Chloroplast genome structure in Ilex (Aquifoliaceae)

Comparative and Phylogenetic Analysis of the Chloroplast Genomes of Four Wild Species of the Genus Prunus

BACKGROUND

Prunus armeniaca, Prunus divaricata, Prunus tianshanica, and Prunus domestica are valuable ancient tree species that have persisted since the end of the Tertiary period within the Tianshan wild fruit forest. However, the evolutionary relationships among Prunus species in the Tianshan wild fruit forest have long posed a challenge.

METHODS

We sequenced and assembled the chloroplast genomes of P. armeniaca, P. divaricata, and P. tianshanica, and incorporated the chloroplast genome data of P. domestica for comparative analysis to elucidate their phylogenetic positions within the genus Prunus.

RESULTS

The lengths of these chloroplast genomes ranged from 157,395 bp to 158,090 bp, with a total of 130 to 131 genes annotated, comprising 85 to 86 protein-coding genes, 8 rRNA genes, and 35 to 36 tRNA genes. Notably, the four wild Prunus species predominantly used high-frequency codons ending in A/U. Additionally, we identified 300 simple repetitive sequences and 166 long repetitive sequences across the four wild Prunus species. The mutation sites were mainly found in the non-coding regions, with seven regions of high mutation frequency identified. The phylogenetic tree revealed five branches: subgenus Armeniaca, subgenus Microcerasus, subgenus Prunus, subgenus Amygdalus, and subgenus Cerasus. The estimated deviation time for the crown group of Prunus is roughly 61.41 million years ago.

CONCLUSIONS

This study provides exhaustive genetic evidence for the classification and systematic relationships of the four wild Prunus species and establishes a crucial foundation for subsequent research into the diversity and evolutionary history of the Prunus genus.

The complete chloroplast genomes and comparative study of the two tung trees of Vernicia (Euphorbiaceae)

BACKGROUND

Vernicia montana and V. fordii are economically important woody oil species in the Euphorbiaceae that have great industrial oil and ornamental greening properties, however, the wild resources of Vernicia trees have been reduced because of their habitat destruction. Considering the diverse economic and ecological importance of Vernicia species, it is important to collect more molecular data to determine the genetic differences between V. montana and V. fordii.

RESULTS

We sequenced, assembled, and annotated the complete chloroplast (CP) genome of two tung trees based on the genome skimming approach. The whole CP genomes of V. montana and V. fordii were 163,518 bp and 161,495 bp in length, both including a pair of inverted repeats separated by a large single-copy and a small single-copy region. We detected a total number of 311 tandem repeats, 100 dispersed repeats, and 255 simple repeats from V. montana and V. fordii CP genomes. The mean value of nucleotide diversity between the two species was 0.0122, and the average Ka/Ks ratio across all coding genes was 0.3483. Comparative chloroplast genome analysis showed that the coding regions were more conserved than the non-coding regions. The phylogenetic relationships yielded by the complete genome sequences showed that V. montana was closely related to V. fordii and is considered as a sister group.

CONCLUSIONS

We sequenced, assembled, annotated, and analyzed the CP genome of two tung trees, which will be useful in investigating the conservation genetics and potential breeding applications of this oil shrub.

Genomic Variability Survey in Ilex aquifolium L., with Reference to Four Insular Populations from Eastern Europe

Cosmopolitan in the western areas of Europe as well as on other continents, the Ilex genus is interesting for its genetic, phenotypic, and biogeographic variabilities. Its insular/local distribution, according to existing data on the periphery of the central and southern European areas, represents a suitable case study with reference to the adaptive plasticity or acclimatization of the Ilex aquifolium L. species to new climatic conditions. The aim of the present study was to analyze the genetic variability at the genome level in four insular populations of Ilex aquifolium L., i.e., in three spontaneous populations from Romania (RO), Serbia (SR), and Bulgaria (BG) and a cultivated population from Hungary (HU). According to the obtained results, the most genetically similar populations among the four considered in this study were those from SR and RO. Genetic variation overlapped genes that were generally associated with metabolic regulation/transport factors, water, and abiotic stress factors. The analysis of single-nucleotide polymorphisms (SNPs) at the levels of the chloroplast and mitochondrion, from the point of view of their distributions at the gene level, identified two clusters: one that includes the native populations (BG, SR, and RO) and a second one including the cultured population from HU.

First indisputable fossil Ilex (Aquifoliales: Aquifoliaceae) flower found in Baltic amber

The genus Ilex (holly) in the monotypic family Aquifoliaceae contains more than 600 species distributed worldwide. Pollen fossils and macrofossils of fruits of Ilex are known from the late Cretaceous (90 Ma) and verified leaves from the upper Miocene (10 Ma), but until now only a few more or less incomplete flower fossils have been suggested as referable to this genus. This paper reviews the fossil flowers earlier attributed to Ilex and presents a complete and indisputable staminate Ilex flower from Baltic amber (34-38 Ma) examined in detail with synchrotron X-ray tomography. This finding may challenge the hypothesis of late Neogene dispersal of the genus from a center of origin in subtropical East Asia.

Comparative analysis of chloroplast genomes in ten holly (Ilex) species: insights into phylogenetics and genome evolution

In order to clarify the chloroplast genomes and structural features of ten Ilex species and provide insights into the phylogeny and genome evolution of the genus Ilex, we conducted a comparative analysis of chloroplast genomes using bioinformatics methods. The chloroplast genomes of ten Ilex species were obtained, and their structural features and variations were compared. The results indicated that all chloroplast genomes in the genus Ilex exhibit a double-stranded circular structure, with sizes ranging from 157,356 to 158,018 bp, showing minimal differences in size. The chloroplast genomes of the ten Ilex species have a relatively conservative gene count, with a total of 134 to 135 genes, including 88 or 89 protein-coding genes, and a conserved number of 8 rRNA genes. Each chloroplast genome contains 3 to 123 SSR (Simple Sequence Repeat) sites, predominantly composed of mononucleotide and trinucleotide repeats, with no detection of pentanucleotide or hexanucleotide repeats. The variation in dispersed repeat sequences among Ilex species is minimal, with a total repeat sequence number ranging from 1 to 14, concentrated in the length range of 30 to 42 base pairs. The expansion and contraction of chloroplast genome boundaries among Ilex species are relatively stable, with only minor variations observed in individual species. Variations in non-coding regions are more pronounced than those in coding regions, with the variability in the Large Single Copy region (LSC) being the highest, while the variability in the Inverted Repeat region A (IRa) is the lowest. The divergence time among Ilex species was estimated using the MCMC-tree module, revealing the evolutionary relationships among these species, their common ancestors, and their differentiation throughout the evolutionary process. The research findings provide a valuable reference for the systematic study and molecular marker development of Ilex plants.

