Complete Chloroplast Genome Sequence of Justicia flava: Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae

Chloroplast genome of Ecbolium viride (Forssk.) Alston: plastome evolution and phylogenomics of Justiceae (Acanthaceae, Acanthoideae)

Justicieae is the most taxonomically complex tribe in Acanthaceae. Here, we sequenced the plastome of Ecbolium viride, a medicinally important species. The genome was analyzed with previously reported plastome of Justiceae. The plastome of E. viride has quadripartite structure with a length of 151 185 bp. The comparative genomic analyses revealed no structural inversion in Justiceae and some regions (rpoC2, ycf2, ycf1, ndhH rps16-trnQ-UGG, and trnL-CAA-ycf15) exhibiting a significant level of nucleotide divergence. The positive selection analyses revealed that some species in the tribe have undergone adaptive evolution. The visualization of the boundaries between the single copy and inverted repeat regions revealed that Justiceae chloroplast genome experienced some levels of variation, which give an insight into the evolution of the species. The longest genome was in the earliest diverged taxa of the tribe Pseuderanthemum haikangense and from this genome, a series of contraction and expansion occurred contributing to the evolution of other lineages. The plastome-based phylogeny revealed and confirmed the monophyly of Justiceae, polyphyly of Justicia and supported the tribal classification Graptophyllinae, Tetrameriinae, and Isoglossinae. We proposed that Declipterinae should be treated as subtribe and the status of Justiciinae can only be confirmed after the resolution of the polyphyletic Justicia.

Chloroplast genome of Justicia procumbens: genomic features, comparative analysis, and phylogenetic relationships among Justicieae species

Justicia procumbens L. is a traditional medicinal plant that is widely distributed in China. However, little is known about the genetic diversity and evolution of this genus, and no genomic studies have been carried out on J. procumbens previously. In this study, we aimed to assemble and annotate the first complete chloroplast genome (cpDNA) of J. procumbens and compare it with all previously published cpDNAs within the tribe Justicieae. Genome structure and comparative and phylogenetic analyses were performed. The 150,454 bp-long J. procumbens cpDNA has a circular and quadripartite structure consisting of a large single copy, a small single copy, and two inverted repeat regions. It contains 133 genes, of which 88 are protein-coding genes, 37 are tRNA genes, and eight are rRNA genes. Twenty-four simple sequence repeats (SSRs) and 81 repeat sequences were identified. Comparative analyses with other Justicieae species revealed that the non-coding regions of J. procumbens cpDNA showed greater variation than did the coding regions. Moreover, phylogenetic analysis based on 14 cpDNA sequences from Justicieae species showed that J. procumbens and J. flava were most closely related. This study provides valuable genetic information to support further research on the genetic diversity and evolutionary development of the tribe Justicieae.

An insight on the complete chloroplast genome of Gomphocarpus siniacus and Duvalia velutina, Asclepiadoideae (Apocynaceae)

Abstract We studied the complete chloroplast genome of Gomphocarpus siniacus and Duvalia velutina from Asclepiadoideae subfamily; due to their medicinal importance and distribution worldwide their interest became high. In this study we analyzed the complete chloroplast genomes of G. siniacus and D. velutina using Illumina sequencing technology. The sequences were compared with the other species from Apocynaceae family. The complete genome of G. siniacus is 162,570 bp while D. velutina has154, 478 bp in length. Both genomes consist of 119 genes; encode 31 tRNA genes, and eight rRNA genes. Comparative studies of the two genomes showed variations in SSR markers in which G. siniacus possesses 223 while D. velutina has 186. This could be used for barcoding in order to aid in easy identification of the species. Phylogenetic analysis on the other hand reaffirms the tribal position of G. siniacus in Asclepiadeae and D. velutina in Ceropegieae. These findings could be used in subsequent research studies of angiosperms identification, genetic engineering, herb genomics and phylogenomic studies of Apocynaceae family.

The complete chloroplast genome and phylogenetic analysis of Acalypha hispida Burm. f. (Euphorbiaceae), an ornamental and medicinal plant

Acalypha hispida Burm. f. (1768) is an evergreen shrub native to New Guinea and the Bismarck Archipelago. Currently, it is widely cultivated as an ornamental and medicinal plant in tropical and subtropical areas worldwide. This study characterized the complete chloroplast genome of A. hispida, which is 172,122 bp in length and consists of large single-copy (LSC) and small single-copy (SSC) regions of 97,025 bp and 19,787 bp, respectively, that are separated by a pair of 27,655 bp inverted repeat (IR) regions. The overall GC content of the genome is 34.22%. The genome contains 131 genes, including 86 protein-coding, 37 tRNA, and eight rRNA genes. Phylogenetic analysis indicates that A. hispida is closely related to Ricinus communis and Cleidiocarpon cavaleriei in the Euphorbiaceae family. The complete chloroplast genome of A. hispida provides genomic resources and potential markers suitable for future species identification and speciation studies of the genus Acalypheae and will also provide important information on the phylogenetic relationships of the Euphorbiaceae family.

Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

BACKGROUND

Justicia L. is the largest genus in Acanthaceae Juss. and widely distributed in tropical and subtropical regions of the world. Previous phylogenetic studies have proposed a general phylogenetic framework for Justicia based on several molecular markers. However, their studies were mainly focused on resolution of phylogenetic issues of Justicia in Africa, Australia and South America due to limited sampling from Asia. Additionally, although Justicia plants are of high medical and ornamental values, little research on its genetics was reported. Therefore, to improve the understanding of its genomic structure and relationships among Asian Justicia plants, we sequenced complete chloroplast (cp.) genomes of 12 Asian plants and combined with the previously published cp. genome of Justicia leptostachya Hemsl. for further comparative genomics and phylogenetic analyses.

RESULTS

All the cp. genomes exhibit a typical quadripartite structure without genomic rearrangement and gene loss. Their sizes range from 148,374 to 151,739 bp, including a large single copy (LSC, 81,434-83,676 bp), a small single copy (SSC, 16,833-17,507 bp) and two inverted repeats (IR, 24,947-25,549 bp). GC contents range from 38.1 to 38.4%. All the plastomes contain 114 genes, including 80 protein-coding genes, 30 tRNAs and 4 rRNAs. IR variation and repetitive sequences analyses both indicated that Justicia grossa C. B. Clarke is different from other Justicia species because its lengths of ndhF and ycf1 in IRs are shorter than others and it is richest in SSRs and dispersed repeats. The ycf1 gene was identified as the candidate DNA barcode for the genus Justicia. Our phylogenetic results showed that Justicia is a polyphyletic group, which is consistent with previous studies. Among them, J. grossa belongs to subtribe Tetramerinae of tribe Justicieae while the other Justicia members belong to subtribe Justiciinae. Therefore, based on morphological and molecular evidence, J. grossa should be undoubtedly recognized as a new genus. Interestingly, the evolutionary history of Justicia was discovered to be congruent with the morphology evolution.

CONCLUSION

Our study not only elucidates basic features of Justicia whole plastomes, but also sheds light on interspecific relationships of Asian Justicia plants for the first time.

Comparitive Analysis of the Chloroplast Genomes of Three Houpoea Plants

The genus Houpoea belongs to the family Magnoliaceae, and the species in this genus have important medicinal values. However, the investigation of the correlation between the evolution of the genus and its phylogeny has been severely hampered by the unknown range of species within the genus and the paucity of research on its chloroplast genome. Thus, we selected three species of Houpoea: Houpoea officinalis var officinalis (OO), Houpoea officinalis var. biloba (OB), and Houpoea rostrata (R). With lengths of 160,153 bp (OO), 160,011 bp (OB), and 160,070 bp (R), respectively, the whole chloroplast genomes (CPGs) of these three Houpoea plants were acquired via Illumina sequencing technology, and the findings were annotated and evaluated. These three chloroplast genomes were revealed by the annotation findings to be typical tetrads. A total of 131, 132, and 120 different genes were annotated. The CPGs of the three species had 52, 47, and 56 repeat sequences, which were primarily found in the ycf2 gene. A useful tool for identifying species is the approximately 170 simple sequence repeats (SSRs) that have been found. The border area of the reverse repetition region (IR) was studied, and it was shown that across the three Houpoea plants, it is highly conservative, with only changes between H. rostrata and the other two plants observed. Numerous highly variable areas (rps3-rps19, rpl32-trnL, ycf1, ccsA, etc.) have the potential to serve as the barcode label for Houpoea, according to an examination of mVISTA and nucleotide diversity (Pi). Phylogenetic relation indicates that Houpoea is a monophyletic taxon, and its genus range and systematic position are consistent with the Magnoliaceae system of Sima Yongkang-Lu Shugang, including five species and varieties of H. officinalis var. officinalis, H. rostrata, H. officinalis var. biloba, Houpoea obovate, and Houpoea tripetala, which evolved and differentiated from the ancestors of Houpoea to the present Houpoea in the above order. This study provides valuable information on the genus Houpoea, enriches the CPG information on Houpoea genus, and provides genetic resources for the further classification of and phylogenetic research on Houpoea.

