CPGAVAS2, an integrated plastome sequence annotator and analyzer

De novo assembly of the complete mitochondrial genome of sweet potato (Ipomoea batatas [L.] Lam) revealed the existence of homologous conformations generated by the repeat-mediated recombination

Sweet potato (Ipomoea batatas [L.] Lam) is an important food crop, an excellent fodder crop, and a new type of industrial raw material crop. The lack of genomic resources could affect the process of industrialization of sweet potato. Few detailed reports have been completed on the mitochondrial genome of sweet potato. In this research, we sequenced and assembled the mitochondrial genome of sweet potato and investigated its substructure. The mitochondrial genome of sweet potato is 270,304 bp with 23 unique core genes and 12 variable genes. We detected 279 pairs of repeat sequences and found that three pairs of direct repeats could mediate the homologous recombination into four independent circular molecules. We identified 70 SSRs in the whole mitochondrial genome of sweet potato. The longest dispersed repeat in mitochondrial genome was a palindromic repeat with a length of 915 bp. The homologous fragments between the chloroplast and mitochondrial genome account for 7.35% of the mitochondrial genome. We also predicted 597 RNA editing sites and found that the rps3 gene was edited 54 times, which occurred most frequently. This study further demonstrates the existence of multiple conformations in sweet potato mitochondrial genomes and provides a theoretical basis for the evolution of higher plants and cytoplasmic male sterility breeding.

Molecular Structure and Phylogenetic Analyses of the Complete Chloroplast Genomes of Three Medicinal Plants Conioselinum vaginatum, Ligusticum sinense, and Ligusticum jeholense

Most plants of Ligusticum have an important medicinal and economic value with a long history, Ligusticum sinense and L. jeholense ("Gaoben") has long been used in traditional Chinese medicine for the treatment of carminative, dispelling cold, dehumidification, and analgesia. While in the market Conioselinum vaginatum (Xinjiang Gaoben) is substitution for Gaoben, and occupies a higher market share. These three Gaoben-related medicinal materials are similar in morphology, and are difficult to distinguish from each other by the commonly used DNA barcodes. The chloroplast genome has been widely used for molecular markers, evolutionary biology, and barcoding identification. In this study, the complete chloroplast genome sequences of C. vaginatum, L. sinense, and L. jeholense were reported. The results showed that the complete chloroplast genomes of these three species have typical quadripartite structures, which were comprised of 148,664, 148,539, and 148,497 bp. A total of 114 genes were identified, including 81 protein-coding genes (PCGs), 29 tRNA genes, and four rRNA genes. Our study indicated that highly variable region ycf2-trnL and accD-ycf4 that can be used as specific DNA barcodes to distinguish and identify C. vaginatum, L. sinense, and L. jeholense. In addition, phylogenetic study showed that C. vaginatum nested in Ligusticum and as a sister group of L. sinense and L. jeholense, which suggested these two genera are both in need of revision. This study offer valuable information for future research in the identification of Gaoben-related medicinal materials and will benefit for further phylogenetic study of Apiaceae.

Characterization of the complete chloroplast genome of Cycas ferruginea, a vulnerable species

Cycas ferruginea F. N. Wei (1994) is recorded in the list of wild plant protection in China as a national first-class protected plant. The complete chloroplast genome of C. ferruginea was analyzed for the first time in this article. The genome is 162,045 bp in length, which contains a pair of inverted repeats (IRs) of 25,048 bp each, a large single-copy (LSC) region of 88,827 bp, and a small single-copy (SSC) region of 23,122 bp. The genome comprises a total of 130 encoded genes, including 85 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The total GC content is 39.44%, and the corresponding values of the LSC, SSC, and IRs are 38.73%, 36.56%, and 42.02%, respectively. The phylogenetic relationships were reconstructed based on the complete chloroplast genome sequences of 16 species. Results showed that C. ferruginea is close to C. debaoensis, C. bifida, and C. szechuanensis.

The first complete chloroplast genome of Briggsia chienii W. Y. Chun and its phylogenetic position within Gesneriaceae

Briggsia chienii W. Y. Chun 1946 is an endemic herbaceous perennial species distributed in southern China. In this study, we firstly characterized the complete chloroplast genome sequence of B. chienii and provided new molecular resources for promoting its conservation and taxonomic assignment. Its complete chloroplast genome is 154,082 bp in length and contains the typical quadripartite structure of angiosperm plastome, including two inverted repeat (IR) regions of 25,447 bp, a large single-copy (LSC) region of 85,035 bp, and a small single-copy (SSC) region of 18,153 bp. The plastome contains 114 genes, consisting of 80 protein-coding genes, 30 tRNA gene, and 4 rRNA genes. The overall GC content in the plastome of B. chienii is 37.4%, which is lower than lots of angiosperm plastome. The phylogenetic result indicated that B. chienii exhibited the closest relationship with Oreocharis cotinifolia W. T. Wang 1983, and provided new information for the phylogeny relationship of genus Briggsia.

The complete chloroplast genome sequence of Picrasma quassioides (D. Don) Benn. 1844 (Simaroubaceae)

Picrasma quassioides is a member of the Simaroubaceae family and is widely used as a medicinal plant. In this study, we sequenced and assembled the complete chloroplast genome of P. quassioides. The chloroplast genome is 160,015 bp in length, with a large single-copy region of 87,136 bp, a small single-copy region of 18,069 bp, and a pair of inverted repeat regions of 27,405 bp. It contains a total of 110 unique genes, including 77 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. Phylogenetic analysis showed that P. quassioides clustered well with Simaroubaceae plants, Eurycoma longifolia, Leitneria floridana, and Ailanthus latissimus.