The complete chloroplast genome sequences of six Hylotelephium species: Comparative genomic analysis and phylogenetic relationships

To evaluate the phylogenetic relationships between Hylotelephium and Orostachys, and to provide important information for further studies, we analyzed the complete chloroplast genomes of six Hylotelephium species and compared the sequences to those of published chloroplast genomes of congeneric species and species of the closely related genus, Orostachys. The total chloroplast genome length of nineteen species, including the six Hylotelephium species analyzed in this study and the thirteen Hylotelephium and Orostachys species analyzed in previous studies, ranged from 150,369 bp (O. minuta) to 151,739 bp (H. spectabile). Their overall GC contents were almost identical (37.7-37.8%). The chloroplast genomes of the nineteen species contained 113 unique genes comprising 79 protein-coding genes (PCGs), 30 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). Among the annotated genes, fourteen genes contained one intron, and two genes contained two introns. The chloroplast genomes of the nineteen Hylotelephium and Orostachys species had identical structures. Additionally, the large single copy (LSC), inverted repeat (IR), and small single copy (SSC) junction regions were conserved in the Hylotelephium and Orostachys species. The nucleotide diversity between the Hylotelephium chloroplast genomes was extremely low in all regions, and only one region showed a high Pi value (>0.03). In all nineteen chloroplast genomes, six regions had a high Pi value (>0.03). The phylogenetic analysis showed that the genus delimitation could not be clearly observed even in this study because Hylotelephium formed a paraphyly with subsect. Orostachys of the genus Orostachys. Additionally, the data supported the taxonomic position of Sedum taqeutii, which was treated as a synonym for H. viridescens in previous studies, as an independent taxon.

Chloroplast genome analysis of three Acanthus species reveal the adaptation of mangrove to intertidal habitats

Acanthus is a distinctive genus that covers three species with different ecological niches including Acanthus mollis (arid terrestrial), Acanthus leucostachyus (damp forest) and Acanthus ilicifolius (coastal intertidal). It is an intriguing question how these species evolved from terrestrial to coastal intertidal. In the present study, we assembled chloroplast genomes of A. ilicifolius, A. leucostachyus and A. mollis, which exhibited typical quadripartite structures. The sizes were 150,758, 154,686 and 150,339 bp that comprised a large single copy (LSC, 82,963, 86,461 and 82,612 bp), a small single copy (SSC, 17,191, 17,511 and 17,019 bp), and a pair of inverted repeats (IRs, 25,302, 25,357 and 25,354 bp), respectively. Gene annotation revealed that A. ilicifolius, A. leucostachyus and A. mollis contained 113, 112 and 108 unique genes, each of which contained 79, 79 and 74 protein-coding genes, 30, 29 and 30 tRNAs, and 4 rRNA genes, respectively. Differential gene analysis revealed plenty of ndhs gene deletions in the terrestrial plant A. mollis. Nucleotide diversity analysis showed that the psbK, ycf1, ndhG, and rpl22 have the highest nucleotide variability. Compared to A. leucostachyus and A. mollis, seven genes in A. ilicifolius underwent positive selection. Among them, the atpF gene showed a strong positive selection throughout terrestrial to marine evolution and was important for adaptation to coastal intertidal habitats. Phylogenetic analysis indicated that A. ilicifolius has a closer genetic relationship with A. leucostachyus than A. mollis which further confirmed the evolutionary direction of Acanthus going from terrestrial to coastal intertidal zones.

The complete chloroplast genome sequences of three lilies: genome structure, comparative genomic and phylogenetic analyses

We sequenced and analyzed the complete chloroplast genomes of Lilium amoenum, Lilium souliei, and Nomocharis forrestii in detail, including the first sequence and structural comparison of Nomocharis forrestii. We found that the lengths and nucleotide composition of the three chloroplast genes showed little variation. The chloroplast genomes of the three Lilium species contain 87 protein coding genes (PCGs), 38 tRNAs, and 8 rRNA genes. The only difference is that Nomocharis forrestii had an additional infA pseudogene. In the sequence analysis of the Lilium chloroplast genomes, 216 SSRs, 143 pairs of long repeats, 571 SNPs, and 202 indels were detected. In addition, we identified seven hypervariable regions that can be used as potential molecular markers and DNA barcodes of Lilium through complete sequence alignment. The phylogenetic tree was constructed from the three chloroplast genome sequences of Lilium obtained here and 40 chloroplast genome sequences from the NCBI database (including 35 Lilium species, 4 Fritillaria species, and one species of Smilax). The analysis showed that the species clustering of the genus Lilium essentially conformed to the classical morphological classification system of Comber, but differences in the classification of individual species remained. In our report, we support the reclassification of Lilium henryi and Lilium rosthorniiy in the genus Lilium. In general, this study not only provides genome data for three Lilium species, but also provides a comparative analysis of the Lilium chloroplast genomes. These advances will help to identify Lilium species, clarify the phylogenetic analysis of the Lilium genus, and help to solve and improve the disputes and deficiencies in the traditional morphological classification.

Characterization of the complete chloroplast genome sequence of Elaeagnus henryi Warb. ex Diels (Elaeagnaceae)

Elaeagnus henryi Warb. ex Diels belongs to the Elaeagnaceae. Here, we reveal the complete chloroplast genome of Elaeagnus henryi. The complete chloroplast genome is 152,244 bp in length and contains a large single-copy (LSC) region of 82,235 bp, a small single-copy (SSC) region of 18,279 bp and a pair of inverted repeats (IRs) of 25,865 bp. There are 126 genes, including 81 protein-coding, 37 transfer RNA (tRNA), and eight ribosomal RNA (rRNA) genes. The total GC content of the chloroplast genome sequence is 37.1%. The maximum-likelihood phylogenetic analysis indicated that E. henryi was sister to Elaeagnus pungens (MW145133). The result may be because the species are advanced and developed from the same ancestor.

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.

Taxonomy, comparative genomics of Mullein (Verbascum, Scrophulariaceae), with implications for the evolution of Verbascum and Lamiales

BACKGROUND

The genus Verbascum L. (Scrophulariaceae) is distributed in Africa, Europe, and parts of Asia, with the Mediterranean having the most species variety. Several researchers have already worked on the phylogenetic and taxonomic analysis of Verbascum by using ITS data and chloroplast genome fragments and have produced different conclusions. The taxonomy and phylogenetic relationships of this genus are unclear.