A Comparative Analysis of the Chloroplast Genomes of Three Lonicera Medicinal Plants

Both Lonicerae japonicae flos and Lonicerae similis flos are important components in traditional Chinese medicine (TCM) with precious medicinal value. However, the absence of studies on their chloroplast genomes and chromatography has considerably hindered the study of their evolutionary and phylogenetic relationships. In this study, the complete chloroplast (cp) genomes of Lonicera acuminata Wall. and Lonicera similis Hemsl. were sequenced using the Illumina sequencing platform and compared with that of Lonicera japonica Thunb., which has been previously reported. Furthermore, the chromatographic fingerprints of the three plants were constructed using HPLC and the content of quality marker (Q-Marker) was calculated. The annotation results showed that the two chloroplast genomes were typical quadripartite structures with lengths of 155,330 bp (L. acuminata) and 155,207 bp (L. similis). A total of 126 different genes were annotated, containing 82 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The expansion and contraction of the inverted repeat (IR) regions suggested that the boundary regions of IR/SC were comparatively conserved in the three species, and six regions (trnH-GUG-psbA, rps2-rpoC2, rbcL-psaI, trnN-GUU-ndhF, rps15-ycf1, and infA) with nucleotide diversity values (Pi) of variable sites higher than 1% were identified. Phylogenetic relation indicated that L. similis had a closer genetic relationship with L. japonica than L. acuminata. Additionally, the chromatographic fingerprints showed that the characteristic peaks of the three medicinal plants were similar, including Neochlorogenic acid, Chlorogenic acid, 4-Dicaffeoylquinic acid, Sweroside, Secoxyloganin, Luteoloside, Isochlorogenic acid A, Isochlorogenic acid B, and Isochlorogenic acid C. The content of chlorogenic acid and total phenolic acid in L. acuminata (7.4633 ± 0.4461%, 14.8953 ± 0.0728%) and L. similis (14.1055 ± 0.2566%, 21.9782 ± 0.1331%) was much higher than that of L. japonica (3.9729 ± 0.0928%, 6.0964 ± 0.1228%), respectively. This study provides appropriate information for species identification, phylogeny, quality assessment, and rational use of three medicinal plants of the genus Lonicera.

Complete chloroplast genome of the desert date (Balanites aegyptiaca (L.) Del. comparative analysis, and phylogenetic relationships among the members of Zygophyllaceae

BACKGROUND

Balanites aegyptiaca (L.) Delile, commonly known as desert date, is a thorny evergreen tree belonging to the family Zygophyllaceae and subfamily Tribuloideae that is widespread in arid and semiarid regions. This plant is an important source of food and medicines and plays an important role in conservation strategies for restoring degraded desert ecosystems.

RESULTS

In the present study, we sequenced the complete plastome of B. aegyptiaca. The chloroplast genome was 155,800 bp, with a typical four-region structure: a large single copy (LSC) region of 86,562 bp, a small single copy (SSC) region of 18,102 bp, and inverted repeat regions (IRa and IRb) of 25,568 bp each. The GC content was 35.5%. The chloroplast genome of B. aegyptiaca contains 107 genes, 75 of which coding proteins, 28 coding tRNA, and 4 coding rRNA. We did not observe a large loss in plastid genes or a reduction in the genome size in B. aegyptiaca, as found previously in some species belonging to the family Zygophyllaceae. However, we noticed a divergence in the location of certain genes at the IR-LSC and IR-SSC boundaries and loss of ndh genes relative to other species. Furthermore, the phylogenetic tree constructed from the complete chloroplast genome data broadly supported the taxonomic classification of B. aegyptiaca as belonging to the Zygophyllaceae family. The plastome of B. aegyptiaca was found to be rich in single sequence repeats (SSRs), with a total of 240 SSRs.

CONCLUSIONS

The genomic data available from this study could be useful for developing molecular markers to evaluate population structure, investigate genetic variation, and improve production programs for B. aegyptiaca. Furthermore, the current data will support future investigation of the evolution of the family Zygophyllaceae.

