Dynamics of chloroplast genomes in green plants

Unraveling the specialized metabolic pathways in medicinal plant genomes: a review

Medicinal plants are important sources of bioactive specialized metabolites with significant therapeutic potential. Advances in multi-omics have accelerated the understanding of specialized metabolite biosynthesis and regulation. Genomics, transcriptomics, proteomics, and metabolomics have each contributed new insights into biosynthetic gene clusters (BGCs), metabolic pathways, and stress responses. However, single-omics approaches often fail to fully address these complex processes. Integrated multi-omics provides a holistic perspective on key regulatory networks. High-throughput sequencing and emerging technologies like single-cell and spatial omics have deepened our understanding of cell-specific and spatially resolved biosynthetic dynamics. Despite these advancements, challenges remain in managing large datasets, standardizing protocols, accounting for the dynamic nature of specialized metabolism, and effectively applying synthetic biology for sustainable specialized metabolite production. This review highlights recent progress in omics-based research on medicinal plants, discusses available bioinformatics tools, and explores future research trends aimed at leveraging integrated multi-omics to improve the medicinal quality and sustainable utilization of plant resources.

Species-wide inventory of Arabidopsis thaliana organellar variation reveals ample phenotypic variation for photosynthetic performance

Efforts to improve photosynthetic performance are increasingly employing natural genetic variation. However, genetic variation in the organellar genomes (plasmotypes) is often disregarded due to the difficulty of studying the plasmotypes and the lack of evidence that this is a worthwhile investment. Here, we systematically phenotyped plasmotype diversity using Arabidopsis thaliana as a model species. A reanalysis of whole-genome resequencing data of 1,541 representative accessions shows that the genetic diversity among the mitochondrial genomes is eight times lower than among the chloroplast genomes. Plasmotype diversity of the accessions divides the species into two major phylogenetic clusters, within which highly divergent subclusters are distinguished. We combined plasmotypes from 60 A. thaliana accessions with the nuclear genomes (nucleotypes) of four A. thaliana accessions to create a panel of 232 cytonuclear genotypes (cybrids). The cybrid plants were grown in a range of different light and temperature conditions and phenotyped using high-throughput phenotyping platforms. Analysis of the phenotypes showed that several plasmotypes alone or in interaction with the nucleotypes have significant effects on photosynthesis and that the effects are highly dependent on the environment. Moreover, we introduce Plasmotype Association Studies (PAS) as a method to reveal plasmotypic effects. Within A. thaliana, several organellar variants can influence photosynthetic phenotypes, which emphasizes the valuable role this variation has on improving photosynthetic performance. The increasing feasibility of producing cybrids in various species calls for further research into how these phenotypes may support breeding goals in crop species.

The complete chloroplast genome of Arachis lutescens Krapov. & Rigoni (Fabaceae)

Arachis lutescens Krapov. & Rigoni 1958 is an important species due to their potentially extensive applications for cultivated peanut breeding. The whole chloroplast genome of A. lutescens was successfully assembled and annotated for the first time. The complete chloroplast genome of A. lutescens is a typically circular structure of 156,398 bp with a GC content of 36.3%. It comprises a large single-copy (LSC) region of 85,950 bp, a small single-copy (SSC) region of 18,800 bp, and two inverted repeat regions (IRs) of 25,824 bp, each. The plastome of A. lutescens contains a total of 125 genes, including 81 protein-coding genes, 36 tRNAs, and eight rRNAs. The phylogenetic analysis strongly supports the close relationship between A. lutescens and cultivated peanut clades. This study contributes to our understanding of the molecular characteristics and evolutionary relationships of this plant species.

Intraspecific differentiation of Lindera obtusiloba as revealed by comparative plastomic and evolutionary analyses

Lindera obtusiloba Blume is the northernmost tree species in the family Lauraceae, and it is a key species in understanding the evolutionary history of this family. The species of L. obtusiloba in East Asia has diverged into the Northern and Southern populations, which are geographically separated by an arid belt. Though the morphological differences between populations have been observed and well documented, intraspecific variations at the plastomic level have not been systematically investigated to date. Here, ten chloroplast genomes of L. obtusiloba individuals were sequenced and analyzed along with three publicly available plastomes. Comparative plastomic analysis suggests that both the Northern and the Southern populations share similar overall structure, gene order, and GC content in their plastomes although the size of the plasome and the level of intraspecific variability do vary between the two populations. The Northern have relatively larger plastomes while the Southern population possesses higher intraspecific variability, which could be attributed to the complexity of the geological environments in the South. Phylogenomic analyses also support the split of the Northern and Southern clades among L. obtusiloba individuals. However, there is no obvious species boundary between var. obtusiloba and var. heterophylla in the Southern population, indicating that gene flow could still occur between these two varieties, and this could be used as a good example of reticulate evolution. It is also found that a few photosynthesis-related genes are under positive selection, which is mainly related to the geological and environmental differences between the Northern and the Southern regions. Our results provide a reference for phylogenetic analysis within species and suggest that phylogenomic analyses with a sufficient number of nuclear and chloroplast genomic target loci from widely distributed individuals could provide a deeper understanding of the population evolution of the widespread species.

The low level of plastome differentiation observed in some lineages of Poales hinders molecular species identification

Chloroplast genomes are a source of information successfully used in various fields of plant genetics, including molecular species identification. However, recent studies indicate an extremely low level of interspecific variability in the plastomes of some taxonomic groups of plants, including the genus Stipa L., which is a representative of the grass family. In this study we aimed to analyze the level of chloroplast genome diversity within particular genera as well as the effectiveness of identifying plant species in the Poaceae family and the other representatives of Poales order. Analysis of complete plastid genome alignments created for 96 genera comprising 793 species and 1707 specimens obtained from the GenBank database allowed defining and categorizing molecular diagnostic characters distinguishing the analyzed species from the other representatives of the genus. The results also demonstrate which species do not have any species-specific mutations, thereby they cannot be identified on the basis of differences between the complete chloroplast genomes. Our research showed a huge diversity of the analyzed species in terms of the number of molecular diagnostic characters and indicated which genera pose a particular challenge in terms of molecular species identification. The results show that a very low level of genetic diversity between plastomes is not uncommon in Poales. This is the first extensive research on super-barcoding that tests this method on a large data set and illustrates its effectiveness against the background of phylogenetic relationships.

Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome

Chloroplast genomes are valuable for inferring evolutionary relationships. We report the complete chloroplast genomes of 36 Corydalis spp. and one Fumaria species. We compared these genomes with 22 other taxa and investigated the genome structure, gene content, and evolutionary dynamics of the chloroplast genomes of 58 species, explored the structure, size, repeat sequences, and divergent hotspots of these genomes, conducted phylogenetic analysis, and identified nine types of chloroplast genome structures among Corydalis spp. The ndh gene family suffered inversion and rearrangement or was lost or pseudogenized throughout the chloroplast genomes of various Corydalis species. Analysis of five protein-coding genes revealed simple sequence repeats and repetitive sequences that can be potential molecular markers for species identification. Phylogenetic analysis revealed three subgenera in Corydalis. Subgenera Cremnocapnos and Sophorocapnos represented the Type 2 and 3 genome structures, respectively. Subgenus Corydalis included all types except type 3, suggesting that chloroplast genome structural diversity increased during its differentiation. Despite the explosive diversification of this subgenus, most endemic species collected from the Korean Peninsula shared only one type of genome structure, suggesting recent divergence. These findings will greatly improve our understanding of the chloroplast genome of Corydalis and may help develop effective molecular markers.

Comparative and phylogenetic analysis of complete chloroplast genome sequences of Salvia regarding its worldwide distribution

Salvia is widely used as medicine, food, and ornamental plants all over the world, with three main distribution centers, the Central and western Asia/Mediterranean (CAM), the East Aisa (EA), and the Central and South America (CASA). Along with its large number of species and world-wide distribution, Salvia is paraphyletic with multiple diversity. Chloroplast genomes (CPs) are useful tools for analyzing the phylogeny of plants at lower taxonomic levels. In this study, we reported chloroplast genomes of five species of Salvia and performed phylogenetic analysis with current available CPs of Salvia. Repeated sequence analysis and comparative analysis of Salvia CPs were also performed with representative species from different distribution centers. The results showed that the genetic characters of the CPs are related to the geographic distribution of plants. Species from CAM diverged first to form a separate group, followed by species from EA, and finally species from CASA. Larger variations of CPs were observed in species from CAM, whereas more deficient sequences and less repeated sequences in the CPs were observed in species from CASA. These results provide valuable information on the development and utilization of the worldwide genetic resources of Salvia.

New insights into polyploid evolution and dynamic nature of Ludwigia section Isnardia (Onagraceae)

BACKGROUND

While polyploids are common in plants, the evolutionary history and natural dynamics of most polyploid groups are still unclear. Owing to plentiful earlier systematic studies, Ludwigia sect. Isnardia (comprising 22 wetland taxa) is an ideal allopolyploid complex to investigate polyploid evolution and natural dynamics within and among taxa. With a considerable sampling, we concentrated on revisiting earlier phylogenies of Isnardia, reevaluating the earlier estimated age of the most recent common ancestor (TMRCA), exploring the correlation between infraspecific genetic diversity and ploidy levels, and inspecting interspecific gene flows among taxa.

RESULTS

Phylogenetic trees and network concurred with earlier phylogenies and hypothesized genomes by incorporating 192 atpB-rbcL and ITS sequences representing 91% of Isnardia taxa. Moreover, we detected three multi-origin taxa. Our findings on L. repens and L. sphaerocarpa were consistent with earlier studies; L. arcuata was reported as a multi-origin taxon here, and an additional evolutionary scenario of L. sphaerocarpa was uncovered, both for the first time. Furthermore, estimated Isnardia TMRCA ages based on our data (5.9 or 8.9 million years ago) are in accordance with earlier estimates, although younger than fossil dates (Middle Miocene). Surprisingly, infraspecific genetic variations of Isnardia taxa did not increase with ploidy levels as anticipated from many other polyploid groups. In addition, the exuberant, low, and asymmetrical gene flows among Isnardia taxa indicated that the reproductive barriers may be weakened owing to allopolyploidization, which has rarely been reported.

CONCLUSIONS

The present research gives new perceptions of the reticulate evolution and dynamic nature of Isnardia and points to gaps in current knowledge about allopolyploid evolution.

Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily

Uncaria species are used in traditional medicine and are considered of high therapeutic value and economic importance. This work describes the assembly and annotation of the chloroplast genomes of U. guianensis and U. tomentosa, as well as a comparative analysis. The genomes were sequenced on MiSeq Illumina, assembled with NovoPlasty, and annotated using CHLOROBOX GeSeq. Addictionaly, comparative analysis were performed with six species from NCBI databases and primers were designed in Primer3 for hypervariable regions based on the consensus sequence of 16 species of the Rubiaceae family and validated on an in-silico PCR in OpenPrimeR. The genome size of U. guianensis and U. tomentosa was 155,505 bp and 156,390 bp, respectively. Both Species have 131 genes and GC content of 37.50%. The regions rpl32-ccsA, ycf1, and ndhF-ccsA showed the three highest values of nucleotide diversity within the species of the Rubiaceae family and within the Uncaria genus, these regions were trnH-psbA, psbM-trnY, and rps16-psbK. Our results indicates that the primer of the region ndhA had an amplification success for all species tested and can be promising for usage in the Rubiaceae family. The phylogenetic analysis recovered a congruent topology to APG IV. The gene content and the chloroplast genome structure of the analyzed species are conserved and most of the genes are under negative selection. We provide the cpDNA of Neotropical Uncaria species, an important genomic resource for evolutionary studies of the group.

The First Complete Chloroplast Genome of Cordia monoica: Structure and Comparative Analysis

Cordia monoica is a member of the Boraginaceae family. This plant is widely distributed in tropical regions and has a great deal of medical value as well as economic importance. In the current study, the complete chloroplast (cp) genome of C. monoica was sequenced, assembled, annotated, and reported. This circular chloroplast genome had a size of 148,711 bp, with a quadripartite structure alternating between a pair of repeated inverted regions (26,897-26,901 bp) and a single copy region (77,893 bp). Among the 134 genes encoded by the cp genome, there were 89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A total of 1387 tandem repeats were detected, with the hexanucleotides class making up 28 percent of the repeats. Cordia monoica has 26,303 codons in its protein-coding regions, and leucine amino acid was the most frequently encoded amino acid in contrast to cysteine. In addition, 12 of the 89 protein-coding genes were found to be under positive selection. The phyloplastomic taxonomical clustering of the Boraginaceae species provides further evidence that chloroplast genome data are reliable not only at family level but also in deciphering the phylogeny at genus level (e.g., Cordia).

Plastid phylogenomics and molecular evolution of Thismiaceae (Dioscoreales)

PREMISE

Species in Thismiaceae can no longer photosynthesize and instead obtain carbon from soil fungi. Here we infer Thismiaceae phylogeny using plastid genome data and characterize the molecular evolution of this genome.

METHODS

We assembled five Thismiaceae plastid genomes from genome skimming data, adding to previously published data for phylogenomic inference. We investigated plastid-genome structural changes, considering locally colinear blocks (LCBs). We also characterized possible shifts in selection pressure in retained genes by considering changes in the ratio of nonsynonymous to synonymous changes (ω).