RESULTS

The complete plastomes (cp) lengths for V. chaixii, V. songaricum, V. phoeniceum, V. blattaria, V. sinaiticum, V. thapsus, and V. brevipedicellatum ranged from 153,014 to 153,481 bp. The cp coded 114 unique genes comprising of 80 protein-coding genes, four ribosomal RNA (rRNA), and 30 tRNA genes. We detected variations in the repeat structures, gene expansion on the inverted repeat, and single copy (IR/SC) boundary regions. The substitution rate analysis indicated that some genes were under purifying selection pressure. Phylogenetic analysis supported the sister relationship of (Lentibulariaceae + Acanthaceae + Bignoniaceae + Verbenaceae + Pedaliaceae) and (Lamiaceae + Phyrymaceae + Orobanchaceae + Paulowniaceae + Mazaceae) in Lamiales. Within Scrophulariaceae, Verbascum was sister to Scrophularia, while Buddleja formed a monophyletic clade from (Scrophularia + Verbascum) with high bootstrap support values. The relationship of the nine species within Verbascum was highly supported.

CONCLUSION

Based on the phylogenetic results, we proposed to reinstate the species status of V. brevipedicellatum (Engl.) Hub.-Mor. Additionally, three genera (Mazus, Lancea, and Dodartia) placed in the Phyrymaceae family formed a separate clade within Lamiaceae. The classification of the three genera was supported by previous studies. Thus, the current study also suggests the circumscription of these genera as documented previously to be reinstated. The divergence time of Lamiales was approximated to be 86.28 million years ago (Ma) (95% highest posterior density (HPD), 85.12-89.91 Ma). The complete plastomes sequence data of the Verbascum species will be important for understanding the Verbascum phylogenetic relationships and evolution in order Lamiales.

The complete chloroplast genome of ornamental and medicinal Callerya dielsiana (Fabaceae)

Callerya dielsiana is a Chinese endemic tropical/subtropical liana. We sequenced the complete chloroplast genome with the Illumina Hiseq X-Ten platform. The genome is obtained with 132,301 bp in length, lacking an inverted repeat (IR) region, contains 4 rRNAs, 30 tRNAs genes, and 76 protein-coding genes. The overall GC content is 33.9%. Based on the whole chloroplast genomes of 14 legume species, a phylogenetic tree is constructed and indicated that C. dielsiana belongs to the well-supported tribe Wisterieae. The tribe is sister to Glycyrrhiza and nested within the IRLC (Inverted Repeat-Lacking Clade) group of the subfamily Papilionoideae (Fabaceae).

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.

Complete chloroplast genome of Ilex dabieshanensis: Genome structure, comparative analyses with three traditional Ilex tea species, and its phylogenetic relationships within the family Aquifoliaceae

Ilex dabieshanensis K. Yao & M. B. Deng is not only a highly valued tree species for landscaping, it is also a good material for making kuding tea due to its anti-inflammatory and lipid-lowering medicinal properties. Utilizing next-generation and long-read sequencing technologies, we assembled the whole chloroplast genome of I. dabieshanensis. The genome was 157,218 bp in length, exhibiting a typical quadripartite structure with a large single copy (LSC: 86,607 bp), a small single copy (SSC: 18,427 bp) and a pair of inverted repeat regions (IRA and IRB: each of 26,092 bp). A total of 121 predicted genes were encoded, including 113 distinctive (79 protein-coding genes, 30 tRNAs, and 4 rRNAs) and 8 duplicated (8 protein-coding genes) located in the IR regions. Overall, 132 SSRs and 43 long repeats were detected and could be used as potential molecular markers. Comparative analyses of four traditional Ilex tea species (I. dabieshanensis, I. paraguariensis, I. latifolia and I. cornuta) revealed seven divergent regions: matK-rps16, trnS-psbZ, trnT-trnL, atpB-rbcL, petB-petD, rpl14-rpl16, and rpl32-trnL. These variations might be applicable for distinguishing different species within the genus Ilex. Phylogenetic reconstruction strongly suggested that I. dabieshanensis formed a sister clade to I. cornuta and also showed a close relationship to I. latifolia. The generated chloroplast genome information in our study is significant for Ilex tea germplasm identification, phylogeny and genetic improvement.

Chromosomal level genome of Ilex asprella and insight into antiviral triterpenoid pathway

Ilex asprella is a widely used herbs in Traditional Chinese Medicine for treating viral infection and relieving inflammation. Due to the earlier fruiting period of I. asprella, it is the major food source for frugivores in summer. Despite its pharmacological and ecological importance, a reference genome for I. asprella is lacking. By using Illumina, stLFR and Omni-C sequencing data, we present the first chromosomal-level assembly for I. asprella. The genome assembly size is 804 Mbp, with Benchmarking Universal Single-Copy Orthologs (BUSCO) score 94.4% for eudicotyledon single copy genes. Transcriptomes of leaves, stems, flowers, premature fruits and roots were analyzed, providing 39,215 gene models. The complete set of genes involved in the triterpenoids production is disclosed for the first time. We have also found the oxidosqualene cyclases (OSCs), CYP716s and UDP-glycosyltransferases (UGTs), which are responsible for the modification of triterpenoid backbones, resulting in the high variety of triterpenoid saponins.

Complete chloroplast genome sequence and phylogenetic analysis of Ilex × attenuata 'Fosteri' (Aquifoliaceae)

Ilex × attenuata ‘Fosteri’ is an important ornamental plant widely distributed in mid-southern China and south-eastern United States. In this study, we assembled the complete chloroplast (cp) genome of I. attenuata by high-throughput sequencing and bioinformatics. The full length of cp genome was 157,833 bp with 37.63% overall GC content, which contained two inverted repeats (IR) of 26,093 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 87,188 bp and 18,459 bp, respectively. The cp genome contained 135 genes, including 88 protein-coding genes, 8 rRNA genes and 39 tRNA genes. Phylogenetic tree showed that the close relationship of three species of Ilex (I. attenuata, I. viridis and I. szechwanensis) in the Aquifoliaceae family.

New Insight into the Phylogeny and Taxonomy of Cultivated and Related Species of Crataegus in China, Based on Complete Chloroplast Genome Sequencing

Hawthorns (Crataegus L.) are one of the most important processing and table fruits in China, due to their medicinal properties and health benefits. However, the interspecific relationships and evolution history of cultivated Crataegus in China remain unclear. Our previously published data showed C. bretschneideri may be derived from the hybridization of C. pinnatifida with C. maximowiczii, and that introgression occurs between C. hupehensis, C. pinnatifida, and C. pinnatifida var. major. In the present study, chloroplast sequences were used to further elucidate the phylogenetic relationships of cultivated Crataegus native to China. The chloroplast genomes of three cultivated species and one related species of Crataegus were sequenced for comparative and phylogenetic analyses. The four chloroplast genomes of Crataegus exhibited typical quadripartite structures and ranged from 159,607 bp (C. bretschneideri) to 159,875 bp (C. maximowiczii) in length. The plastomes of the four species contained 113 genes consisting of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Six hypervariable regions (ndhC-trnV(UAC)-trnM(CAU), ndhA, atpH-atpI, ndhF, trnR(UCU)-atpA, and ndhF-rpl32), 196 repeats, and a total of 386 simple sequence repeats were detected as potential variability makers for species identification and population genetic studies. In the phylogenomic analyses, we also compared the entire chloroplast genomes of three published Crataegus species: C. hupehensis (MW201730.1), C. pinnatifida (MN102356.1), and C. marshallii (MK920293.1). Our phylogenetic analyses grouped the seven Crataegus taxa into two main clusters. One cluster included C. bretschneideri, C. maximowiczii, and C. marshallii, whereas the other included C. hupehensis, C. pinnatifida, and C. pinnatifida var. major. Taken together, our findings indicate that C. maximowiczii is the maternal origin of C. bretschneideri. This work provides further evidence of introgression between C. hupehensis, C. pinnatifida, and C. pinnatifida var. major, and suggests that C. pinnatifida var. major might have been artificially selected and domesticated from hybrid populations, rather than evolved from C. pinnatifida.

