic vanilloids. Almost all these protein genes show accelerated base substitution rates compared to the photosynthetic vanilloids. Two of the twenty genes in the mycoheterotrophic species faced strong "relaxed selection" pressure (p-value < 0.05).

The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae).

The genus Zoysia Willd. (Chloridoideae) is widely distributed from the temperate regions of Northeast Asia-including China, Japan, and Korea-to the tropical regions of Southeast Asia. Among these, four species-Zoysia japonica Steud., Zoysia sinica Hance, Zoysia tenuifolia Thiele, and Zoysia macrostachya Franch. & Sav.-are naturally distributed in the Korean Peninsula. In this study, we report the complete plastome sequences of these Korean Zoysia species (NCBI acc. nos. MF953592, MF967579~MF967581). The length of Zoysia plastomes ranges from 135,854 to 135,904 bp, and the plastomes have a typical quadripartite structure, which consists of a pair of inverted repeat regions (20,962~20,966 bp) separated by a large (81,348~81,392 bp) and a small (12,582~12,586 bp) single-copy region. In terms of gene order and structure, Zoysia plastomes are similar to the typical plastomes of Poaceae. The plastomes encode 110 genes, of which 76 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Fourteen genes contain single introns and one gene has two introns. Three evolutionary hotspot spacer regions-atpB~rbcL, rps16~rps3, and rpl32~trnL-UAG-were recognized among six analyzed Zoysia species. The high divergences in the atpB~rbcL spacer and rpl16~rpl3 region are primarily due to the differences in base substitutions and indels. In contrast, the high divergence between rpl32~trnL-UAG spacers is due to a small inversion with a pair of 22 bp stem and an 11 bp loop. Simple sequence repeats (SSRs) were identified in 59 different locations in Z. japonica, 63 in Z. sinica, 62 in Z. macrostachya, and 63 in Z. tenuifolia plastomes. Phylogenetic analysis showed that the Zoysia (Zoysiinae) forms a monophyletic group, which is sister to Sporobolus (Sporobolinae), with 100% bootstrap support. Within the Zoysia clade, the relationship of (Z. sinica, Z japonica), (Z. tenuifolia, Z. matrella), (Z. macrostachya, Z. macrantha) was suggested.

Three complete plastome sequences from the families of Lamiaceae, Mazaceae, and Phrymaceae (Lamiales).

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 single-copy 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.

Corrigendum: Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences.

[This corrects the article DOI: 10.3389/fpls.2020.00022.].

Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences.

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. Forty-two 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 124 orchid species confirmed the relationship of {Apostasioideae [Vanilloideae (Cypripedioideae (Orchidoideae, Epidendroideae))]} at the subfamily level and the phylogenetic relationships of 17 tribes were also established. Molecular clock analysis based on the whole plastome sequences suggested that Orchidaceae diverged from its sister family 99.2 mya, and the estimated divergence times of five subfamilies are as follows: Apostasioideae (79.91 mya), Vanilloideae (69.84 mya), Cypripedioideae (64.97 mya), Orchidoideae (59.16 mya), and Epidendroideae (59.16 mya). We also released the first nuclear ribosomal (nr) DNA unit (18S-ITS1-5.8S-ITS2-28S-NTS-ETS) sequences for the 42 species of Orchidaceae. Finally, the phylogenetic tree based on the nrDNA unit sequences is compared to the tree based on the 42 identical plastome sequences, and the differences between the two datasets are discussed in this paper.

Plastome evolution and phylogeny of subtribe Aeridinae (Vandeae, Orchidaceae).

Subtribe Aeridinae (Vandeae, Epidendroideae, Orchidaceae) consists of 83 genera and 2,345 species. The present study completely decoded the plastomes and nuclear ribosomal (nr) RNA gene clusters of seven species of Aeridinae belonging to Gastrochilus, Neofinetia, Pelatantheria, and Thrixspermum and compared them with existing data to investigate their genome evolution and phylogeny. Although no large structural variations were observed among the Aeridinae plastomes, 14 small inversions (SI) were found in Orchidaceae for the first time. Therefore, the evolutionary trends and usefulness of SI as molecular identification markers were evaluated. Since all 11 ndh genes in the Aeridinae plastome were lost or pseudogenized, the evolutionary trends of ndh genes are discussed at the tribe and family levels. In the maximum likelihood tree reconstructed from 83 plastome genes, the five Orchidaceae subfamilies were shown to have diverged in the following order: Apostasioideae, Vanilloideae, Cypripedioideae, Orchioideae, Epidendroideaeae. Divergence times for major lineages were found to be more recent, 5-10 Mya, than previous studies, which only used two or three genes. Vandeae, which includes Aeridinae, formed a sister group with Cymbidieae and Epidendreae. The Vandeae, Cymbidieae, and Epidendreae lineages were inferred to have diverged at 25.31 Mya; thus, numerous speciation events within Aeridineae occurred since then. Furthermore, the present study reconstructed a phylogenetic tree from 422 nrITS sequences belonging to Aerdinae and allied taxa and uses it to discuss the phylogenetic positions and species identities of five endangered species.