RESULTS

Thismiaceae experienced two major pulses of gene loss around the early diversification of the family, with subsequent scattered gene losses across descendent lineages. In addition to massive size reduction, Thismiaceae plastid genomes experienced occasional inversions, and there were likely two independent losses of the plastid inverted repeat (IR) region. Retained plastid genes remain under generally strong purifying selection (ω << 1), with significant and sporadic weakening or strengthening in several instances. The bifunctional trnE-UUC gene of Thismia huangii may retain a secondary role in heme biosynthesis, despite a probable loss of functionality in protein translation. Several cis-spliced group IIA introns have been retained, despite the loss of the plastid intron maturase, matK.

CONCLUSIONS

We infer that most gene losses in Thismiaceae occurred early and rapidly, following the initial loss of photosynthesis in its stem lineage. As a species-rich, fully mycoheterotrophic lineage, Thismiaceae provide a model system for uncovering the unique and divergent ways in which plastid genomes evolve in heterotrophic plants.

Multiple domestication events explain the origin of Gossypium hirsutum landraces in Mexico

Several Mesoamerican crops constitute wild-to-domesticated complexes generated by multiple initial domestication events, and continuous gene flow among crop populations and between these populations and their wild relatives. It has been suggested that the domestication of cotton (Gossypium hirsutum) started in the northwest of the Yucatán Peninsula, from where it spread to other regions inside and outside of Mexico. We tested this hypothesis by assembling chloroplast genomes of 23 wild, landraces, and breeding lines (transgene-introgressed and conventional). The phylogenetic analysis showed that the evolutionary history of cotton in Mexico involves multiple events of introgression and genetic divergence. From this, we conclude that Mexican landraces arose from multiple wild populations. Our results also revealed that their structural and functional chloroplast organizations had been preserved. However, genetic diversity decreases as a consequence of domestication, mainly in transgene-introgressed (TI) individuals (π = 0.00020, 0.00001, 0.00016, 0, and 0, of wild, TI-wild, landraces, TI-landraces, and breeding lines, respectively). We identified homologous regions that differentiate wild from domesticated plants and indicate a relationship among the samples. A decrease in genetic diversity associated with transgene introgression in cotton was identified for the first time, and our outcomes are therefore relevant to both biosecurity and agrobiodiversity conservation.

Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure

The chloroplast genomes of angiosperms usually have a stable circular quadripartite structure that exhibits high consistency in genome size and gene order. As one of the most diverse genera of angiosperms, Carex is of great value for the study of evolutionary relationships and speciation within its genus, but the study of the structure of its chloroplast genome is limited due to its highly expanded and restructured genome with a large number of repeats. In this study, we provided a more detailed account of the chloroplast genomes of Carex using a hybrid assembly of second- and third-generation sequencing and examined structural variation within this genus. The study revealed that chloroplast genomes of four Carex species are significantly longer than that of most angiosperms and are characterized by high sequence rearrangement rates, low GC content and gene density, and increased repetitive sequences. The location of chloroplast genome structural variation in the species of Carex studied is closely related to the positions of long repeat sequences; this genus provides a typical example of chloroplast structural variation and expansion caused by long repeats. Phylogenetic relationships constructed based on the chloroplast protein-coding genes support the latest taxonomic system of Carex, while revealing that structural variation in the chloroplast genome of Carex may have some phylogenetic significance. Moreover, this study demonstrated a hybrid assembly approach based on long and short reads to analyze complex chloroplast genome assembly and also provided an important reference for the analysis of structural rearrangements of chloroplast genomes in other taxa.

Complete chloroplast genome sequences of Myristicaceae species with the comparative chloroplast genomics and phylogenetic relationships among them

BACKGROUND

Myristicaceae was widly distributed from tropical Asia to Oceania, Africa, and tropical America. There are 3 genera and 10 species of Myristicaceae present in China, mainly distributed in the south of Yunnan Province. Most research on this family focuses on fatty acids, medicine, and morphology. Based on the morphology, fatty acid chemotaxonomy, and a few of molecular data, the phylogenetic position of Horsfieldia pandurifolia Hu was controversial.

RESULTS

In this study, the chloroplast genomes of two Knema species, Knema globularia (Lam.) Warb. and Knema cinerea (Poir.) Warb., were characterized. Comparing the genome structure of these two species with those of other eight published species, including three Horsfieldia species, four Knema species, and one Myristica species, it was found that the chloroplast genomes of these species were relatively conserved, retaining the same gene order. Through sequence divergence analysis, there were 11 genes and 18 intergenic spacers were subject to positive selection, which can be used to analyze the population genetic structure of this family. Phylogenetic analysis showed that all Knema species were clustered in the same group and formed a sister clade with Myristica species support by both high maximum likelihood bootstrap values and Bayesian posterior probabilities; among Horsfieldia species, Horsfieldia amygdalina (Wall.) Warb., Horsfieldia kingii (Hook.f.) Warb., Horsfieldia hainanensis Merr. and Horsfieldia tetratepala C.Y.Wu. were grouped together, but H. pandurifolia formed a single group and formed a sister clade with genus Myristica and Knema. Through the phylogenetic analysis, we support de Wilde' view that the H. pandurifolia should be separated from Horsfieldia and placed in the genus Endocomia, namely Endocomia macrocoma subsp. prainii (King) W.J.de Wilde.

CONCLUSION

The findings of this study provide a novel genetic resources for future research in Myristicaceae and provide a molecular evidence for the taxonomic classification of Myristicaceae.

The Complete Chloroplast Genome of Hypoestes forskaolii (Vahl) R.Br: Insights into Comparative and Phylogenetic Analyses within the Tribe Justiceae