Characterization of the complete chloroplast genome of Ilex crenata Thunb. (Aquifoliaceae)

Ilex crenata Thunb. is a species of Aquifoliaceae with high ornamental and ecological values. In this study, the complete chloroplast (cp) genome of I. crenata was assembled and characterized through Illumina sequencing data. The entire cp genome of I. crenata was 157,988 bp in length with 37.64% overall GC content, containing a large single-copy (LSC) region of 87,414 bp and a small single-copy (SSC) region of 18,422 bp, which were separated by a pair of 26,076 bp inverted repeat (IR) regions. A total of 135 genes were annotated, including 88 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 78 conserved protein-coding genes demonstrated that I. crenata is closely related to I. viridis and I. szechwanensis.

Phylogenetic position of Bupleurum sikangense inferred from the complete chloroplast genome sequence

Bupleurum sikangense is an endemic species to China distributed in Xizang (Tibet), which has high saikosaponin content and potential medicinal value. Morphologically, it extremely resembles B. commelynoideum. In order to get a better understanding of the relationship between B. sikangense and B. commelynoideum, and on the phylogenetic status of the two species in the genus, the complete chloroplast (cp) genomes of them were sequenced. The genome organization, repeat sequences, codon usage, RNA-editing sites, and variation of their cp genomes revealed high similarity between the species. Some highly variable regions like trnK-UUU_rps16, rps16_trnQ-UUG, ndhC_trnV-UAC, petA_psbJ, accD_psaI, and petL_psbE were identified, providing potential molecular markers for differentiating the two species. Phylogenetic analysis indicated that B. commelynoideum has a closer relationship to B. chinese than that to B. sikangense. Overall, this study will not only improve our knowledge about cp genomes of these two species, and but also provide data for further research on species identification, safe medical application, conservation genetics, etc., of Bupleurum plants.

Screening and verification of extranuclear genetic markers in green tide algae from the Yellow Sea

Over the past decade, Ulva compressa, a cosmopolitan green algal species, has been identified as a component of green tides in the Yellow Sea, China. In the present study, we sequenced and annotated the complete chloroplast genome of U. compressa (alpha-numeric code: RD9023) and focused on the assessment of genome length, homology, gene order and direction, intron size, selection strength, and substitution rate. We compared the chloroplast genome with the mitogenome. The generated phylogenetic tree was analyzed based on single and aligned genes in the chloroplast genome of Ulva compared to mitogenome genes to detect evolutionary trends. U. compressa and U. mutabilis chloroplast genomes had similar gene queues, with individual genes exhibiting high homology levels. Chloroplast genomes were clustered together in the entire phylogenetic tree and shared several forward/palindromic/tandem repetitions, similar to those in U. prolifera and U. linza. However, U. fasciata and U. ohnoi were more divergent, especially in sharing complementary/palindromic repetitions. In addition, phylogenetic analyses of the aligned genes from their chloroplast genomes and mitogenomes confirmed the evolutionary trends of the extranuclear genomes. From phylogenetic analysis, we identified the petA chloroplast genes as potential genetic markers that are similar to the tufA marker. Complementary/forward/palindromic interval repetitions were more abundant in chloroplast genomes than in mitogenomes. Interestingly, a few tandem repetitions were significant for some Ulva subspecies and relatively more evident in mitochondria than in chloroplasts. Finally, the tandem repetition [GAAATATATAATAATA × 3, abbreviated as TRg)] was identified in the mitogenome of U. compressa and the conspecific strain U. mutabilis but not in other algal species of the Yellow Sea. Owing to the high morphological plasticity of U. compressa, the findings of this study have implications for the rapid non-sequencing detection of this species during the occurrence of green tides in the region.

The complete chloroplast genome sequence of Ilex chinensis Sims. (Aquifoliaceae), a folk herbal medicine plant in China

The complete chloroplast (cp) genome of Ilex chinensis, an important economic plant with ornamental and ecological values, was sequenced to investigate its phylogenetic relationship. The entire cp genome of I. chinensis was 157,885 bp in length with 37.61% overall GC content, including a large single-copy (LSC) region of 87,289 bp, and a small single-copy (SSC) region of 18,388 bp, which were separated by a pair of inverted repeats (IRs) of 52,208 bp. The cp genome contained 135 genes, including 90 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on whole cp genome sequences showed that I. chinensis was closely related to I. szechwanensis and I. viridis species.

Cytological and Transcriptomic Analysis Provide Insights into the Formation of Variegated Leaves in Ilex × altaclerensis 'Belgica Aurea'

Ilex × altaclerensis 'Belgica Aurea' is an attractive ornamental plant bearing yellow-green variegated leaves. However, the mechanisms underlying the formation of leaf variegation in this species are still unclear. Here, the juvenile yellow leaves and mature variegated leaves of I. altaclerensis 'Belgica Aurea' were compared in terms of leaf structure, pigment content and transcriptomics. The results showed that no obvious differences in histology were noticed between yellow and variegated leaves, however, ruptured thylakoid membranes and altered ultrastructure of chloroplasts were found in yellow leaves (yellow) and yellow sectors of the variegated leaves (variegation). Moreover, the yellow leaves and the yellow sectors of variegated leaves had significantly lower chlorophyll compared to green sectors of the variegated leaves (green). In addition, transcriptomic sequencing identified 1675 differentially expressed genes (DEGs) among the three pairwise comparisons (yellow vs. green, variegation vs. green, yellow vs. variegation). Expression of magnesium-protoporphyrin IX monomethyl ester (MgPME) [oxidative] cyclase, monogalactosyldiacylglycerol (MGDG) synthase and digalactosyldiacylglycerol (DGDG) synthase were decreased in the yellow leaves. Altogether, chlorophyll deficiency might be the main factors driving the formation of leaf variegation in I.altaclerensis 'Belgica Aurea'.