The complete chloroplast genome sequence of Lindera fragrans (Lauraceae): genome structure and phylogenetic analysis

Lindera fragrans, naturally distributed in southern China, is economic and ecological tree. Its leaves are one of the primary raw materials for processing Hawk tea. Here, we assembled the complete chloroplast genome of L. fragrans using Illumina pair-end sequencing. The chloroplast genome size was 152,739 base pairs (bp) with 39% GC content, containing a pair of inverted repeats (IRA/B) of 20,067 bp, separated by a large- and a small single-copy region (LSC/SSC) of 93,711 bp and 18,894 bp, respectively. The genome encoded 126 genes, including 82 protein-coding, 36 transfer RNA (tRNA), and eight ribosomal RNA (rRNA) genes. Phylogenetic analysis based on chloroplast genome sequences of 22 species suggested that L. fragrans was closely related to species of Lindera genus than other genera in Lauraceae. These results can be a valuable genome resource for further genetics and molecular biology studies.

Complete chloroplast genome of Nyctocalos pinnatum: chloroplast features and phylogenetic relationships within Bignoniaceae

Nyctocalos is a genus of flowering lianas belonging to the family Bignoniaceae, and occurring from South-Central China to Malesia. In this study, we assembled the first complete chloroplast genome of N. pinnatum. The total length of the chloroplast genome is 159591 bp, with a GC content of 38.04%, which includes a pair of inverted repeats of 30,480 bp, a small single-copy region of 12,774 bp and a large single-copy region of 85,857 bp. The chloroplast genome contains 135 genes, consisting of 89 protein-coding genes, 38 transfer RNAs, and 8 ribosomal RNAs. We constructed a phylogenomic tree with representative chloroplast genomes from Bignoniaceae. N. pinnatum is revealed to be sister to Oroxylum in the tribe Oroxyleae, with a high bootstrap support. This is the first chloroplast genome assembled in Nyctocalos, and it provides essential information for further ecology and evolutionary studies in this genus and Bignoniaceae.

The complete chloroplast genome sequence of Begonia arachnoidea (Begoniaceae)

There are more than 2035 Begonia species (Begoniaceae) reported currently in the world. Begonia arachnoidea was found as a new species within a small area in Southern China. In this study, we are reporting for the first time its chloroplast genome for the purpose to compare with the chloroplast genomic data from other plant taxa which were closely related to this new species. Our results show that the circular chloroplast genome of B. arachnoidea is 169,725 bp in length, with 35.49% GC content. The whole structure of the genome has 76,431 bp in a large single-copy (LSC) region, 18,146 bp in a small single-copy (SSC) region, and the two inverted repeat (IRs) regions are both 37,574 bp. There are 90 protein-coding genes, 8 rRNA genes, and 42 tRNA genes encoded in this genome. Final phylogenetic analysis revealed that B. arachnoidea is genetically closest to B. pulchrifolia and B. coptidifolia.

The complete chloroplast genome of Epimedium trifoliolatobinatum (Koidz.) Koidz. (Berberidaceae)

Epimedium L. is an important genus in the family Berberidaceae. Epimedium trifoliolatobinatum (Koidz.) Koidz. 1939 is inhabited on the west side of the Shikoku, Japan. In this study, the first complete chloroplast genome of E. trifoliolatobinatum was assembled with Illumina paired-end sequencing data, which was 157,272 bp in length with a total GC content of 38.70%. A total of 112 unique genes were annotated, comprising 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis suggested that E. trifoliolatobinatum was sister to E. koreanum. The current results provided fundamental information for further conducting molecular systematics and phylogenetic research of Epimedium genus.

The complete chloroplast genome of Clematis hexapetala (Ranunculaceae) and its phylogenetic analysis

Clematis hexapetala Pall. (1776) is a traditional Chinese medicine belonging to the Ranunculaceae. In this study, the complete chloroplast genome was sequenced through Illumina platform, cp was circular DNA molecule of 159,538 bp in length with a typical quadripartite structure, consisting of four regions: two copies of inverted repeat region (IRs: 31,039 bp), a large single-copy (LSC: 79,333 bp) region, a small single-copy (SSC: 18,127 bp) region. The chloroplast genome encodes a total of 135 genes, including 91 CDS genes, 36 tRNA genes, 8 rRNA genes. Phylogenetic analysis based on complete genes shows that C. hexapetala closely related to C. taeguensis in the genus Clematis. This study improves our comprehension of the chloroplast genome and its phylogenetic relationships within Ranunculaceae.

The complete chloroplast genome of Epimedium muhuangense (Berberidaceae)

Epimedium muhuangense S. Z. He & Y. Y. Wang 2017, one of the rare unifoliolate species in the Epimedium genus of Berberidaceae, is distributed in the Guizhou province of China. In present research, we sequenced the complete chloroplast genome of E. muhuangense with Illumina sequencing technology. The whole genome was 157,264 bp in length, which consisted of a large single-copy region (LSC, 88,588 bp), a small single-copy region (SSC, 17,036 bp), and a pair of inverted repeat regions (IRa and IRb, 25,820 bp). A total of 112 unique genes were successfully annotated, consisting of 78 protein-encoding genes, 30 rRNA, and four tRNA. Phylogenetic analysis demonstrated that E. muhuangense is closely related to E. elachyphyllum.