Characterization of 20 complete plastomes from the tribe Laureae (Lauraceae) and distribution of small inversions.

Lindera Thunb. (Lauraceae) consists of approximately 100 species, mainly distributed in the temperate and tropical regions of East Asia. In this study, we report 20 new, complete plastome sequences including 17 Lindera species and three related species, Actinodaphne lancifolia, Litsea japonica and Sassafras tzumu. The complete plastomes of Lindera range from 152,502 bp (L. neesiana) to 154,314 bp (L. erythrocarpa) in length. Eleven small inversion (SI) sites are documented among the plastomes. Six of the 11 SI sites are newly reported and they locate in rpoB-trnC, psbC-trnS, petA-psbJ, rpoA and ycf2 regions. The distribution patterns of SIs are useful for species identification. An average of 83 simple sequence repeats (SSRs) were detected in each plastome. The mono-SSRs accounted for 72.7% of total SSRs, followed by di- (12.4%), tetra- (9.4%), tri- (4.2%), and penta-SSRs (1.3%). Of these SSRs, 64.6% were distributed in an intergenic spacer (IGS) region. In addition, 79.8% of the SSRs are located in a large single copy (LSC) region. In contrast, almost no SSRs are distributed in inverted repeat (IR) regions. The SSR loci are useful to identifying species but the phylogenetic value is low because the majority of them show autapomorphic status or highly homoplastic characteristics. The nucleotide diversity (Pi) values also indicated the conserved nature of the IR region compared to LSC and small single copy (SSC) regions. Five spacer regions with high Pi values, trnH-psbA, petA-psbJ and ndhF-rpl32, rpl32-trnL and Ψycf1-ndhF, have a potential use for the molecular identification study of Lindera and related species. Lindera species form a paraphyletic group in the plastome tree because of the inclusion of related genera such as Actinodaphne, Laurus, Litsea and Neolitsea. A former member of tribe Laureae, Sassafras, forms a clade with the tribe Cinnamomeae. The SIs do not affect the phylogenetic relationship of Laureae. This result indicated that ancient plastome captures may have contribute to the mixed intergeneric relationship of Laureae. Alternatively, the result may indicate that the morphological characters defined the genera of Lauraceae originated for several times.

Extensive Losses of Photosynthesis Genes in the Plastome of a Mycoheterotrophic Orchid, Cyrtosia septentrionalis (Vanilloideae: Orchidaceae).

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 ycf2. A block consisting of four rrn genes and rps7 and rps12 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.

The complete plastome sequence of Carissa macrocarpa (Eckl.) A. DC. (Apocynaceae).

In this study, we determined the complete plastome sequence of Carissa macrocarpa (Eckl.) A. DC. (Apocynaceae) (NCBI acc. no. KX364402). The gene order and structure of the C. macrocarpa plastome are similar to those of a typical angiosperm. The complete plastome is 155,297 bp in length, and consists of a large single-copy region of 85,586 bp and a small single-copy region of 18,131 bp, which are separated by two inverted repeats of 25,792 bp. The plastome contains 113 genes, of which 79 are protein-coding genes, 30 are tRNA genes and 4 are rRNA genes. Sixteen genes contained one intron and two genes have two introns. The average A-T content of the plastome is 62.0%. A total of 31 simple sequence repeat loci were identified within the genome. Phylogenetic analysis revealed that C. macrocarpa is a member of the paraphyletic subfamily Rauvolfioideae of Apocynaceae. The sister group relationship of C. macrocarpa to the Apocynoideae-Asclepiadoideae clade is supported by 100% bootstrap values.

The complete plastome sequence of the endangered orchid Kuhlhasseltia nakaiana (Orchidaceae).

In this study, we report the complete plastome sequence of Kuhlhasseltia nakaiana (F.Maek.) Ormerod (Orchidaceae) (NCBI acc. no. KY354041), an endangered plant species protected by the national law of Korea. The gene order and number in the K. nakaiana plastome were similar to a typical orchid plastome. The complete plastome was 147,614 bp in length and consisted of a large single copy region of 81,617 bp and a small single copy region of 13,673 bp, separated by two inverted repeats of 26,162 bp. The plastome contained 103 genes, of which 69 were protein-coding genes, 30 were tRNA genes, and four were rRNA genes. Fourteen genes contained one intron and two genes (clpP and ycf3) had two introns. The AT content of the plastome was 60.5%. A total of 74 simple sequence repeat regions were identified from the plastome. Phylogenetic analysis determined that K. nakaiana was a member of the tribe Cranichideae and revealed the sister group relationship between K. nakaiana and Ludisia discolor within the tribe Cranichideae.