The complete chloroplast genome sequence and phylogenetic analysis of Ilex × Koehneana 'Wirt L. Winn' (Aquifoliaceae)

Ilex × Koehneana ‘Wirt L. Winn’, an important ornamental tree, has been widely distributed in southeastern China. In this study, we assembled and characterized the complete chloroplast (cp) genome of I. Koehneana to investigate its phylogenetic relationship. The whole cp genome of I. Koehneana is 157,538 bp, which contained a large single-copy (LSC) region of 87,055 bp and a small single-copy (SSC) region of 18,429 bp, and a pair of inverted repeats (IR) of 52,054 bp. A total of 137 genes, including 90 protein-coding genes, eight rRNAs, and 39 tRNAs, were identified. Phylogenetic analysis based on 74 conserved protein-coding genes revealed that I. Koehneana is closely related to I. ‘tall boy’.

Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes

Ilex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genomes of all 19 Ilex types that are native to Hong Kong. The genomes are conserved in structure, gene content and arrangement. The chloroplast genomes range in size from 157,119 bp in Ilex graciliflora to 158,020 bp in Ilex kwangtungensis. All these genomes contain 125 genes, of which 88 are protein-coding and 37 are tRNA genes. Four highly varied sequences (rps16-trnQ, rpl32-trnL, ndhD-psaC and ycf1) were found. The number of repeats in the Ilex genomes is mostly conserved, but the number of repeating motifs varies. The phylogenetic relationship among the 19 Ilex genomes, together with eight other available genomes in other studies, was investigated. Most of the species could be correctly assigned to the section or even series level, consistent with previous taxonomy, except Ilex rotunda var. microcarpa, Ilex asprella var. tapuensis and Ilex chapaensis. These species were reclassified; I. rotunda was placed in the section Micrococca, while the other two were grouped with the section Pseudoaquifolium. These studies provide a better understanding of Ilex phylogeny and refine its classification.

The complete plastid genome sequence of Ilex suaveolens (H. Lév.) Loes, the most abundant medicinal holly in Mount Huangshan

Holly (Ilex L.) is a woody dioecious genus cultivated as pharmaceutical, ornamentals, and industrial materials. Ilex suaveolens (H. Lév.) Loes is an endemic medicinal holly with a predominant distribution in Mount Huangshan, China. In the present work, the complete plastid genome of I. suaveolens was de novo sequenced by high-throughput sequencing technology. The newly-assembled plastid genome holds 37.6% of the overall GC content and a length of 157,857 bp, comprising a large single-copy (LSC, 87,255 bp), a small single-copy (SSC, 18,398 bp), and a pair of inverted repeat (IRs, 26,102 bp) regions. The plastid genome annotation suggested the presence of a total of 89 protein-encoding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The plastome-mediated phylogenetic topology revealed that I. suaveolens clustered together with I. szechwanenesis and I. viridis in the same clade, and a strong relationship between clades and biogeography was found. These data contribute to the understanding of genetic diversity and conservation study of Ilex in Mount Huangshan.

The complete chloroplast genome of Plateau herb Chesneya acaulis (Fabaceae)

Chesneya acaulis is a perennial herb, which restricts in Xizang (Tibet) of China, Afghanistan, and Pakistan. The complete chloroplast genome was sequenced using the Illumina Hiseq X-Ten platform. The genome lacks an inverted repeat (IR) region, containing 75 protein-coding genes, 29 tRNAs genes, and 4 rRNAs. The overall GC content is 34.6%. A phylogenetic tree based on the whole chloroplast genomes of 15 species indicated that C. acaulis had a close relationship with the genus Hedysarum, and it nested in the inverted repeat-lacking clade (IRLC), of the subfamily Papilionoideae (Leguminosae).

The complete chloroplast genome sequence and phylogenetic analysis of Ilex 'Beryl', a hybrid of Ilex cornuta × Ilex latifolia (Aquifoliaceae)

Ilex ‘Beryl’ is an ornamental and ecological tree widespread in southeastern China. In this study, the complete chloroplast (cp) genome of Ilex ‘Beryl’ was assembled and characterized to investigate its phylogenetic relationship. The entire cp genome of ‘Beryl’ was a typical quadripartite structure with 157,575 bp in length, including a large single-copy (LSC) region of 87,080 bp and a small single-copy (SSC) region of 18,427 bp, which were separated by a pair of inverted repeats (IRs) of 52,068 bp. There are 135 genes annotated, including 90 protein-coding genes, eight rRNA genes and 37 tRNA genes. Phylogenetic analysis based on whole cp genome sequences showed that ‘Beryl’ is closest to I. ‘Emily Bruner’ and I. ‘tall boy’.

The complete chloroplast genome of Ilex 'Tall Boy', Ilex aquifolium × Ilex latifolia (Aquifoliaceae)

Thecomplete chloroplast (cp) genome of Ilex ‘Tall Boy’, an important economic plant with ornamental and ecological values, was sequenced to investigate its phylogenetic relationship. The entire cp genome of ‘Tall Boy’ was 157,527 bp in length with 37.65% overall GC content, including a large single-copy (LSC) region of 87,044 bp and a small single-copy (SSC) region of 18,429 bp, which were separated by a pair of inverted repeats (IRs) of 52,054 bp. The cp genome contained 135 genes, including 90 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on whole cp genome sequences showed that ‘Tall Boy’ is closest to I. latifolia Thunb. species.

Comparative Survey of Morphological Variations and Plastid Genome Sequencing Reveals Phylogenetic Divergence between Four Endemic Ilex Species

Holly (Ilex L.), from the monogeneric Aquifoliaceae, is a woody dioecious genus cultivated as pharmaceutical and culinary plants, ornamentals, and industrial materials. With distinctive leaf morphology and growth habitats, but uniform reproductive organs (flowers and fruits), the evolutionary relationships of Ilex remain an enigma. To date, few contrast analyses have been conducted on morphology and molecular patterns in Ilex. Here, the different phenotypic traits of four endemic Ilex species (I. latifolia, I. suaveolens, I. viridis, and I. micrococca) on Mount Huangshan, China, were surveyed through an anatomic assay and DNA image cytometry, showing the unspecified link between the examined morphology and the estimated nuclear genome size. Concurrently, the newly-assembled plastid genomes in four Ilex have lengths ranging from 157,601 bp to 157,857 bp, containing a large single-copy (LSC, 87,020–87,255 bp), a small single-copy (SSC, 18,394–18,434 bp), and a pair of inverted repeats (IRs, 26,065–26,102 bp) regions. The plastid genome annotation suggested the presence of numerable protein-encoding genes (89–95), transfer RNA (tRNA) genes (37–40), and ribosomal RNA (rRNA) genes (8). A comprehensive comparison of plastomes within eight Ilex implicated the conserved features in coding regions, but variability in the junctions of IRs/SSC and the divergent hotspot regions potentially used as the DNA marker. The Ilex topology of phylogenies revealed the incongruence with the traditional taxonomy, whereas it informed a strong association between clades and geographic distribution. Our work herein provided novel insight into the variations in the morphology and phylogeography in Aquifoliaceae. These data contribute to the understanding of genetic diversity and conservation in the medicinal Ilex of Mount Huangshan.