The complete chloroplast genome and phylogenetic analysis of Astragalus sinicus Linne 1767

Astragalus sinicus Linne 1767 is a traditional winter-growing green manure, that plays an important role in upgrading soil fertility and maintaining crop yield and quality for rice fields. This study reports the complete chloroplast genome of A. sinicus. The chloroplast genome contained 110 complete genes, including 76 protein-coding genes, 4 ribosomal RNA genes, and 30 tRNA genes with 123,830 bp in length and a 34.66% GC content with IR loss. The evolutionary history, referred to as the maximum-likelihood (ML), showed that A. sinicus and Astragalus bhotanensis were most closely related. The chloroplast genome analysis of A. sinicus will serve as a reference for future studies on species evolution, plant conservation, and molecular phylogeny in Astragalus.

The complete chloroplast genome sequence of Potentilla bifurca L

Potentilla bifurca L. is a perennial herb in China, which has high ecological and economic values. Its complete chloroplast genome was reported in this study for the first time. The whole chloroplast genome was 157, 902 base pairs in length with 129 genes, including 84 protein-coding genes, 37 tRNAs, and 8 rRNAs. The maximum likelihood phylogenetic analysis revealed that the species of P. bifurca was isolated first among the genus Potentilla. This result will be helpful for the conservation and phylogeny programs of the genus Potentilla.

Complete chloroplast genome characterization and phylogenetic analysis of Clematis mandshurica (Ranunculaceae)

The complete chloroplast genome sequence of Clematis mandshurica Ruprecht (1867), a specie of the Ranunculaceae family, and its phylogenetic relationships with other species have been reported in this study. The complete chloroplast genome of C. mandshurica is 159,563 bp in length, including a large single-copy (LSC) region of 79,360 bp, a small single-copy (SSC) region of 18,121 bp, and a pair of identical inverted repeat regions (IRs) of 31,041 bp. The genome encodes a total of 132 genes, including 90 protein-coding genes, 34 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis reveals that C. mandshurica was found to be closest to Clematis taeguensis. The complete chloroplast genome of C. mandshurica contributes to a better understanding of phylogenetic relationships among Clematis species.

Complete chloroplast genome of Gentianopsis barbata and comparative analysis with related species from Gentianaceae

Gentianopsis barbata is an essential medicinal plant in China with high ornamental and medicinal values. Unfortunately, the study of the chloroplast genome of this plant still has a gap. This study sequenced and characterized the complete chloroplast genome of G. barbata. The complete chloroplast genome of G. barbata is a typical circular structure with 151,123 bp. It consists of a large single-copy region (82,690 bp) and a small single-copy region (17,887 bp) separated by a pair of inverted repeats (25,273 bp), which covers 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. Repeat analysis showed the highest frequency of palindrome. Thirty-seven simple sequence repeats were identified, most of which were single nucleotides. The bayesian inference tree, maximum likelihood tree, and neighbor joining tree suggested that G. barbata is grouped with Gentianopsis grandis and Gentianopsis paludosa. The divergence time analysis showed that G. barbata diverged at 1.243 Mya. Comparative chloroplast analysis can reveal interspecific diversity, and regions with high variation can be used to develop molecular markers applicable to various research areas. Our results provide new insight into plastome evolution and valuable resource for further studies on G. barbata.

The complete chloroplast genome of Psychotria asiatica, Linnaeus 1759 (Rubiaceae)

Psychotria asiatica is a typical traditional medicinal plant. Herein, we acquired and characterized the complete chloroplast (cp) genome sequence of P. asiatica to provide genomic resources for conservation genetics and phylogenetic studies of P. asiatica. The cp genome of P. asiatica is 154,652 bp in length and consists of a large single-copy (LSC) region with 85,106 bp, a small single-copy (SSC) region with 17,960 bp, and two inverted repeat regions (IRs) with 25,793 bp. The cp genome of P. asiatica comprises 127 genes, including 82 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic result confirmed that P. asiatica was closely related to Psychotria kirkii within the Rubiaceae.

The complete chloroplast genome of Piper sarmentosum Roxburgh, 1820 (Piperaceae)

Piper sarmentosum Roxb. (Piperaceae) is a traditional medicinal herb native to Southeast Asia. The complete genome of P. sarmentosum was sequenced and characterized in this study with the aim of providing genomic resources for the evolution and molecular breeding of P. sarmentosum. It has a typical quadripartite structure, with a large single-copy (LSC) region of 88,979 bp, a small single-copy (SSC) region of 18,274 bp, and two copies of 27,068 bp inverted-repeat regions (IRa and IRb). A total of 130 genes were annotated, comprising 85 protein-coding genes (PCGs), 8 ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. The phylogenetic tree showed that P. sarmentosum in the current study is closely related to Piper longum.

The complete chloroplast genome of two traditional medical plants: Asparagus cochinchinensis (Lour.) Merr. and Asparagus dauricus Fisch. ex Link

Asparagus cochinchinensis (Lour.) Merr. and Asparagus dauricus Fisch. ex Link are two traditional medical plants with therapeutic effects, distributed in mountainous regions of China. In the current study, the complete chloroplast (cp) genomes of A. cochinchinensis and A. dauricus were sequenced on the Illumina Hiseq 2500, and obtained with a length of 157,095 bp and 156,918 bp, respectively, both containing a large single-copy region and a small single-copy region separated by a pair of inverted repeat regions. The cp genome of A. cochinchinensis has 132 annotated genes including 86 protein-coding genes, 38 tRNA, and eight rRNA genes. A. dauricus has 112 annotated genes containing 78 protein genes, 30 tRNA, and four rRNA genes. The maximum-likelihood tree was reconstructed with 17 species, indicating that A. cochinchinensis is a sister group to the clade including A. officinalis to A. racemosa. This clade includes five species of Asparagus.