Gene Losses and Plastome Degradation in the Hemiparasitic Species Plicosepalus acaciae and Plicosepalus curviflorus: Comparative Analyses and Phylogenetic Relationships among Santalales Members

The Plicosepalus genus includes hemiparasitic mistletoe and belongs to the Loranthaceae family, and it has several medicinal uses. In the present study, we sequenced the complete plastomes of two species, Plicosepalus acaciae and Plicosepalus curviflorus, and compared them with the plastomes of photosynthetic species (hemiparasites) and nonphotosynthetic species (holoparasites) in the order Santalales. The complete chloroplast genomes of P. acaciae and P. curviflorus are circular molecules with lengths of 120,181 bp and 121,086 bp, respectively, containing 106 and 108 genes and 63 protein-coding genes, including 25 tRNA and 4 rRNA genes for each species. We observed a reduction in the genome size of P. acaciae and P. curviflorus and the loss of certain genes, although this reduction was less than that in the hemiparasite and holoparasitic cp genomes of the Santalales order. Phylogenetic analysis supported the taxonomic state of P. acaciae and P. curviflorus as members of the family Loranthaceae and tribe Lorantheae; however, the taxonomic status of certain tribes of Loranthaceae must be reconsidered and the species that belong to it must be verified. Furthermore, available chloroplast genome data of parasitic plants could help to strengthen efforts in weed management and encourage biotechnology research to improve host resistance.

Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species

BACKGROUND

The large genus Ficus comprises approximately 800 species, most of which possess high ornamental and ecological values. However, its evolutionary history remains largely unknown. Plastome (chloroplast genome) analysis had become an essential tool for species identification and for unveiling evolutionary relationships between species, genus and other rank groups. In this work we present the plastomes of ten Ficus species.

RESULTS

The complete chloroplast (CP) genomes of eleven Ficus specimens belonging to ten species were determined and analysed. The full length of the Ficus plastome was nearly 160 kbp with a similar overall GC content, ranging from 35.88 to 36.02%. A total of 114 unique genes, distributed in 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, were annotated in each of the Ficus CP genome. In addition, these CP genomes showed variation in their inverted repeat regions (IR). Tandem repeats and mononucleotide simple sequence repeat (SSR) are widely distributed across the Ficus CP genome. Comparative genome analysis showed low sequence variability. In addition, eight variable regions to be used as potential molecular markers were proposed for future Ficus species identification. According to the phylogenetic analysis, these ten Ficus species were clustered together and further divided into three clades based on different subgenera. Simultaneously, it also showed the relatedness between Ficus and Morus.

CONCLUSION

The chloroplast genome structure of 10 Ficus species was similar to that of other angiosperms, with a typical four-part structure. Chloroplast genome sizes vary slightly due to expansion and contraction of the IR region. And the variation of noncoding regions of the chloroplast genome is larger than that of coding regions. Phylogenetic analysis showed that these eleven sampled CP genomes were divided into three clades, clustered with species from subgenus Urostigma, Sycomorus, and Ficus, respectively. These results support the Berg classification system, in which the subgenus Ficus was further decomposed into the subgenus Sycomorus. In general, the sequencing and analysis of Ficus plastomes, especially the ones of species with no or limited sequences available yet, contribute to the study of genetic diversity and species evolution of Ficus, while providing useful information for taxonomic and phylogenetic studies of Ficus.

Comparative Analysis and Phylogenetic Relationships of Ceriops Species (Rhizophoraceae) and Avicennia lanata (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests

Ceriops and Avicennia are true mangroves in the middle and seaward zones of mangrove forests, respectively. The chloroplast genomes of Ceriops decandra, Ceriops zippeliana, and Ceriops tagal were assembled into lengths of 166,650, 166,083 and 164,432 bp, respectively, whereas Avicennia lanata was 148,264 bp in length. The gene content and gene order are highly conserved among these species. The chloroplast genome contains 125 genes in A. lanata and 129 genes in Ceriops species. Three duplicate genes (rpl2, rpl23, and trnM-CAU) were found in the IR regions of the three Ceriops species, resulting in expansion of the IR regions. The rpl32 gene was lost in C. zippeliana, whereas the infA gene was present in A. lanata. Short repeats (<40 bp) and a lower number of SSRs were found in A. lanata but not in Ceriops species. The phylogenetic analysis supports that all Ceriops species are clustered in Rhizophoraceae and A. lanata is in Acanthaceae. In a search for genes under selective pressures of coastal environments, the rps7 gene was under positive selection compared with non-mangrove species. Finally, two specific primer sets were developed for species identification of the three Ceriops species. Thus, this finding provides insightful genetic information for evolutionary relationships and molecular markers in Ceriops and Avicennia species.

Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution

BACKGROUND

The large and diverse Coffeeae alliance clade of subfamily Ixoroideae (Rubiaceae) consists of 10 tribes, > 90 genera, and > 2000 species. Previous molecular phylogenetics using limited numbers of markers were often unable to fully resolve the phylogenetic relationships at tribal and generic levels. Also, the structural variations of plastomes (PSVs) within the Coffeeae alliance tribes have been poorly investigated in previous studies. To fully understand the phylogenetic relationships and PSVs within the clade, highly reliable and sufficient sampling with superior next-generation analysis techniques is required. In this study, 71 plastomes (40 newly sequenced and assembled and the rest from the GenBank) were comparatively analyzed to decipher the PSVs and resolve the phylogenetic relationships of the Coffeeae alliance using four molecular data matrices.

RESULTS

All plastomes are typically quadripartite with the size ranging from 153,055 to 155,908 bp and contained 111 unique genes. The inverted repeat (IR) regions experienced multiple contraction and expansion; five repeat types were detected but the most abundant was SSR. The size of the Coffeeae alliance clade plastomes and its elements are affected by the IR boundary shifts and the repeat types. However, the emerging PSVs had no taxonomic and phylogenetic implications. Eight highly divergent regions were identified within the plastome regions ndhF, ccsA, ndhD, ndhA, ndhH, ycf1, rps16-trnQ-UUG, and psbM-trnD. These highly variable regions may be potential molecular markers for further species delimitation and population genetic analyses for the clade. Our plastome phylogenomic analyses yielded a well-resolved phylogeny tree with well-support at the tribal and generic levels within the Coffeeae alliance.

CONCLUSIONS

Plastome data could be indispensable in resolving the phylogenetic relationships of the Coffeeae alliance tribes. Therefore, this study provides deep insights into the PSVs and phylogenetic relationships of the Coffeeae alliance and the Rubiaceae family as a whole.

Characterization and comparative analysis of the plastome sequence from Justicia ventricosa (Lamiales: Acanthaceae)

Justicia ventricosa is a characteristic ethnic herb commonly used to treat Orthopedic pains. Here, to confirm its phylogenetic position and to develop molecular markers that can distinguish different Justicia species, we obtained and analyzed the plastome of Justicia ventricosa. The plastome was sequenced using the Illumina HiSeq sequencing platform, assembled with NOVOPlasty, and annotated with CPGAVAS2. The genome has a circular structure of 149,700 bp, containing a large single-copy region of 82,324 bp, a small single-copy region of 17,260 bp, and two reverse repeat regions of 25,058 bp each. It encodes 112 unique genes, including 76 protein-coding genes, eight ribosomal RNA genes, and 28 transfer RNA genes. Twenty cis-splicing genes were found. In total, we predicted 19 microsatellite repeats and 13 tandem repeat sequences. For distributed repeats, four were palindrome repeats and five were direct repeats. To find the highly variable intergenic spacer (IGS) regions, we calculated the K2P distances for IGS regions from four Justicia species. The K2P values ranged from 6.11 to 57.82. The largest K2P distances were found for ccsA-ndhD, petB-petD, psbK-psbI, and ycf4-cemA. Phylogenetic analysis results showed that J. ventricosa was most closely related to J. leptostachya. To determine how Justicia species adapt to the environment, we performed selection pressure analysis. Nine genes were found to have undergone positive selection. Lastly, we performed a genome-wise DNA barcode prediction, seven pairs of primers were found. The results provide valuable information that can be used for molecular marker development and bioprospecting in Justicia species.

Peculiarities of the inverted repeats in the complete chloroplast genome of Strobilanthes bantonensis Lindau

Strobilanthes bantonensis Lindau belongs to the family Acanthaceae. It is an antiviral herb that can be used to prevent Influenza virus infections in the border areas between China and Vietnam. Local people call it ‘Purple Ban-lan-gen’ because its root is very similar to that of Strobilanthes cusia (Nees) Kuntze, which is called ‘Southern Ban-lan-gen’ and is listed in Chinese Pharmacopeia. The two species have been used interchangeably locally. However, their pharmacological equivalence has caused concern for years. We have sequenced the chloroplast genome of S. cusia previously. In this study, we sequenced the complete chloroplast genome sequence of S. bantonensis to preform in-depth comparative genetic analysis of the two Strobilanthes species. The chloroplast genome of S. bantonensis is a circular DNA molecule with a total length of 144,591 bp and encodes 84 protein-coding, 8 ribosomes, and 37 transfer RNA genes. The chloroplast genome has a conservative quadripartite structure, including a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeat (IR) regions, with lengths of 92,068 bp, 17,767 bp, and 17,378 bp, respectively. Phylogenetic analysis confirmed that S. bantonensis is closely related to the S. cusia. Compared with other species from Acanthaceae, S. bantonensis has a significantly shortened IR region, suggesting the occurrence of IR contraction events. This study will help future taxonomic, evolutionary, phylogenetic, and bioprospecting studies of the sizeable Strobilanthes genus, which contains over 400 species.

Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

Avicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its comparison with related species in family Acanthaceae. Detailed next-generation sequencing and analysis showed a complete chloroplast genome of 150,279 bp, comprising 38.6% GC. Genome architecture is quadripartite revealing large single copy (82,522 bp), small single copy (17,523 bp), and pair of inverted repeats (25,117 bp). Furthermore, the genome contains 132 different genes, including 87 protein-coding genes, 8 rRNA, 37 tRNA genes, and 126 simple sequence repeats (122 mononucleotide, 2 dinucleotides, and 2 trinucleotides). Interestingly, about 25 forward, 15 reversed and 14 palindromic repeats were also found in the A. marina. High degree synteny was observed in the pairwise alignment with related genomes. The chloroplast genome comparative assessment showed a high degree of sequence similarity in coding regions and varying divergence in the intergenic spacers among ten Acanthaceae species. The pairwise distance showed that A. marina exhibited the highest divergence (0.084) with Justicia flava and showed lowest divergence with Aphelandra knappiae (0.059). Current genomic datasets are a valuable resource for investigating the population and evolutionary genetics of family Acanthaceae members' specifically A. marina and related species.

Comparative analyses of chloroplast genomes from 13 Lagerstroemia (Lythraceae) species: identification of highly divergent regions and inference of phylogenetic relationships

Seven divergence hotspots as plastid markers for DNA barcoding was selected, and the phylogeny of 13 Lagerstroemia species based on the cp genome data was reconstructed within Myrtales. The Lagerstroemia species used in this study originated in China and have high economic and ecological value. The shared interspecific morphological characteristics and intraspecific morphological variation resulting from hybridization among Lagerstroemia taxa have made resolving their classification problems and phylogenetic relationships difficult. Systematic comparative genomic analysis has been shown to resolve phylogenetic relationships. We sequenced and annotated 6 Lagerstroemia cp genomes (Lagerstroemia excelsa, Lagerstroemia limii, Lagerstroemia siamica, Lagerstroemia tomentosa, Lagerstroemia venusta, and Lagerstroemia calyculata) for the first time and combined them with previously published genomes for Lagerstroemia species. Bioinformatics was used to analyse the 13 cp genomes in terms of gene structure and organization, codon usage, contraction and expansion of inverted repeat regions, repeat structure, divergence hotspots, species pairwise Ka/Ks ratios and phylogenetic relationships. The length varied between 152,049 bp in Lagerstroemia subcostata and 152,521 bp in L. venusta. We selected seven divergence hotspots in the cp genomes that had the potential to act as plastid markers to distinguish Lagerstroemia species. The phylogenetic relationships within Myrtales inferred from the cp genomes of 13 Lagerstroemia species and 27 other Myrtales species were highly supported, which illustrated several novel relationships within Myrtales. Taken together, our results provide comprehensive chloroplast genomic resources, which can be used further for species identification and molecular breeding of Lagerstroemia species.

Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae

Paphiopedilum delenatii is a native orchid of Vietnam with highly attractive floral traits. Unfortunately, it is now listed as a critically endangered species with a few hundred individuals remaining in nature. In this study, we performed next-generation sequencing of P. delenatii and assembled its complete chloroplast genome. The whole chloroplast genome of P. delenatii was 160,955 bp in size, 35.6% of which was GC content, and exhibited typical quadripartite structure of plastid genomes with four distinct regions, including the large and small single-copy regions and a pair of inverted repeat regions. There were, in total, 130 genes annotated in the genome: 77 coding genes, 39 tRNA genes, 8 rRNA genes, and 6 pseudogenes. The loss of ndh genes and variation in inverted repeat (IR) boundaries as well as data of simple sequence repeats (SSRs) and divergent hotspots provided useful information for identification applications and phylogenetic studies of Paphiopedilum species. Whole chloroplast genomes could be used as an effective super barcode for species identification or for developing other identification markers, which subsequently serves the conservation of Paphiopedilum species.