The complete chloroplast genome of Ilex 'Emily Bruner', Ilex cornuta 'Burfordii' × Ilex latifolia (Aquifoliaceae)

Ilex ‘Emily Bruner’ is an important economic plant with ornamental and ecological functions in southeastern China. In this study, we characterized the complete chloroplast (cp) genome sequence of ‘Emily Bruner’ to investigate its phylogenetic relationship. The entire cp genome of ‘Emily Bruner’ was 157,216 bp in length with 37.68% overall GC content, including a large single-copy (LSC) region of 86,721 bp and a small single-copy (SSC) region of 18,427 bp, which were separated by a pair of inverted repeats (IRs) of 52,068 bp. The cp genome contained 135 genes, including 90 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on whole cp genome sequences showed that ‘Emily Bruner’ is closest to I. cornuta species.

Complete chloroplast genomes of four Physalis species (Solanaceae): lights into genome structure, comparative analysis, and phylogenetic relationships

BACKGROUND

Physalis L. is a genus of herbaceous plants of the family Solanaceae, which has important medicinal, edible, and ornamental values. The morphological characteristics of Physalis species are similar, and it is difficult to rapidly and accurately distinguish them based only on morphological characteristics. At present, the species classification and phylogeny of Physalis are still controversial. In this study, the complete chloroplast (cp) genomes of four Physalis species (Physalis angulata, P. alkekengi var. franchetii, P. minima and P. pubescens) were sequenced, and the first comprehensive cp genome analysis of Physalis was performed, which included the previously published cp genome sequence of Physalis peruviana.

RESULTS

The Physalis cp genomes exhibited typical quadripartite and circular structures, and were relatively conserved in their structure and gene synteny. However, the Physalis cp genomes showed obvious variations at four regional boundaries, especially those of the inverted repeat and the large single-copy regions. The cp genomes' lengths ranged from 156,578 bp to 157,007 bp. A total of 114 different genes, 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, were observed in four new sequenced Physalis cp genomes. Differences in repeat sequences and simple sequence repeats were detected among the Physalis cp genomes. Phylogenetic relationships among 36 species of 11 genera of Solanaceae based on their cp genomes placed Physalis in the middle and upper part of the phylogenetic tree, with a monophyletic evolution having a 100% bootstrap value.

CONCLUSION

Our results enrich the data on the cp genomes of the genus Physalis. The availability of these cp genomes will provide abundant information for further species identification, increase the taxonomic and phylogenetic resolution of Physalis, and assist in the investigation and utilization of Physalis plants.

Unraveling the Chloroplast Genomes of Two Prosopis Species to Identify Its Genomic Information, Comparative Analyses and Phylogenetic Relationship

Genus Prosopis (family Fabaceae) are shrubby trees, native to arid and semi-arid regions of Asia, Africa, and America and known for nitrogen fixation. Here, we have sequenced the complete chloroplast (cp) genomes of two Prosopis species (P. juliflora and P. cineraria) and compared them with previously sequenced P. glandulosa, Adenanthera microsperma, and Parkia javanica belonging to the same family. The complete genome sequences of Prosopis species and related species ranged from 159,389 bp (A. microsperma) to 163,677 bp (P. cineraria). The overall GC contents of the genomes were almost the similar (35.9–36.6%). The P. juliflora and P. cineraria genomes encoded 132 and 131 genes, respectively, whereas both the species comprised of 85 protein-coding genes higher than other compared species. About 140, 134, and 129 repeats were identified in P. juliflora, P. cineraria and P. glandulosa cp genomes, respectively. Similarly, the maximum number of simple sequence repeats were determined in P. juliflora (88), P. cineraria (84), and P. glandulosa (78). Moreover, complete cp genome comparison determined a high degree of sequence similarity among P. juliflora, P. cineraria, and P. glandulosa, however some divergence in the intergenic spacers of A. microsperma and Parkia javanica were observed. The phylogenetic analysis showed that P. juliflora is closer to P. cineraria than P. glandulosa.

Complete chloroplast genome sequence and phylogenetic analysis of Ilex viridis Champ. ex Benth

Ilex viridis Champ. ex Benth. is domestic to southern China. In the present work, the complete chloroplast (cp) genome sequence of Ilex viridis was assembled and characterized by high-throughput sequencing analyses. The chloroplast genome was 157,701 bp in length, consisting of large single-copy (LSC) and small single-copy (SSC) regions of 87,177 bp and 18,394 bp, respectively, which were separated by a pair of 26,065 bp inverted repeat (IR) regions. The genome was predicted to contain 134 genes, including 89 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the genome is 37.7%. The phylogenetic tree reconstructed using 13 chloroplast genomes reveals that I. viridis is mostly related to Ilex szechwanensis.

The complete plastid genome sequence of Ilex micrococca Maxim

Ilex micrococca Maxim. is a widely distributed species of Aquifoliaceae in Eastern Asia. In this study, the complete chloroplast (cp) genome sequence of I. micrococca was assembled and characterized by high-throughput sequencing data. The entire cp genome was 157,782 bp in length, containing a large single-copy region (LSC) of 87,200 bp, and a small single-copy region (SSC) of 18,434 bp, which were separated by a pair of 26,074 bp inverted repeat (IR) regions. The cp genome contained 134 genes, including 89 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. Eighteen genes occur in double copies. The overall GC content is 37.6%. The phylogenetic tree reconstructed by 13 chloroplast genomes reveals that I. micrococca is most related with Ilex wilsonii. The complete cp genome provides valuable information for further phylogenetic and cp genetic engineering studies of this important Ilex species I. micrococca.

Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae

In this study, we assembled and annotated the chloroplast (cp) genome of the Euonymus species Euonymus fortunei, Euonymus phellomanus, and Euonymus maackii, and performed a series of analyses to investigate gene structure, GC content, sequence alignment, and nucleic acid diversity, with the objectives of identifying positive selection genes and understanding evolutionary relationships. The results indicated that the Euonymus cp genome was 156,860-157,611bp in length and exhibited a typical circular tetrad structure. Similar to the majority of angiosperm chloroplast genomes, the results yielded a large single-copy region (LSC) (85,826-86,299bp) and a small single-copy region (SSC) (18,319-18,536bp), separated by a pair of sequences (IRA and IRB; 26,341-26,700bp) with the same encoding but in opposite directions. The chloroplast genome was annotated to 130-131 genes, including 85-86 protein coding genes, 37 tRNA genes, and eight rRNA genes, with GC contents of 37.26-37.31%. The GC content was variable among regions and was highest in the inverted repeat (IR) region. The IR boundary of Euonymus happened expanding resulting that the rps19 entered into IR region and doubled completely. Such fluctuations at the border positions might be helpful in determining evolutionary relationships among Euonymus. The simple-sequence repeats (SSRs) of Euonymus species were composed primarily of single nucleotides (A)n and (T)n, and were mostly 10-12bp in length, with an obvious A/T bias. We identified several loci with suitable polymorphism with the potential use as molecular markers for inferring the phylogeny within the genus Euonymus. Signatures of positive selection were seen in rpoB protein encoding genes. Based on data from the whole chloroplast genome, common single copy genes, and the LSC, SSC, and IR regions, we constructed an evolutionary tree of Euonymus and related species, the results of which were consistent with traditional taxonomic classifications. It showed that E. fortunei sister to the Euonymus japonicus, whereby E. maackii appeared as sister to Euonymus hamiltonianus. Our study provides important genetic information to support further investigations into the phylogenetic development and adaptive evolution of Euonymus species.