The complete chloroplast genome of Euonymus alatus (Celastraceae)

Euonymus alatus, Celastraceae, is a deciduous tree species valued for its ornamental and medicinal properties. Here, the species’ whole chloroplast genome sequence was generated by assembling the Illumina paired-end sequencing reads. The circular genome was 157,611 bp in length, exhibiting a typical quadripartite structure with a large single-copy (LSC: 85,892 bp), a small single-copy (SSC: 18,419 bp), and a pair of inverted repeat regions (IRA and IRB: each of 26,650 bp). The chloroplast genome encoded 131 genes, including 87 protein-coding (78 protein-coding gene species), 36 transfer RNA (29 tRNA species), and 8 ribosomal RNA genes (4 rRNA species). The overall GC content was 37.3%, while the corresponding values of the LSC, SSC and IR regions were 35.1, 31.7 and 42.7%, respectively. Phylogenetic analysis of 12 species complete chloroplast genomes suggested that E. alatus was relatively close to E. japonicus. This complete chloroplast genome is expected to provide valuable insight into further phylogenetic reconstruction of the Celastraceae species.

Characterization of the complete chloroplast genome of Dendrobium findlayanum Par. et Rchb. f. 1874 (Orchidaceae)

Dendrobium findlayanum Par. et Rchb. f. 1874 has the high ornamental and medicinal value. Here, we report the first complete chloroplast genome of D. findlayanum. The complete chloroplast genome of D. findlayanum is 153,713 bp in length with 120 genes, including 75 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The total content of GC of the whole genome is 37.46%. Phylogenetic analysis indicated that D. findlayanum was closely related to other species in Dendrobium, and this study provides new genetic resources for species identification and phylogenetic analyses in Dendrobium.

The complete chloroplast genome of Laportea bulbifera (Sieb. et Zucc.) Wedd. and its phylogenetic analysis

The circle complete chloroplast genome of Laportea bulbifera (Sieb. et Zucc.) Wedd. was sequenced for the first time. The genome length of L. bulbifera is 150,042 bp with 36.80% of GC content. The genome consists of a large single copy (LSC) region of 82,414 bp, a small single copy (SSC) region of 17,714 bp, and two inverted repeat (IRa and IRb) regions of 24,957 bp each. A total of 129 genes were annotated, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis was conducted by 29 species from the Rosales, the results presented a closed relationship between the species Laportea bulbifera and Poikilospermum lanceolatum.

The complete chloroplast genome of Medicago arabica (Fabaceae)

Medicago arabica (Linnaeus, 1762) Huds. is an important annual legume forage that grows in a wide range of climates, from subtropical to temperate. This study aimed to sequence the chloroplast genome of M. arabica and compare it with other legumes. In this study, we sequenced the entire chloroplast genome of M. arabica, which has 125,056 base pairs. The total GC content of the chloroplast genome of M. arabica was 34.4%. From the 110 unique genes of the circular genome, 30 tRNA genes, four rRNA genes, and 76 protein-coding genes were successfully annotated. A maximum likelihood (ML) tree was constructed using the model species and 17 species of the Medicago genus. M. arabica was shown to be phylogenetically closely related to M. polymorpha. The nucleotide diversity of the chloroplast genome may provide valuable molecular markers to study chloroplast, genetic breeding, and plant molecular evolution. These findings provide a solid foundation for future research on the molecular biology of the chloroplast.

The Complete Chloroplast Genomes of Primula obconica Provide Insight That Neither Species nor Natural Section Represent Monophyletic Taxa in Primula (Primulaceae)

The genus Primula (Primulaceae) comprises more than 500 species, with 300 species distributed in China. The contradictory results between systematic analyses and morphology-based taxonomy make taxonomy studies difficult. Furthermore, frequent introgression between closely related species of Primula can result in non-monophyletic species. In this study, the complete chloroplast genome of sixteen Primula obconica subsp. obconica individuals were assembled and compared with 84 accessions of 74 species from 21 sections of the 24 sections of the genus in China. The plastome sizes of P. obconica subsp. obconica range from 153,584 bp to 154,028 bp. Genome-wide variations were detected, and 1915 high-quality SNPs and 346 InDels were found. Most SNPs were detected in downstream and upstream gene regions (45.549% and 41.91%). Two cultivated accessions, ZP1 and ZP2, were abundant with SSRs. Moreover, 12 SSRs shared by 9 accessions showed variations that may be used as molecular markers for population genetic studies. The phylogenetic tree showed that P. obconica subsp. obconica cluster into two independent clades. Two subspecies have highly recognizable morphological characteristics, isolated geographical distribution areas, and distinct phylogenetic relationships compared with P. obconica subsp. obconica. We elevate the two subspecies of P. obconica to separate species. Our phylogenetic tree is largely inconsistent with morphology-based taxonomy. Twenty-one sections of Primula were mainly divided into three clades. The monophyly of Sect. Auganthus, Sect. Minutissimae, Sect. Sikkimensis, Sect. Petiolares, and Sect. Ranunculoides are well supported in the phylogenetic tree. The Sect. Obconicolisteri, Sect. Monocarpicae, Sect. Carolinella, Sect. Cortusoides, Sect. Aleuritia, Sect. Denticulata, Sect. Proliferae Pax, and Sect. Crystallophlomis are not a monophyletic group. The possible explanations for non-monophyly may be hybridization, polyploidization, recent introgression, incorrect taxonomy, or chloroplast capture. Multiple genomic data and population genetic studies are therefore needed to reveal the evolutionary history of Primula. Our results provided valuable information for intraspecific variation and phylogenetic relationships within Primula.