Hypoestes forskaolii is one of the most important species of the family Acanthaceae, known for its high economic and medicinal importance. It is well distributed in the Arab region as well as on the African continent. Previous studies on ethnomedicine have reported that H. forskaolii has an anti-parasitic effect as well as antimalarial and anthelmintic activities. Previous studies mainly focused on the ethnomedicinal properties, hence, there is no information on the genomic architecture and phylogenetic positions of the species within the tribe Justiceae. The tribe Justicieae is the most taxonomically difficult taxon in Acanthoideae due to its unresolved infratribal classification. Therefore, by sequencing the complete chloroplast genome (cp genome) of H. forskaolii, we explored the evolutionary patterns of the cp genome and reconstructed the phylogeny of Justiceae. The cp genome is quadripartite and circular in structure and has a length of 151,142 bp. There are 130 genes (86 coding for protein, 36 coding for tRNA and 8 coding for rRNA) present in the plastome. Analyses of long repeats showed only three types of repeats: forward, palindromic and reverse were present in the genome. Microsatellites analysis revealed 134 microsatellites in the cp genome with mononucleotides having the highest frequency. Comparative analyses within Justiceae showed that genomes structure and gene contents were highly conserved but there is a slight distinction in the location of the genes in the inverted repeat and single copy junctions. Additionally, it was discovered that the cp genome includes variable hotspots that can be utilized as DNA barcodes and tools for determining evolutionary relationships in the Justiceae. These regions include: atpH-atpI, trnK-rps16, atpB-rbcL, trnT-trnL, psbI-trnS, matK, trnH-psbA, and ndhD. The Bayesian inference phylogenetic tree showed that H. forskaolii is a sister to the Dicliptra clade and belongs to Diclipterinae. The result also confirms the polyphyly of Justicia and inclusion of Diclipterinae within justicioid. This research has revealed the phylogenetic position of H. forskaolii and also reported the resources that can be used for evolutionary and phylogenetic studies of the species and the Justicieae.

DNA-Based Identification of Eurasian Vicia Species Using Chloroplast and Nuclear DNA Barcodes

Many legume species of the Vicia L. genus (Fabaceae Lindl.) are key components of the Mediterranean diet and have an integral role in sustainable agriculture. Given the importance of the Vicia species for Eurasian culture, it is necessary to implement methodologies, such as DNA barcoding, that can enable the effective authentication and identification of species in the genus. In this study, we analysed the chloroplast trnL and rpoC1, as well as the nuclear ITS2 DNA barcoding regions, to identify 71 Vicia specimens of Eurasian descent. Both the trnL and ITS2 regions were highly effective in discriminating the analysed taxa, while the more conserved rpoC1 region could not identify all of the selected species due to high sequence conservation or non-annotated or absent rpoC1 species sequences in GenBank. A dendrographic representation of the generated trnL data showed sufficient clustering for most of the analysed taxa, although some topological discrepancies were observed. ITS2 and rpoC1 reconstructions were also used for resolving the topological discrepancies observed in the trnL tree. Our analysis suggests that a combination of DNA barcoding regions is essential for accurate species discrimination within the Vicia genus, while single-locus analyses do not provide the necessary resolution.

The plastome of Melocactus glaucescens Buining & Brederoo reveals unique evolutionary features and loss of essential tRNA genes

The plastome of Melocactus glaucescens shows unique rearrangements, IR expansion, and unprecedented gene losses in Cactaceae. Our data indicate tRNA import from the cytosol to the plastids in this species. Cactaceae represents one of the richest families in keystone species of arid and semiarid biomes. This family shows various specific features comprehending morphology, anatomy, and metabolism, which allow them to grow under unfavorable environmental conditions. The subfamily Cactoideae contains the most divergence of species, which are highly variable in growth habit and morphology. This subfamily includes the endangered species Melocactus glaucescens (tribe Cereeae), which is a cactus endemic to the biome Caatinga in Brazil. Aiming to analyze the plastid evolution and develop molecular markers, we sequenced and analyzed in detail the plastome of M. glaucescens. Our analyses revealed that the M. glaucescens plastome is the most divergent among the species of the family Cactaceae sequenced so far. We characterized here unique rearrangements, expanded IRs containing an unusual set of genes, and several gene losses. Some genes related to the ndh complex were lost during the plastome evolution, while others have lost their functionality. Additionally, the loss of three tRNA genes (trnA-UGC, trnV-UAC, and trnV-GAC) suggests tRNA import from the cytosol to the plastids in M. glaucescens. Moreover, we identified high gene divergence, several putative positive signatures, and possible unique RNA-editing sites. Furthermore, we mapped 169 SSRs in the plastome of M. glaucescens, which are helpful to access the genetic diversity of natural populations and conservation strategies. Finally, our data provide new insights into the evolution of plastids in Cactaceae, which is an outstanding lineage adapted to extreme environmental conditions and a notorious example of the atypical evolution of plastomes.

Comparative Genomics, Phylogenetics, Biogeography, and Effects of Climate Change on Toddalia asiatica (L.) Lam. (Rutaceae) from Africa and Asia

In the present study, two samples of Toddalia asiatica species, both collected from Kenya, were sequenced and comparison of their genome structures carried out with T. asiatica species from China, available in the NCBI database. The genome size of both species from Africa was 158, 508 base pairs, which was slightly larger, compared to the reference genome of T. asiatica from Asia (158, 434 bp). The number of genes was 113 for both species from Africa, consisting of 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Toddalia asiatica from Asia had 115 genes with 81 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Both species compared displayed high similarity in gene arrangement. The gene number, orientation, and order were highly conserved. The IR/SC boundary structures were the same in all chloroplast genomes. A comparison of pairwise sequences indicated that the three regions (trnH-psbA, rpoB, and ycf1) were more divergent and can be useful in developing effective genetic markers. Phylogenetic analyses of the complete cp genomes and 79 protein-coding genes indicated that the Toddalia species collected from Africa were sister to T. asiatica collected from Asia. Both species formed a sister clade to the Southwest Pacific and East Asian species of Zanthoxylum. These results supported the previous studies of merging the genus Toddalia with Zanthoxylum and taxonomic change of Toddalia asiatica to Zanthoxylum asiaticum, which should also apply for the African species of Toddalia. Biogeographic results demonstrated that the two samples of Toddalia species from Africa diverged from T. asiatica from Asia (3.422 Mya, 95% HPD). These results supported an Asian origin of Toddalia species and later dispersal to Africa and Madagascar. The maxent model analysis showed that Asia would have an expansion of favorable areas for Toddalia species in the future. In Africa, there will be contraction and expansion of the favorable areas for the species. The availability of these cp genomes will provide valuable genetic resources for further population genetics and biogeographic studies of these species. However, more T. asiatica species collected from a wide geographical range are required.