The complete plastome sequences of Mangifera indica L. (Anacardiaceae).

In this study, we determined the complete plastome sequence of Mangifera indica L. (Anacardiaceae) (NCBI acc. no. KX871231). The complete plastome is 157,780 bp in length, and consists of a large single copy of 86,673 bp and a small single copy of 18,349 bp, separated by two inverted repeats of 25,792 bp. The plastome contains 112 genes, of which 78 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Sixteen genes contain one intron and two genes have two introns. The average A-T content of the plastome is 62.1%. The M. indica plastome has approximately 15 kb inversion between trnT-UGU and trnT-GGU. We identify a palindromic repeat of 18 bp (ATTCTTTTTTTTTTTTTT/AAAAAAAAAAAAAAGAAT) near the inversion breakpoints of M. indica plastome. Phylogenetic analysis revealed that M. indica is a sister group of Rhus chinensis with 100% bootstrap support. Anacardiaceae clade is a sister group of Boswellia sacra (Burseraceae) with 100% bootstrap support.

The complete plastome sequence of the endangered orchid Habenaria radiata (Orchidaceae).

In this study, we determined the complete chloroplast sequence of Habenaria radiata (Thunb.) Spreng. (Orchidaceae) (NCBI acc. no. KX871237), an endangered plant species protected by the national law of Korea. The gene order and gene content of the H. radiata plastome are similar to those of typical angiosperm plastomes. The 11 ndh genes, which are usually lost in orchid plastomes, are intact in the H. radiata plastome. The complete plastome is 155,353 bp in length and consists of a large single copy of 84,833 bp and a small single copy of 17,718 bp, separated by two inverted repeats of 26,401 bp. The plastome contains 113 genes, of which 79 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Sixteen genes contain one intron and two genes (clpP, ycf3) have two introns. A total of 76 simple sequence repeat (SSR) loci, which consist of 58 mono-SSR, 17 di-SSR, and 1 tri-SSR, are scattered along the H. radiata plastome. Some of these plastome SSR and high sequence divergent regions may be useful for development of genetic markers for the populations of H. radiata and other congeneric species. Phylogenetic analysis identified the sister relationship between H. radiata and H. pantlingiana within the tribe Orchideae.

The complete plastome sequence of the endangered orchid Oberonia japonica (Orchidaceae).

In this study, we report the complete chloroplast sequence of Oberonia japonica (Maxim.) Makino (Orchidaceae) (NCBI acc. no. KX871235), which is an endangered plant species currently protected by the National Law of Korea. The gene order and content of the O. japonica plastome are similar to those of a typical orchid plastome. The 11 ndh genes are pseudogenized or lost completely from the plastome of O. japonica. The plastome contains 102 genes, of which 68 are protein-coding genes, 30 and four are transfer RNA (tRNA) and ribosomal RNA (rRNA) genes, respectively. Sixteen genes contain one intron and two genes (clpP and ycf3) have two introns. The complete plastome is 142,996 bp long and consists of one large and small single copy each of 81,669 and 10,969 bp, respectively, separated by two inverted repeats of 25,179 bp. The AT content of the O. japonica plastome is 62.6%. Sixty-five simple sequence repeat (SSR) loci, consisting of 56 mono-SSR, seven di-SSR, and two tri-SSR are scattered along the O. japonica plastome. Some of these plastome SSR loci may be useful for developing genetic markers for the O. japonica populations. Phylogenetic analysis has shown that O. japonica is a member of the Malaxideae. The genus Oberonia forms a monophyletic clade with Dendrobium.

The complete plastome sequence of the endangered orchid Cymbidium macrorhizon (Orchidaceae).

In this study, we determined the complete chloroplast sequence of Cymbidium macrorhizon Lindl. (Orchidaceae) (NCBI acc. no. KY354040), an endangered plant species protected by the national law of Korea. The gene order and number in the C. macrorhizon plastome were similar to a typical Orchid plastome. The complete plastome was 149,859 bp in length and consisted of a large single copy region of 85,187 bp and a small single copy region of 13,766 bp; these were separated by two inverted repeats of 25,453 bp. The plastome contained 103 genes of which 69 were protein-coding genes, 30 were tRNA genes and four were rRNA genes. Fourteen genes contained one intron and two genes (clpP, and ycf3) had two introns. The AT content of the C. macrorhizon plastome was 60.0% and a total of 62 simple sequence repeat regions were identified in the plastome. Phylogenetic analysis also identified C. lancifolium as a closely related sister to C. macrorhizon, suggesting that the hemisaprophytic nature of C. macrorhizon is derived recently from a common leafy ancestor.