Strategies for molecular authentication of herbal products: from experimental design to data analysis

Molecular herbal authentication has gained worldwide popularity in the past decade. DNA-based methods, including DNA barcoding and species-specific amplification, have been adopted for herbal identification by various pharmacopoeias. Development of next-generating sequencing (NGS) drastically increased the throughput of sequencing process and has sped up sequence collection and assembly of organelle genomes, making more and more reference sequences/genomes available. NGS allows simultaneous sequencing of multiple reads, opening up the opportunity of identifying multiple species from one sample in one go. Two major experimental approaches have been applied in recent publications of identification of herbal products by NGS, the PCR-dependent DNA metabarcoding and PCR-free genome skimming/shotgun metagenomics. This review provides a brief introduction of the use of DNA metabarcoding and genome skimming/shotgun metagenomics in authentication of herbal products and discusses some important considerations in experimental design for botanical identification by NGS, with a specific focus on quality control, reference sequence database and different taxon assignment programs. The potential of quantification or abundance estimation by NGS is discussed and new scientific findings that could potentially interfere with accurate taxon assignment and/or quantification is presented.

Actinostephanus (Gesneriaceae), a new genus and species from Guangdong, South China

Actinostephanus, a new genus from southern China, is described and colorfully illustrated with a single species, A.enpingensis. This new genus is morphologically most similar to Boeica and Leptoboea, nevertheless, it can be easily distinguished from the latter two by the following characteristics, such as leaves in whorls of three, all closely clustered at the top; corolla bowl-shaped, 5-lobed, actinomorphic; capsule hard, oblong-ovoid, short, 3-4 mm long, densely appressed villous, wrapped by persistent densely pubescent calyx lobes, style persistent. The new genus and related genera were sequenced using the next-generation sequencing technique. The whole plastid genome of the new genus is 154, 315 - 154, 344 bp in length. We reconstructed phylogenetic trees using the dataset of 80 encoded protein genes of the whole plastid genome from 47 accessions based on ML and BI analyses. The result revealed that the new genus was recovering in a polytomy including Boeica, Rhynchotechum, and Leptoboea with strong support, congruent to the morphological evidence. A global conservation assessment was also performed and classifies A.enpingensis as Least Concern (LC). In addition, after a review of recently described species of Gesneriaceae, we propose that plant enthusiasts, especially Gesneriad fans, have been playing an increasingly important role in the process of new taxa-discoveries.

Complete chloroplast genome sequences of three aroideae species (Araceae): lights into selective pressure, marker development and phylogenetic relationships

Background

Colocasia gigantea, Caladium bicolor and Xanthosoma sagittifolium are three worldwide famous ornamental and/or vegetable plants in the Araceae family, these species in the subfamily Aroideae are phylogenetically perplexing due to shared interspecific morphological traits and variation.

Result

This study, for the first time ever, assembled and analyzed complete chloroplast genomes of C. gigantea, C. bicolor and X. sagittifolium with genome sizes of 165,906 bp, 153,149 bp and 165,169 bp in length, respectively. The genomes were composed of conserved quadripartite circular structures with a total of 131 annotated genes, including 8 rRNA, 37 tRNA and 86 protein-coding genes. A comparison within Aroideae showed seven protein-coding genes (accD, ndhF, ndhK, rbcL, rpoC1, rpoC2 and matK) linked to environmental adaptation. Phylogenetic analysis confirmed a close relationship of C. gigantea with C. esculenta and S. colocasiifolia, and the C. bicolor with X. sagittifolium. Furthermore, three DNA barcodes (atpH-atpI + psaC-ndhE, atpH-atpI + trnS-trnG, atpH-atpI + psaC-ndhE + trnS-trnG) harbored highly variable regions to distinguish species in Aroideae subfamily.

Conclusion

These results would be beneficial for species identification, phylogenetic relationship, genetic diversity, and potential of germplasm resources in Aroideae.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08400-3.

The complete plastomes of seven Peucedanum plants: comparative and phylogenetic analyses for the Peucedanum genus

BACKGROUND

The Peucedanum genus is the backbone member of Apiaceae, with many economically and medically important plants. Although the previous studies on Peucedanum provide us with a good research basis, there are still unclear phylogenetic relationships and many taxonomic problems in Peucedanum, and a robust phylogenetic framework of this genus still has not been obtained, which severely hampers the improvement and revision of taxonomic system for this genus. The plastid genomes possessing more variable characters have potential for reconstructing a robust phylogeny in plants.

RESULTS

In the current study, we newly sequenced and assembled seven Peucedanum plastid genomes. Together with five previously published plastid genomes of Peucedanum, we performed a comprehensively comparative analyses for this genus. Twelve Peucedanum plastomes were similar in terms of genome structure, codon bias, RNA editing sites, and SSRs, but varied in genome size, gene content and arrangement, and border of SC/IR. Fifteen mutation hotspot regions were identified among plastid genomes that can serve as candidate DNA barcodes for species identification in Peucedanum. Our phylogenetic analyses based on plastid genomes generated a phylogeny with high supports and resolutions for Peucedanum that robustly supported the non-monophyly of genus Peucedanum.

CONCLUSION

The plastid genomes of Peucedanum showed both conservation and diversity. The plastid genome data were efficient and powerful for improving the supports and resolutions of phylogeny for the complex Peucedanum genus. In summary, our study provides new sights into the plastid genome evolution, taxonomy, and phylogeny for Peucedanum species.