Comparative Genomics, Phylogenetics, Biogeography, and Effects of Climate Change on Toddalia asiatica (L.) Lam. (Rutaceae) from Africa and Asia

In the present study, two samples of Toddalia asiatica species, both collected from Kenya, were sequenced and comparison of their genome structures carried out with T. asiatica species from China, available in the NCBI database. The genome size of both species from Africa was 158, 508 base pairs, which was slightly larger, compared to the reference genome of T. asiatica from Asia (158, 434 bp). The number of genes was 113 for both species from Africa, consisting of 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Toddalia asiatica from Asia had 115 genes with 81 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Both species compared displayed high similarity in gene arrangement. The gene number, orientation, and order were highly conserved. The IR/SC boundary structures were the same in all chloroplast genomes. A comparison of pairwise sequences indicated that the three regions (trnH-psbA, rpoB, and ycf1) were more divergent and can be useful in developing effective genetic markers. Phylogenetic analyses of the complete cp genomes and 79 protein-coding genes indicated that the Toddalia species collected from Africa were sister to T. asiatica collected from Asia. Both species formed a sister clade to the Southwest Pacific and East Asian species of Zanthoxylum. These results supported the previous studies of merging the genus Toddalia with Zanthoxylum and taxonomic change of Toddalia asiatica to Zanthoxylum asiaticum, which should also apply for the African species of Toddalia. Biogeographic results demonstrated that the two samples of Toddalia species from Africa diverged from T. asiatica from Asia (3.422 Mya, 95% HPD). These results supported an Asian origin of Toddalia species and later dispersal to Africa and Madagascar. The maxent model analysis showed that Asia would have an expansion of favorable areas for Toddalia species in the future. In Africa, there will be contraction and expansion of the favorable areas for the species. The availability of these cp genomes will provide valuable genetic resources for further population genetics and biogeographic studies of these species. However, more T. asiatica species collected from a wide geographical range are required.

ORTHOSKIM: in silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications

Low-coverage whole genome shotgun sequencing (or genome skimming) has emerged as a cost-effective method for acquiring genomic data in non-model organisms. This method provides sequence information on chloroplast genome (cpDNA), mitochondrial genome (mtDNA) and nuclear ribosomal regions (rDNA), which are over-represented within cells. However, numerous bioinformatic challenges remain to accurately and rapidly obtain such data in organisms with complex genomic structures and rearrangements, in particular for mtDNA in plants or for cpDNA in some plant families. Here we introduce the pipeline ORTHOSKIM, which performs in silico capture of targeted sequences from genomic and transcriptomic libraries without assembling whole organelle genomes. ORTHOSKIM proceeds in three steps: 1) global sequence assembly, 2) mapping against reference sequences, and 3) target sequence extraction; importantly it also includes a range of quality control tests. Different modes are implemented to capture both coding and non-coding regions of cpDNA, mtDNA and rDNA sequences, along with predefined nuclear sequences (e.g. ultra-conserved elements) or collections of single-copy ortholog genes. Moreover, aligned DNA matrices are produced for phylogenetic reconstructions, by performing multiple alignments of the captured sequences. While ORTHOSKIM is suitable for any eukaryote, a case study is presented here, using 114 genome-skimming libraries and 4 RNAseq libraries obtained for two plant families, Primulaceae and Ericaceae, the latter being a well-known problematic family for cpDNA assemblies. ORTHOSKIM recovered with high success rates cpDNA, mtDNA and rDNA sequences, well suited to accurately infer evolutionary relationships within these families. ORTHOSKIM is released under a GPL-3 license and is available at: https://github.com/cpouchon/ORTHOSKIM.

Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants

The plastid organelle is essential for many vital cellular processes and the growth and development of plants. The availability of a large number of complete plastid genomes could be effectively utilized to understand the evolution of the plastid genomes and phylogenetic relationships among plants. We comprehensively analyzed the plastid genomes of Viridiplantae comprising 3,654 taxa from 298 families and 111 orders and compared the genomic organizations in their plastid genomic DNA among major clades, which include gene gain/loss, gene copy number, GC content, and gene blocks. We discovered that some important genes that exhibit similar functions likely formed gene blocks, such as the psb family presumably showing co-occurrence and forming gene blocks in Viridiplantae. The inverted repeats (IRs) in plastid genomes have doubled in size across land plants, and their GC content is substantially higher than non-IR genes. By employing three different data sets [all nucleotide positions (nt123), only the first and second codon positions (nt12), and amino acids (AA)], our phylogenomic analyses revealed Chlorokybales + Mesostigmatales as the earliest-branching lineage of streptophytes. Hornworts, mosses, and liverworts forming a monophylum were identified as the sister lineage of tracheophytes. Based on nt12 and AA data sets, monocots, Chloranthales and magnoliids are successive sister lineages to the eudicots + Ceratophyllales clade. The comprehensive taxon sampling and analysis of different data sets from plastid genomes recovered well-supported relationships of green plants, thereby contributing to resolving some long-standing uncertainties in the plant phylogeny.

Chloroplast Phylogenomic Analyses Reveal a Maternal Hybridization Event Leading to the Formation of Cultivated Peanuts

Peanuts (Arachis hypogaea L.) offer numerous healthy benefits, and the production of peanuts has a prominent role in global food security. As a result, it is in the interest of society to improve the productivity and quality of peanuts with transgenic means. However, the lack of a robust phylogeny of cultivated and wild peanut species has limited the utilization of genetic resources in peanut molecular breeding. In this study, a total of 33 complete peanut plastomes were sequenced, analyzed and used for phylogenetic analyses. Our results suggest that sect. Arachis can be subdivided into two lineages. All the cultivated species are contained in Lineage I with AABB and AA are the two predominant genome types present, while species in Lineage II possess diverse genome types, including BB, KK, GG, etc. Phylogenetic studies also indicate that all allotetraploid cultivated peanut species have been derived from a possible maternal hybridization event with one of the diploid Arachis duranensis accessions being a potential AA sub-genome ancestor. In addition, Arachis monticola, a tetraploid wild species, is placed in the same group with all the cultivated peanuts, and it may represent a transitional species, which has been through the recent hybridization event. This research could facilitate a better understanding of the taxonomic status of various Arachis species/accessions and the evolutionary relationship among them, and assists in the correct and efficient use of germplasm resources in breeding efforts to improve peanuts for the benefit of human beings.

Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes

Sorghum [Sorghum bicolor (L.) Moench] is an important food crop with a diverse gene pool residing in its wild relatives. A total of 15 sorghum accessions from the unexploited wild gene pool of the Sorghum genus, representing the five subgenera, were sequenced, and the complete chloroplast genomes and 99 common single-copy concatenated nuclear genes were assembled. Annotation of the chloroplast genomes identified a total of 81 protein-coding genes, 38 tRNA, and four rRNA genes. The gene content and gene order among the species was identical. A total of 153 nonsynonymous amino acid changes in 40 genes were identified across the species. Phylogenetic analysis of both the whole chloroplast genome and nuclear genes revealed a similar topology with two distinct clades within the genus. The species within the subgenera Eusorghum, Chaetosorghum, and Heterosorghum clustered in one clade, whereas the species within the subgenera Parasorghum and Stiposorghum clustered in a second clade. However, the subgenera Parasorghum and Stiposorghum were not monophyletic, suggesting the need for further research to resolve the relationships within this group. The close relationship between the two monotypic subgenera Chaetosorghum and Heterosorghum suggests that species within these subgenera could be considered as one group. This analysis provides an improved understanding of the genetic relationships within the Sorghum genus and defines diversity in wild sorghum species that may be useful for crop improvement.