Exceptionally high rates of positive selection on the rbcL gene in the genus Ilex (Aquifoliaceae)

Background

The genus Ilex (Aquifoliaceae) has a near-cosmopolitan distribution in mesic habitats from tropical to temperate lowlands and in alpine forests. It has a high rate of hybridization and plastid capture, and comprises four geographically structured plastid groups. A previous study showed that the plastid rbcL gene, coding for the large subunit of Rubisco, has a particularly high rate of non-synonymous substitutions in Ilex, when compared with other plant lineages. This suggests a strong positive selection on rbcL, involved in yet unknown adaptations. We therefore investigated positive selection on rbcL in 240 Ilex sequences from across the global range.

Results

The rbcL gene shows a much higher rate of positive selection in Ilex than in any other plant lineage studied so far (> 3000 species) by tests in both PAML and SLR. Most positively selected residues are on the surface of the folded large subunit, suggesting interaction with other subunits and associated chaperones, and coevolution between positively selected residues is prevalent, indicating compensatory mutations to recover molecular stability. Coevolution between positively selected sites to restore global stability is common.

Conclusions

This study has confirmed the predicted high incidence of positively selected residues in rbcL in Ilex, and shown that this is higher than in any other plant lineage studied so far. The causes and consequences of this high incidence are unclear, but it is probably associated with the similarly high incidence of hybridization and introgression in Ilex, even between distantly related lineages, resulting in large cytonuclear discordance in the phylogenies.

Comparative analysis of the complete chloroplast genome among Prunus mume, P. armeniaca, and P. salicina

Prunus mume Sieb. et Zucc., P. armeniaca L., and P. salicina L. are economically important fruit trees in temperate regions. These species are taxonomically perplexing because of shared interspecific morphological traits and variation, which are mainly attributed to hybridization. The chloroplast is cytoplasmically inherited and often used for evolutionary studies. We sequenced the complete chloroplast genomes of P. mume, P. armeniaca, and P. salicina using Illumina sequencing followed by de novo assembly. The three chloroplast genomes exhibit a typical quadripartite structure with conserved genome arrangement, structure, and moderate divergence. The lengths of the genomes are 157,815, 157,797, and 157,916 bp, respectively. The length of the large single-copy region (LSC) region is 86,113, 86,283, and 86,122 bp, and the length of the SSC region is 18,916, 18,734, and 19,028 bp; the IR region is 26,393, 26,390, and 26,383 bp, respectively. Each of the three chloroplast genomes encodes 133 genes, including 94 protein-coding, 31 tRNA, and eight rRNA genes. Differential gene analysis for the three species revealed that trnY-ATA is a unique gene in P. armeniaca; in contrast, the gene trnI-TAT is only present in P. mume and P. salicina, though the position of the gene in these chloroplast genomes differs. Further comparative analysis of the complete chloroplast genome sequences revealed that the ORF genes and the sequences of linked regions rps16 and atpA, atpH and atpI, trnc-GCA and psbD, ycf3 and atpB, and rpL32 and ndhD are significantly different and may be used as molecular markers in taxonomic studies. Phylogenetic evolution analysis of the three species suggests that P. mume has a closer genetic relationship to P. armeniaca than to P. salicina.

Complete chloroplast genomes of medicinally important Teucrium species and comparative analyses with related species from Lamiaceae

Teucrium is one of the most economically and ecologically important genera in the Lamiaceae family; however, it is currently the least well understood at the plastome level. In the current study, we sequenced the complete chloroplast (cp) genomes of T. stocksianum subsp. stenophyllum R.A.King (TSS), T. stocksianum subsp. stocksianum Boiss. (TS) and T. mascatense Boiss. (TM) through next-generation sequencing and compared them with the cp genomes of related species in Lamiaceae (Ajuga reptans L., Caryopteris mongholica Bunge, Lamium album L., Lamium galeobdolon (L.) Crantz, and Stachys byzantina K.Koch). The results revealed that the TSS, TS and TM cp genomes have sizes of 150,087, 150,076 and 150,499 bp, respectively. Similarly, the large single-copy (LSC) regions of TSS, TS and TM had sizes of 81,707, 81,682 and 82,075 bp, respectively. The gene contents and orders of these genomes were similar to those of other angiosperm species. However, various differences were observed at the inverted repeat (IR) junctions, and the extent of the IR expansion into ψrps19 was 58 bp, 23 bp and 61 bp in TSS, TS and TM, respectively. Similarly, in all genomes, the pbsA gene was present in the LSC at varying distances from the JLA (IRa-LSC) junction. Furthermore, 89, 72, and 92 repeats were identified in the TSS, TM and TS cp genomes, respectively. The highest number of simple sequence repeats was found in TSS (128), followed by TS (127) and TM (121). Pairwise alignments of the TSS cp genome with related cp genomes showed a high degree of synteny. However, relatively lower sequence identity was observed when various coding regions were compared to those of related cp genomes. The average pairwise divergence among the complete cp genomes showed that TSS was more divergent from TM (0.018) than from TS (0.006). The current study provides valuable genomic insight into the genus Teucrium and its subspecies that may be applied to a more comprehensive study.

The complete chloroplast genomes of rare medical herb Glycyrrhiza inflata and its relative G. aspera (Fabaceae)

Glycyrrhiza inflata is a threatened perennial herb with medicinal value, which restricts in NW China and Mongolia. Its ally species, G. aspera, is widely distributed from northern China to Turkey. The complete chloroplast genomes were sequenced using the Illumina Hiseq X-Ten platform. Each of the genomes lacks an inverted repeat (IR) region, containing 76 protein-coding genes, 30 tRNAs genes, and 4 rRNAs. The overall GC contents are both 34.3%. A phylogenetic tree based on the whole chloroplast genomes of 15 species indicated that G. aspera and G. inflata belonged to a monophyletic Glycyrrhiza, which was nested in IRLC group of the subfamily Papilionoideae (Leguminosae).