The complete chloroplast genome of Epimedium campanulatum Ogisu (Berberidaceae), a rare plant species endemic to China

Epimedium L. is an important medicinal herbaceous genus that belongs to the family Berberidaceae. Epimedium campanulatum Ogisu is a plant species only inhabited in the northwestern part of Sichuan province, China. Here, we reported the complete chloroplast genome sequence, assembly, and characterization of E. campanulatum. The chloroplast genome of E. campanulatum was 157,343 bp in length, and a total of 112 unique genes were identified. Phylogenetic results revealed that E. campanulatum formed a sister relationship with the cluster of Epimedium ecalcaratum, Epimedium davidii, and Epimedium chlorandrum. Our findings provided valuable data for future taxonomic and phylogenetic research within the genus Epimedium.

The complete chloroplast genome of a karst-dwelling plant Primulina tenuituba (Gesneriaceae)

Primulina tenuituba is a species in the Gesneriaceae family that is widely distributed in China. It is a karst-dwelling species with an enormous tolerance for extreme drought and high temperatures. The species is also used in traditional Chinese medicine. In this study, the complete chloroplast genome of P. tenuituba was assembled and characterized for the first time. The complete chloroplast genome exhibited a typical quadripartite cycle of 153,236 bp in length, including a pair of inverted repeats (IRs) of 25,494 bp, which were separated by a large single-copy (LSC) region of 84,364 bp and a small single copy (SSC) region of 17,884 bp. The GC content was 37.6%. The complete chloroplast genome of P. tenuituba contains 114 genes, including 80 protein-coding genes, 30 tRNAs genes, and four rRNAs. The phylogenetic analysis showed that P. tenuituba is closely related to P. eburnea. The newly reported chloroplast genome of P. tenuituba would provide valuable data for further studies on its evolution and adaptation mechanism.

The complete chloroplast genome of Medicago scutellata (Fabaceae)

Medicago scutellata (Linnaeus, 1753) is one of the essential leguminous forages distributed across tropical and subtropical regions of the world. In our study, we obtained the complete chloroplast genome of M. scutellata with a length of 124,082 bp. The total GC content of the entire chloroplast genome of M. scutellata was 33.9%. Among the 110 unique genes in the circular genome, 30 tRNA, 4 rRNA, and 76 protein-coding genes were successfully annotated. A phylogenetic tree constructed using common protein-coding genes revealed that M. scutellata is closely related to M. truncatula from the Fabaceae family.

The comparative studies of complete chloroplast genomes in Actinidia (Actinidiaceae): novel insights into heterogenous variation, clpP gene annotation and phylogenetic relationships

The genus Actinidia, also called kiwifruit, is characterized with abundant balanced nutritional metabolites, including exceptionally high vitamin C content. However, the traditional classification could not fully reflect the actual Actinidia species' relationships, which need further revision through more accurate approaches. Compared to the nuclear genome, the chloroplast genome has simple heredity characteristics, conserved genome structure and small size, suitable for deciphering complicated species' phylogenetic relationships. Here, the genome-wide comprehensive comparative analyses were performed over 29 independent chloroplast genomes' sequences derived from 25 Actinidia taxa. The average genome size is 156,673.38 bp, with an average 37.20% GC content. The long repeat sequences rather than SSRs (simple sequence repeats) in Actinidia were revealed to be the causal agent leading to the chloroplast genome size expansion. The clpP gene sequences with exon merge and intron deletion were annotated in all the 29 chloroplast genomes tested, which has been previously reported to be lost in Actinidia species. Comprehensive sequence analyses indicated the distinct variation at the clpP gene locus was Actinidiaceae-specific, emerging after the Actinidiaceae-other Ericales species divergence. Four highly divergent sequences (i.e., rps16 ~ trnQ-UUG, rps4 ~ trnT-UGU, petA ~ psbJ, and rps12 ~ psbB) evolved in the LSC (large single-copy) and SSC (small single-copy) regions embodying rps12 ~ psbB (including clpP gene and its up/downstream noncoding sequence) were identified as variation hot spots in Actinidia species. Based on either LSC region alone, combined sequences of LSC and SSC or the whole chloroplast genome sequences, three identical phylogenetic trees of the 25 Actinidia taxa with relatively improved resolution were reconstructed, consistently supporting the reticulate evolutionary lineage in Actinidia. Our findings could help to better understand the evolution characteristics of chloroplast genomes and phylogenetic relationships among Actinidia species.

Identification of Medicinal Bidens Plants for Quality Control Based on Organelle Genomes

Bidens plants are annuals or perennials of Asteraceae and usually used as medicinal materials in China. They are difficult to identify by using traditional identification methods because they have similar morphologies and chemical components. Universal DNA barcodes also cannot identify Bidens species effectively. This situation seriously hinders the development of medicinal Bidens plants. Therefore, developing an accurate and effective method for identifying medicinal Bidens plants is urgently needed. The present study aims to use phylogenomic approaches based on organelle genomes to address the confusing relationships of medicinal Bidens plants. Illumina sequencing was used to sequence 12 chloroplast and eight mitochondrial genomes of five species and one variety of Bidens. The complete organelle genomes were assembled, annotated and analysed. Phylogenetic trees were constructed on the basis of the organelle genomes and highly variable regions. The organelle genomes of these Bidens species had a conserved gene content and codon usage. The 12 chloroplast genomes of the Bidens species were 150,489 bp to 151,635 bp in length. The lengths of the eight mitochondrial genomes varied from each other. Bioinformatics analysis revealed the presence of 50–71 simple sequence repeats and 46–181 long repeats in the organelle genomes. By combining the results of mVISTA and nucleotide diversity analyses, seven candidate highly variable regions in the chloroplast genomes were screened for species identification and relationship studies. Comparison with the complete mitochondrial genomes and common protein-coding genes shared by each organelle genome revealed that the complete chloroplast genomes had the highest discriminatory power for Bidens species and thus could be used as a super barcode to authenticate Bidens species accurately. In addition, the screened highly variable region trnS-GGA-rps4 could be also used as a potential specific barcode to identify Bidens species.