The complete plastome of tropical fruit Garcinia mangostana (Clusiaceae).

The complete plastome sequence of Garcinia mangostana L. (Clusiaceae) is completed in this study (NCBI acc. no. KX822787). This is a first complete plastome sequence from the Clusiaceae. The complete plastome size is 158,179 bp in length and consists of a large single copy of 86,458 bp and a small single copy of 17,703 bp, separated by two inverted repeats of 27,009 bp. The G. mangostana plastome shows four minor structural modifications including infA gene loss, rpl32 gene loss, ycf3 gene intron loss and a 363 bp inversion between trnV-UAC and atpE gene. The plastome contains 111 genes, of which 77 are protein-coding genes, 30 are tRNA genes and four are rRNA genes. The average A-T content of the plastome is 63.9%. A total of 110 simple sequence loci are identified from the genome. Phylogenetic analysis reveals that G. mangostana is a sister group of Erythroxylum novogranatense (Erythroxylaceae) with 78% bootstrap support.

The complete plastome sequence of Durian, Durio zibethinus L. (Malvaceae).

The complete plastome sequence of Durio zibethinus L. (Malvaceae) is determined in this study (NCBI acc. no. MG138151). D. zibethinus is an important fruit crop in Southeastern Asia and known as the 'king of fruit'. Our D. zibethinus plastome is the first reported sequences from the subfamily Helicteroideae of Malvaceae. The plastome sequence of D. zibethinus is 163,974 bp in length and it is composed of a pair of 23,679 bp inverted repeat regions separated by large and small single-copy regions of 95,704 bp and 20,912 bp, respectively. The gene order and structure of the D. zibethinus are similar to those of the typical plastome of land plants. The plastome encodes 113 genes, of which 79 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Fifteen genes contain single intron and two genes have two introns. A total of 144 simple sequence repeats (SSR) were identified in the genome. Phylogenetic analysis show that D. zibethinus (Helicteroideae) is sister group of Tilia (Tilioideae) clade with 100% bootstrap support.

Complete plastome sequence of Averrhoa carambola L. (Oxalidaceae).

In this study, we determined the complete plastome sequence of Averrhoa carambola L. (Oxalidaceae) (NCBI acc. no. KX364202). To the best of our knowledge, this is the first reported complete plastome sequence from the order Oxalidales. The gene order and structure of the A. carambola plastome are collinear with the typical plastome of land plants. The complete plastome size is 155,965 bp in length and consists of a large single copy region of 87,217 bp and a small single copy region of 17,496 bp, which are separated by a pair of 25,626-bp-long inverted repeat regions. The overall A-T content of the plastome sequence is 61.2%. The plastome contains 111 genes, of which 77 are protein-coding genes, 30 are tRNA genes, and 4 are rRNA genes. Sixteen genes contain one intron and two genes have two introns. A total of 91 simple sequence loci were identified from the genome. Phylogenetic analysis revealed that A. carambola is a sister group of Euonymus japonicus with 100% bootstrap support.

The first complete plastome sequence from the family Sapotaceae, Pouteria campechiana (Kunth) Baehni.

In this study, we determined the complete plastome sequence of Pouteria campechiana (Kunth) Baehni (Sapotaceae) (NCBI acc. no. KX426215). This is the first time a plastome from the Sapotaceae has been sequenced. The gene order and structure of the P. campechiana plastome are collinear with those of the typical plastome of land plants. The complete plastome size is 157,922 bp in length and consists of a large single-copy region of 87,122 bp and a small single-copy region of 18,559 bp, which are separated by a pair of 26,120 bp-long inverted repeat regions. The overall A-T content of the plastome sequence is 63.2%. The plastome contains 113 genes, of which 79 are protein-coding genes, 30 are tRNA genes, and 4 are rRNA genes. Sixteen genes contain one intron and two genes have two introns. A total of 91 simple sequence repeat loci were identified within the genome. Phylogenetic analysis revealed that P. campechiana is a sister group of the Primulaceae-Ebenaceae clade with 100% bootstrap support.

Complete plastome sequence of Psidium guajava L. (Myrtaceae).

In this study, we determined the complete plastome sequence of Psidium guajava L. (Myrtaceae) (NCBI acc. no. KX364403). The gene order and structure of the P. guajava plastome are similar to those of a typical angiosperm. The complete plastome is 158,841 bp in length, and consists of a large single copy of 87,675 bp and a small single copy of 18,464 bp, separated by two inverted repeats of 26,351 bp. The overall AT content of the sequence is 63.0%. The plastome contains 112 genes, of which 78 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Sixteen genes contain one intron and two genes have two introns. A total of 100 simple sequence loci were identified from the genome. Phylogenetic analysis revealed that P. guajava is a sister group of Eugenia uniflora with 100% bootstrap support.