Structural rearrangements in plastid genomes of Apiaceae as phylogenetic markers

Apiaceae belong to angiosperm families with frequent plastome structural rearrangements, some of which are generally regarded as synapomorphic for large clades, although typically with limited taxon sampling. Our study aims to improve understanding of the structural rearrangements in plastome within the Tordylieae tribe (ApiaceaeApioideae) with a dense sampling scheme of its species. We showed that presence of psbA pseudogene in inverted repeats near the border with a large single-copy region, which is found in the Tordylieae tribe, may be a clade-specific synapomorphy.

Complete Chloroplast Genomes of Acanthochlamys bracteata (China) and Xerophyta (Africa) (Velloziaceae): Comparative Genomics and Phylogenomic Placement

Acanthochlamys P.C. Kao is a Chinese endemic monotypic genus, whereas Xerophyta Juss. is a genus endemic to Africa mainland, Arabian Peninsula and Madagascar with ca.70 species. In this recent study, the complete chloroplast genome of Acanthochlamys bracteata was sequenced and its genome structure compared with two African Xerophyta species (Xerophyta spekei and Xerophyta viscosa) present in the NCBI database. The genomes showed a quadripartite structure with their sizes ranging from 153,843 bp to 155,498 bp, having large single-copy (LSC) and small single-copy (SSC) regions divided by a pair of inverted repeats (IR regions). The total number of genes found in A. bracteata, X. spekei and X. viscosa cp genomes are 129, 130, and 132, respectively. About 50, 29, 28 palindromic, forward and reverse repeats and 90, 59, 53 simple sequence repeats (SSRs) were found in the A. bracteata, X. spekei, and X. viscosa cp genome, respectively. Nucleotide diversity analysis in all species was 0.03501, Ka/Ks ratio average score was calculated to be 0.26, and intergeneric K2P value within the Order Pandanales was averaged to be 0.0831. Genomic characterization was undertaken by comparing the genomes of the three species of Velloziaceae and it revealed that the coding regions were more conserved than the non-coding regions. However, key variations were noted mostly at the junctions of IRs/SSC regions. Phylogenetic analysis suggests that A. bracteata species has a closer genetic relationship to the genus Xerophyta. The present study reveals the complete chloroplast genome of A. bracteata and gives a genomic comparative analysis with the African species of Xerophyta. Thus, can be useful in developing DNA markers for use in the study of genetic variabilities and evolutionary studies in Velloziaceae.

Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae

The genus Blumea (Asteroideae, Asteraceae) comprises about 100 species, including herbs, shrubs, and small trees. Previous studies have been unable to resolve taxonomic issues and the phylogeny of the genus Blumea due to the low polymorphism of molecular markers. Therefore, suitable polymorphic regions need to be identified. Here, we de novo assembled plastomes of the three Blumea species B. oxyodonta, B. tenella, and B. balsamifera and compared them with 26 other species of Asteroideae after correction of annotations. These species have quadripartite plastomes with similar gene content, genome organization, and inverted repeat contraction and expansion comprising 113 genes, including 80 protein-coding, 29 transfer RNA, and 4 ribosomal RNA genes. The comparative analysis of codon usage, amino acid frequency, microsatellite repeats, oligonucleotide repeats, and transition and transversion substitutions has revealed high resemblance among the newly assembled species of Blumea. We identified 10 highly polymorphic regions with nucleotide diversity above 0.02, including rps16-trnQ, ycf1, ndhF-rpl32, petN-psbM, and rpl32-trnL, and they may be suitable for the development of robust, authentic, and cost-effective markers for barcoding and inference of the phylogeny of the genus Blumea. Among these highly polymorphic regions, five regions also co-occurred with oligonucleotide repeats and support use of repeats as a proxy for the identification of polymorphic loci. The phylogenetic analysis revealed a close relationship between Blumea and Pluchea within the tribe Inuleae. At tribe level, our phylogeny supports a sister relationship between Astereae and Anthemideae rooted as Gnaphalieae, Calenduleae, and Senecioneae. These results are contradictory to recent studies which reported a sister relationship between "Senecioneae and Anthemideae" and "Astereae and Gnaphalieae" or a sister relationship between Astereae and Gnaphalieae rooted as Calenduleae, Anthemideae, and then Senecioneae using nuclear genome sequences. The conflicting phylogenetic signals observed at the tribal level between plastidt and nuclear genome data require further investigation.

Integrated analysis of three newly sequenced fern chloroplast genomes: Genome structure and comparative analysis

BACKGROUND

Some ferns have medicinal properties and are used in therapeutic interventions. However, the classification and phylogenetic relationships of ferns remain incompletely reported. Considering that chloroplast genomes provide ideal information for species identification and evolution, in this study, three unpublished and one published ferns were sequenced and compared with other ferns to obtain comprehensive information on their classification and evolution.

MATERIALS AND METHODS

The complete chloroplast genomes of Dryopteris goeringiana (Kunze) Koidz, D. crassirhizoma Nakai, Athyrium brevifrons Nakai ex Kitagawa, and Polystichum tripteron (Kunze) Presl were sequenced using the Illumina HiSeq 4,000 platform. Simple sequence repeats (SSRs), nucleotide diversity analysis, and RNA editing were investigated in all four species. Genome comparison and inverted repeats (IR) boundary expansion and contraction analyses were also performed. The relationships among the ferns were studied by phylogenetic analysis based on the whole chloroplast genomes.

RESULTS

The whole chloroplast genomes ranged from 148,539 to 151,341 bp in size and exhibited typical quadripartite structures. Ten highly variable loci with parsimony informative (Pi) values of > 0.02 were identified. A total of 75-108 SSRs were identified, and only six SSRs were present in all four ferns. The SSRs contained a higher number of A + T than G + C bases. C-to-U conversion was the most common type of RNA editing event. Genome comparison analysis revealed that single-copy regions were more highly conserved than IR regions. IR boundary expansion and contraction varied among the four ferns. Phylogenetic analysis showed that species in the same genus tended to cluster together with and had relatively close relationships.

CONCLUSION

The results provide valuable information on fern chloroplast genomes that will be useful to identify and classify ferns, and study their phylogenetic relationships and evolution.