The complete chloroplast genome of Ficus pumila, a functional plant in East Asia

Ficus pumila L. is a climbing fig commonly used as an ornamental plant. In this study, we sequenced and assembled the complete chloroplast genome of F. pumila. The complete chloroplast genome of F. pumila is 160,248 bp in length which includes a pair of inverted repeats (IRs) of 25,871 bp separated by a large single-copy (LSC) region of 88,405 bp and a small single-copy (SSC) region of 20,101 bp. The overall guanine–cytosine (GC) content of F. pumila cp genome is 35.98%, while the corresponding values of LSC, SSC, and IR sequences are 33.65, 29.05, and 42.65%, respectively. The phylogenetic tree was shown to be consistent with the traditional morphology-based taxonomy of Moraceae. Five plants from the genus Ficus formed a well-supported monophyletic clade with 100% bootstrap value, and F. pumila is closely related to F. hirta, F. carica, and F. racemosa, with a support value of 97%. The complete chloroplast of F. pumila contributes to the growing number of chloroplast genomes for phylogenetic and evolutionary studies in Moraceae.

The complete chloroplast genome sequence of Camellia sinensis cultivar ‘Qiancha1’ from Guizhou Province, China

The complete chloroplast genome sequence of Camellia sinensis cultivar ‘Qiancha 1’ (QC1), an excellent tea plant cultivar was determined in this study. The cp genome of QC1 is 157,024 bp in length and includes a large single copy (LSC, 86,585 bp), a small single copy (SSC, 18,277 bp) and a pair of inverted repeats (IRa and IRb, 26,081 bp). The overall GC content is 37.3%. A total of 137 genes were annotated, including 92 protein coding, 37 tRNA, and eight rRNA genes. Phylogenetic analysis showed that QC1 has the closest evolutionary relationship with C. sinensis cultivar ‘Anhua’ from Hunan, China. The complete cp genome of QC1 provides a resource for further research on the phylogeny and taxonomy of Sect. Thea (L.) Dyer.

The complete chloroplast genome of two related fig species Ficus squamosa and Ficus heterostyla

The Ficus squamosa and Ficus heterostyla share an undescribed pollinating fig wasp Ceratosolen sp. in Xishuangbanna region, which constitutes the most excellent model to study the role of convergent evolution and hybridization in the species-specific fig-wasp mutualism. The plastomes were 160,350 bp for Ficus squamosa and 160,300 bp for F. heterostyla, both in length with the typical quadripartite structure. In the two genomes, the LSC region was 88,615 bp (F. squamosa) and 88,535 bp (F. heterostyla), the SSC region was 20,071 bp (F. squamosa) and 20,101 bp (F. heterostyla), and the IR regions of both figs were 25,832 bp. They contained 113 unique genes, including a set of 78 protein-coding genes, 30 transfer RNA (tRNA) genes, four ribosomal RNA (rRNA) genes, and one pseudogene (infA). Phylogenetic analysis based on the complete chloroplast (cp) genomes within the Ficus genus suggests that they are closely related sister species.

The complete chloroplast genome sequence of Clerodendranthus spicatus, a medicinal plant for preventing and treating kidney diseases from Lamiaceae family

BACKGROUND

Clerodendranthus spicatus (Thunb.) C. Y. Wu ex H. W. Li is one of the most important medicines for the treatment of nephrology in the southeast regions of China. To understand the taxonomic classification of Clerodendranthus species and identify species discrimination markers, we sequenced and characterized its chloroplast genome in the current study.

METHODS AND RESULTS

Total genomic DNA were isolated from dried leaves of C. spicatus and sequenced using an Illumina sequencing platform. The data were assembled and annotated by the NOVOPlasty software and CpGAVAS2 web service. The complete chloroplast genome of C. spicatus was 152,155 bp, including a large single-copy region of 83,098 bp, a small single-copy region of 17,665 bp, and a pair of inverted repeat regions of 25,696 bp. The Isoleucine codons are the most abundant, accounting for 4.17% of all codons. The codons of AUG, UUA, and AGA demonstrated a high degree of usage bias. Twenty-eight simple sequence repeats, thirty-six tandem repeats, and forty interspersed repeats were identified. The distribution of the specific rps19, ycf1, rpl2, trnH, psbA genes were analyzed. Analysis of the genetic distance of the intergenic spacer regions shows that ndhG-ndhI, accD-psaI, rps15-ycf1, rpl20-clpP, ccsA-ndhD regions have high K2p values. Phylogenetic analysis showed that C. spicatu is closely related to two Lamiaceae species, Tectona grandis, and Glechoma longituba.

CONCLUSIONS

In this study, we sequenced and characterized the chloroplast genome of C. spicatus. Phylogenomic analysis has identified species closely related to C. spicatus, which represent potential candidates for the development of drugs improving renal functions.

The complete chloroplast genome sequence of begonia (Begoniaceae)

Begonia L. (Begoniaceae) is the sixth largest genus in the world which consists of more than 2,039 species. Many species of Begonia have highly ornamental leaves and flowers, so they are mainly used for ornamental purposes, and some species can also be used as medicines or vegetables. Begonia gulongshanensis is a newly discovered species in 2018 which occurs exclusively in Jingxi county in Southern China, however, there are few studies on the molecular biology and phylogeny of this species currently. Therefore, we report its complete chloroplast genome sequence for the first time, hoping to provide a foundation for its future phylogenetic analysis. The chloroplast genome of B. gulongshanensis was 169,153 bp in size, which contained a large single-copy region of 75,998 bp, a small single-copy region of 18,063 bp, and two inverted repeat regions of the same 37,546 bp. The total GC content was 35.51%. The genome encodes 42 transfer RNA genes, 8 ribosomal RNA genes and 90 protein-coding genes. The phylogenetic analysis indicated that the genetic relationship between B. gulongshanensis and the other three begonias was very close, but there was still certain distance.