The Complete Chloroplast Genome of Euphrasia regelii, Pseudogenization of ndh Genes and the Phylogenetic Relationships Within Orobanchaceae

Euphrasia (Orobanchaceae) is a genus which is widely distributed in temperate regions of the southern and northern hemisphere. The taxonomy of Euphrasia is still controversial due to the similarity of morphological characters and a lack of genomic resources. Here, we present the first complete chloroplast (cp) genome of this taxonomically challenging genus. The cp genome of Euphrasia regelii consists of 153,026 bp, including a large single-copy region (83,893 bp), a small single-copy region (15,801 bp) and two inverted repeats (26,666 bp). There are 105 unique genes, including 71 protein-coding genes, 30 tRNA and 4 rRNA genes. Although the structure and gene order is comparable to the one in other angiosperm cp genomes, genes encoding the NAD(P)H dehydrogenase complex are widely pseudogenized due to mutations resulting in frameshifts, and stop codon positions. We detected 36 dispersed repeats, 7 tandem repeats and 65 simple sequence repeat loci in the E. regelii plastome. Comparative analyses indicated that the cp genome of E. regelii is more conserved compared to other hemiparasitic taxa in the Pedicularideae and Buchnereae. No structural rearrangements or loss of genes were detected. Our analyses suggested that three genes (clpP, ycf2 and rps14) were under positive selection and other genes under purifying selection. Phylogenetic analysis of monophyletic Orobanchaceae based on 45 plastomes indicated a close relationship between E. regelii and Neobartsia inaequalis. In addition, autotrophic lineages occupied the earliest diverging branches in our phylogeny, suggesting that autotrophy is the ancestral trait in this parasitic family.

The complete chloroplast genome sequences of four Viola species (Violaceae) and comparative analyses with its congeneric species

We report the complete chloroplast genomes of four Viola species (V. mirabilis, V. phalacrocarpa, V. raddeana, and V. websteri) and the results of a comparative analysis between these species and the published plastid genome of the congeneric species V. seoulensis. The total genome length of the five Viola species, including the four species analyzed in this study and the species analyzed in the previous study, ranged from 156,507 (V. seoulensis) to 158,162 bp (V. mirabilis). The overall GC contents of the genomes were almost identical (36.2-36.3%). The five Viola plastomes each contained 111 unique genes comprising 77 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Among the annotated genes, 16 contained one or two introns. Based on the results of a chloroplast genome structure comparison using MAUVE, all five Viola plastomes were almost identical. Additionally, the large single copy (LSC), inverted repeat (IR), and small single copy (SSC) junction regions were conserved among the Viola species. A total of 259 exon, intron, and intergenic spacer (IGS) fragments were compared to verify the divergence hotspot regions. The nucleotide diversity (Pi) values ranged from 0 to 0.7544. The IR region was relatively more conserved than the LSC and SSC regions. The Pi values in ten noncoding regions were relatively high (>0.03). Among these regions, all but rps19-trnH, petG-trnW, rpl16-rps3, and rpl2-rpl23 represent useful molecular markers for phylogenetic studies and will be helpful to resolve the phylogenetic relationships of Viola. The phylogenetic tree, which used 76 protein-coding genes from 21 Malpighiales species and one outgroup species (Averrhoa carambola), revealed that Malpighiales is divided into five clades at the family level: Erythroxylaceae, Chrysobalanaceae, Euphorbiaceae, Salicaceae, and Violaceae. Additionally, Violaceae was monophyletic, with a bootstrap value of 100% and was divided into two subclades.

Flora do Parque Estadual do Ibitipoca, Minas Gerais, Brasil: Aquifoliaceae

Resumo É apresentado um tratamento florístico de Aquifoliaceae no Parque Estadual do Ibitipoca (PEIB), localizado no sudeste de Minas Gerais (Brasil). A área de estudo faz parte da Serra da Mantiqueira, na Floresta Atlântica Brasileira, e sua vegetação compreende um mosaico de fitofisionomias, com predomínio dos campos rupestres. A família está representada na área por quatro espécies: Ilex dumosa, I. paraguariensis, I. subcordata e I. theezans. Descrições, chave de identificação, ilustrações de caracteres diagnósticos e comentários taxonômicos, ecológicos e de distribuição geográfica são apresentados para as espécies.

The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae)

Panax stipuleanatus (Araliaceae) is an endangered and medicinally important plant endemic to China. However, phylogenetic relationships within the genus Panax have remained unclear. In this study, we sequenced the complete plastome of P. stipuleanatus and included previously reported Panax plastomes to better understand the relationships between species and plastome evolution within the genus Panax. The plastome of P. stipuleanatus is 156,069 base pairs (bp) in length, consisting of a pair of inverted repeats (IRs, each 25,887 bp) that divide the plastome into a large single copy region (LSC, 86,126 bp) and a small single copy region (SSC, 8169 bp). The plastome contains 114 unigenes (80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes). Comparative analyses indicated that the plastome gene content and order, as well as the expansion/contraction of the IR regions, are all highly conserved within Panax. No significant positive selection in the plastid protein-coding genes was observed across the eight Panax species, suggesting the Panax plastomes may have undergone a strong purifying selection. Our phylogenomic analyses resulted in a phylogeny with high resolution and supports for Panax. Nine protein-coding genes and 10 non-coding regions presented high sequence divergence, which could be useful for identifying different Panax species.

First reported chloroplast genome sequence of Punica granatum (cultivar Helow) from Jabal Al-Akhdar, Oman: phylogenetic comparative assortment with Lagerstroemia

Pomegranate (Punica granatum L.) is one of the oldest known edible fruits. It has grown in popularity and is a profitable fruit crop due to its attractive features including a bright red appearance and its biological activities. Scientific exploration of the genetics and evolution of these beneficial traits has been hampered by limited genomic information. In this study, we sequenced the complete chloroplast (cp) genome of the native P. granatum (cultivar Helow) cultivated in the mountains of Jabal Al-Akhdar, Oman. The results revealed a P. granatum cp genome length of 158,630 bp, characterized by a relatively conserved structure containing 2 inverted repeat regions of 25,466 bp, an 18,686 bp small single copy regions, and an 89,015 bp large single copy region. The 86 protein-coding genes included 37 transfer RNA genes and 8 ribosomal RNA genes. Comparison of the P. granatum whole cp genome with seven Lagerstroemia species revealed an overall high degree of sequence similarity with divergence among intergenic spacers. The location, distribution, and divergence of repeat sequences and shared genes of the Punica and Lagerstroemia species were highly similar. Analyses of nucleotide substitution, insertion/deletions, and highly variable regions in these cp genomes identified potential plastid markers for taxonomic and phylogenetic studies in Myrtales. A phylogenetic study of the cp genomes and 76 shared coding regions generated similar cladograms. The complete cp genome of P. granatum will aid in taxonomical studies of the family Lythraceae.