Characterization of the complete chloroplast genome of Zephyranthes phycelloides (Amaryllidaceae, tribe Hippeastreae) from Atacama region of Chile

Sporadic rains in the Atacama Desert reveal a high biodiversity of plant species that only occur there. One of these rare species is the “Red añañuca” (Zephyranthes phycelloides), formerly known as Rhodophiala phycelloides. Many species of Zephyranthes in the Atacama Desert are dangerously threatened, due to massive extraction of bulbs and cutting of flowers. Therefore, studies of the biodiversity of these endemic species, which are essential for their conservation, should be conducted sooner rather than later. There are some chloroplast genomes available for Amaryllidaceae species, however there is no complete chloroplast genome available for any of the species of Zephyranthes subgenus Myostemma. The aim of the present work was to characterize and analyze the chloroplast of Z. phycelloides by NGS sequencing. The chloroplast genome of the Z. phycelloides consists of 158,107 bp, with typical quadripartite structures: a large single copy (LSC, 86,129 bp), a small single copy (SSC, 18,352 bp), and two inverted repeats (IR, 26,813 bp). One hundred thirty-seven genes were identified: 87 coding genes, 8 rRNA, 38 tRNA and 4 pseudogenes. The number of SSRs was 64 in Z. phycelloides and a total of 43 repeats were detected. The phylogenetic analysis of Z. phycelloides shows a distinct subclade with respect to Z. mesochloa. The average nucleotide variability (Pi) between Z. phycelloides and Z. mesochloa was of 0.02000, and seven loci with high variability were identified: psbA, trnS^GCU-trnG^UCC, trnD^GUC-trnY^GUA, trnL^UAA-trnF^GAA, rbcL, psbE-petL and ndhG-ndhI. The differences between the species are furthermore confirmed by the high amount of SNPs between these two species. Here, we report for the first time the complete cp genome of one species of the Zephyranthes subgenus Myostemma, which can be used for phylogenetic and population genomic studies.

Chloroplast phylogenomics in Camelina (Brassicaceae) reveals multiple origins of polyploid species and the maternal lineage of C. sativa

The genus Camelina (Brassicaceae) comprises 7-8 diploid, tetraploid, and hexaploid species. Of particular agricultural interest is the biofuel crop, C. sativa (gold-of-pleasure or false flax), an allohexaploid domesticated from the widespread weed, C. microcarpa. Recent cytogenetics and genomics work has uncovered the identity of the parental diploid species involved in ancient polyploidization events in Camelina. However, little is known about the maternal subgenome ancestry of contemporary polyploid species. To determine the diploid maternal contributors of polyploid Camelina lineages, we sequenced and assembled 84 Camelina chloroplast genomes for phylogenetic analysis. Divergence time estimation was used to infer the timing of polyploidization events. Chromosome counts were also determined for 82 individuals to assess ploidy and cytotypic variation. Chloroplast genomes showed minimal divergence across the genus, with no observed gene-loss or structural variation. Phylogenetic analyses revealed C. hispida as a maternal diploid parent to the allotetraploid Camelina rumelica, and C. neglecta as the closest extant diploid contributor to the allohexaploids C. microcarpa and C. sativa. The tetraploid C. rumelica appears to have evolved through multiple independent hybridization events. Divergence times for polyploid lineages closely related to C. sativa were all inferred to be very recent, at only ~65 thousand years ago. Chromosome counts confirm that there are two distinct cytotypes within C. microcarpa (2n = 38 and 2n = 40). Based on these findings and other recent research, we propose a model of Camelina subgenome relationships representing our current understanding of the hybridization and polyploidization history of this recently-diverged genus.

The complete chloroplast genome of Acer negundo (Aceraceae)

Acer negundo L. is popular as ornamental shade trees. In this study, we sequenced, assembled and characterized the complete chloroplast genome of A. negundo. The genome sequence of A. negundo was 155,910 bp, consisting of a large single-copy region with 85,650 bp (LSC), a small single-copy region with 18,092 bp (SSC), and two inverted repeat regions with 26,084 and 26,090 bp (IRs). The GC content in the chloroplast genome of A. negundo was 37.9%. A total of 127 functional genes were predicted, including 83 protein-coding genes, 40 tRNA genes, and 4 rRNA genes. As shown in the phylogenetic tree, A. negundo was clustered into a monophyletic cluster.

The complete chloroplast genome sequence of Rhaponticum uniflorum, the first of the genus Rhaponticum

Rhaponticum uniflorum is commonly used as a source for traditional medicines with the main effect of clearing heat. Here, we sequenced the complete chloroplast (cp) genome of R. uniflorum to develop molecular markers for taxonomic classification and species determination of R. uniflorum. It was 152,760 bp in size and has a typical circular structure, including a pair of inverted repeats with 25,205 bp, a large single-copy region with 83,687 bp, and a small single copy region with 18,663 bp. The genome encodes 110 unique genes, including 80 protein-coding, four rRNA and 26 tRNA genes. Phylogenomic analysis shows that R. uniflorum is closely related to the Saussurea. The study is useful for phylogenetic and population genetic studies of Rhaponticum plants.