Mutational Dynamics of Aroid Chloroplast Genomes II

The co-occurrence among single nucleotide polymorphisms (SNPs), insertions-deletions (InDels), and oligonucleotide repeats has been reported in prokaryote, eukaryote, and chloroplast genomes. Correlations among SNPs, InDels, and repeats have been investigated in the plant family Araceae previously using pair-wise sequence alignments of the chloroplast genomes of two morphotypes of one species, Colocasia esculenta belonging to subfamily Aroideae (crown group), and four species from the subfamily Lemnoideae, a basal group. The family Araceae is a large family comprising 3,645 species in 144 genera, grouped into eight subfamilies. In the current study, we performed 34 comparisons using 27 species from 7 subfamilies of Araceae to determine correlation coefficients among the mutational events at the family, subfamily, and genus levels. We express strength of the correlations as: negligible or very weak (0.10–0.19), weak (0.20–0.29), moderate (0.30–0.39), strong (0.40–0.69), very strong (0.70–0.99), and perfect (1.00). We observed strong/very strong correlations in most comparisons, whereas a few comparisons showed moderate correlations. The average correlation coefficient was recorded as 0.66 between “SNPs and InDels,” 0.50 between “InDels and repeats,” and 0.42 between “SNPs and repeats.” In qualitative analyses, 95–100% of the repeats at family and sub-family level, while 36–86% of the repeats at genus level comparisons co-occurred with SNPs in the same bins. Our findings show that such correlations among mutational events exist throughout Araceae and support the hypothesis of distribution of oligonucleotide repeats as a proxy for mutational hotspots.

Chloroplast Genome Evolution in Four Montane Zingiberaceae Taxa in China

Chloroplasts are critical to plant survival and adaptive evolution. The comparison of chloroplast genomes could provide insight into the adaptive evolution of closely related species. To identify potential adaptive evolution in the chloroplast genomes of four montane Zingiberaceae taxa (Cautleya, Roscoea, Rhynchanthus, and Pommereschea) that inhabit distinct habitats in the mountains of Yunnan, China, the nucleotide sequences of 13 complete chloroplast genomes, including five newly sequenced species, were characterized and compared. The five newly sequenced chloroplast genomes (162,878-163,831 bp) possessed typical quadripartite structures, which included a large single copy (LSC) region, a small single copy (SSC) region, and a pair of inverted repeat regions (IRa and IRb), and even though the structure was highly conserved among the 13 taxa, one of the rps19 genes was absent in Cautleya, possibly due to expansion of the LSC region. Positive selection of rpoA and ycf2 suggests that these montane species have experienced adaptive evolution to habitats with different sunlight intensities and that adaptation related to the chloroplast genome has played an important role in the evolution of Zingiberaceae taxa.

Comparative and Evolutionary Analyses on the Complete Plastomes of Five Kalanchoe Horticultural Plants

Many species of the genus Kalanchoe are important horticultural plants. They have evolved the Crassulacean acid metabolism (CAM) photosynthetic pathway to allow them to be better adapted to dry environments. Despite their importance, it is still debating whether Kalanchoe is monophyletic, and understanding the past diversification of this genus requires a tremendous amount of effort and work being devoted to the studies of morphological and molecular characters of this genus. However, molecular information, plastic sequence data, in particular, reported on Kalanchoe species is scarce, and this has posed a great challenge in trying to interpret the evolutionary history of this genus. In this study, plastomes of the five Kalanchoe species, including Kalanchoe daigremontiana, Kalanchoe delagoensis, Kalanchoe fedtschenkoi, Kalanchoe longiflora, and Kalanchoe pinnata, were sequenced and analyzed. The results indicate that the five plastomes are comparable in size, guanine-cytosine (GC) contents and the number of genes, which also demonstrate an insignificant difference in comparison with other species from the family Crassulaceae. About 224 simple sequence repeats (SSRs) and 144 long repeats were identified in the five plastomes, and most of these are distributed in the inverted repeat regions. In addition, highly divergent regions containing either single nucleotide polymorphism (SNP) or insertion or deletion (InDel) mutations are discovered, which could be potentially used for establishing phylogenetic relationships among members of the Kalanchoe genus in future studies. Furthermore, phylogenetic analyses suggest that Bryophyllum should be placed into one single genus as Kalanchoe. Further genomic analyses also reveal that several genes are undergone positive selection. Among them, 11 genes are involved in important cellular processes, such as cell survival, electron transfer, and may have played indispensable roles in the adaptive evolution of Kalanchoe to dry environments.

Chloroplast genome assembly of Handroanthus impetiginosus: comparative analysis and molecular evolution in Bignoniaceae

Bignoniaceae species have conserved chloroplast structure, with hotspots of nucleotide diversity. Several genes are under positive selection, and can be targets for evolutionary studies. Bignoniaceae is one of the most species-rich family of woody plants in Neotropical seasonally dry forests. Here we report the assembly of Handroanthus impetiginosus chloroplast genome and evolutionary comparative analyses of ten Bignoniaceae species representing the genera for which whole-genome chloroplast sequences were available. The chloroplast genome of H. impetiginosus is 159,462 bp in size and has a similar structure compared to the other nine species. The total number of genes was slightly variable amongst the Bignoniaceae, ranging from 124 in H. impetiginosus to 144 in Anemopaegma acutifolium. The inverted repeat (IR) size was variable, ranging from 24,657 bp (Tecomaria capensis) to 40,481 bp (A. acutifolium), due to the contraction and retraction at its boundaries. However, gene boundaries were very similar among the ten species. We found 98 forward and palindromic dispersed repeats, and 85 simple sequence repeats (SSRs). In general, chloroplast sequences were highly conserved, with few nucleotide diversity hotspots in the genes accD, clpP, rpoA, ycf1, ycf2. The phylogenetic analysis based on 77 coding genes was highly consistent with Angiosperm Phylogeny Group (APG) IV. Our results also indicate that most genes are under negative selection or neutral evolution. We found no evidence of branch-site selection, implying that H. impetiginosus is not evolving faster than the other species analyzed, notwithstanding we found site positive selection signal in several genes. These genes can provide targets for evolutionary studies in Bignoniaceae and Lamiales species.

Complete Chloroplast Genome of Argania spinosa: Structural Organization and Phylogenetic Relationships in Sapotaceae

Argania spinosa (Sapotaceae), an important endemic Moroccan oil tree, is a primary source of argan oil, which has numerous dietary and medicinal proprieties. The plant species occupies the mid-western part of Morocco and provides great environmental and socioeconomic benefits. The complete chloroplast (cp) genome of A. spinosa was sequenced, assembled, and analyzed in comparison with those of two Sapotaceae members. The A. spinosa cp genome is 158,848 bp long, with an average GC content of 36.8%. The cp genome exhibits a typical quadripartite and circular structure consisting of a pair of inverted regions (IR) of 25,945 bp in length separating small single-copy (SSC) and large single-copy (LSC) regions of 18,591 and 88,367 bp, respectively. The annotation of A. spinosa cp genome predicted 130 genes, including 85 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. A total of 44 long repeats and 88 simple sequence repeats (SSR) divided into mononucleotides (76), dinucleotides (7), trinucleotides (3), tetranucleotides (1), and hexanucleotides (1) were identified in the A. spinosa cp genome. Phylogenetic analyses using the maximum likelihood (ML) method were performed based on 69 protein-coding genes from 11 species of Ericales. The results confirmed the close position of A. spinosa to the Sideroxylon genus, supporting the revisiting of its taxonomic status. The complete chloroplast genome sequence will be valuable for further studies on the conservation and breeding of this medicinally and culinary important species and also contribute to clarifying the phylogenetic position of the species within Sapotaceae.

Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)

Species of the genus Nicotiana (Solanaceae), commonly referred to as tobacco plants, are often cultivated as non-food crops and garden ornamentals. In addition to the worldwide production of tobacco leaves, they are also used as evolutionary model systems due to their complex development history tangled by polyploidy and hybridization. Here, we assembled the plastid genomes of five tobacco species: N. knightiana, N. rustica, N. paniculata, N. obtusifolia and N. glauca. De novo assembled tobacco plastid genomes had the typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions (25,323-25,369 bp each) separated by a large single-copy (LSC) region (86,510-86,716 bp) and a small single-copy (SSC) region (18,441-18,555 bp). Comparative analyses of Nicotiana plastid genomes with currently available Solanaceae genome sequences showed similar GC and gene content, codon usage, simple sequence and oligonucleotide repeats, RNA editing sites, and substitutions. We identified 20 highly polymorphic regions, mostly belonging to intergenic spacer regions (IGS), which could be suitable for the development of robust and cost-effective markers for inferring the phylogeny of the genus Nicotiana and family Solanaceae. Our comparative plastid genome analysis revealed that the maternal parent of the tetraploid N. rustica was the common ancestor of N. paniculata and N. knightiana, and the later species is more closely related to N. rustica. Relaxed molecular clock analyses estimated the speciation event between N. rustica and N. knightiana appeared 0.56 Ma (HPD 0.65-0.46). Biogeographical analysis supported a south-to-north range expansion and diversification for N. rustica and related species, where N. undulata and N. paniculata evolved in North/Central Peru, while N. rustica developed in Southern Peru and separated from N. knightiana, which adapted to the Southern coastal climatic regimes. We further inspected selective pressure on protein-coding genes among tobacco species to determine if this adaptation process affected the evolution of plastid genes. These analyses indicate that four genes involved in different plastid functions, including DNA replication (rpoA) and photosynthesis (atpB, ndhD and ndhF), came under positive selective pressure as a result of specific environmental conditions. Genetic mutations in these genes might have contributed to better survival and superior adaptations during the evolutionary history of tobacco species.

Comparative Plastomics of Ashwagandha (Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants

Within the family Solanaceae, Withania is a small genus belonging to the Solanoideae subfamily. Here, we report the de novo assembled chloroplast genome sequences of W. coagulans, W. adpressa, and W. riebeckii. The length of these genomes ranged from 154,162 to 154,364 base pairs (bp). These genomes contained a pair of inverted repeats (IRa and IRb) ranging from 25,029 to 25,071 bp that were separated by a large single-copy (LSC) region of 85,635-85,765 bp and a small single-copy (SSC) region of 18,457-18,469 bp. We analyzed the structural organization, gene content and order, guanine-cytosine content, codon usage, RNA-editing sites, microsatellites, oligonucleotide and tandem repeats, and substitutions of Withania plastomes, which revealed high similarities among the species. Comparative analysis among the Withania species also highlighted 10 divergent hotspots that could potentially be used for molecular marker development, phylogenetic analysis, and species identification. Furthermore, our analyses showed that even three mutational hotspots (rps4-trnT, trnM-atpE, and rps15) were sufficient to discriminate the Withania species included in current study.

Complete chloroplast genome sequence of Barleria prionitis, comparative chloroplast genomics and phylogenetic relationships among Acanthoideae

BACKGROUND

The plastome of medicinal and endangered species in Kingdom of Saudi Arabia, Barleria prionitis was sequenced. The plastome was compared with that of seven Acanthoideae species in order to describe the plastome, spot the microsatellite, assess the dissimilarities within the sampled plastomes and to infer their phylogenetic relationships.

RESULTS

The plastome of B. prionitis was 152,217 bp in length with Guanine-Cytosine and Adenine-Thymine content of 38.3 and 61.7% respectively. It is circular and quadripartite in structure and constitute of a large single copy (LSC, 83, 772 bp), small single copy (SSC, 17, 803 bp) and a pair of inverted repeat (IRa and IRb 25, 321 bp each). 131 genes were identified in the plastome out of which 113 are unique and 18 were repeated in IR region. The genome consists of 4 rRNA, 30 tRNA and 80 protein-coding genes. The analysis of long repeat showed all types of repeats were present in the plastome and palindromic has the highest frequency. A total number of 98 SSR were also identified of which mostly were mononucleotide Adenine-Thymine and are located at the non coding regions. Comparative genomic analysis among the plastomes revealed that the pair of the inverted repeat is more conserved than the single copy region. In addition high variation is observed in the intergenic spacer region than the coding region. The genes, ycf1and ndhF and are located at the border junction of the small single copy region and IRb region of all the plastome. The analysis of sequence divergence in the protein coding genes indicates that the following genes undergo positive selection (atpF, petD, psbZ, rpl20, petB, rpl16, rps16, rpoC, rps7, rpl32 and ycf3). Phylogenetic analysis indicated sister relationship between Ruellieae and Justcieae. In addition, Barleria, Justicia and Ruellia are paraphyletic, suggesting that Justiceae, Ruellieae, Andrographideae and Barlerieae should be treated as tribes.

CONCLUSIONS

This study sequenced and assembled the first plastome of the taxon Barleria and reported the basics resources for evolutionary studies of B. prionitis and tools for phylogenetic relationship studies within the core Acanthaceae.

Complete chloroplast genome sequence determination of Rheum species and comparative chloroplast genomics for the members of Rumiceae

Complete plastomes of Rheum species facilitated to clarify the phylogeny of Polygonaceae, and comparative chloroplast genomics contributed to develop genetic markers for the authentication of Rheum species. Rheum (Polygonaceae) is widely distributed throughout the temperate and subtropical areas of Asian interior. Rheum species are usually perennial herbs, and half of them are endemic to China with important medicinal properties. On account of similar morphological characteristics, species delimitation of Rheum still remains unclear. Chloroplast genomes of eight Rheum species, Rumex crispus and Oxyria digyna were characterized. Based on the comparison of genome structure of these species and the two published Rheum species, it is shown that plastome sequences of these species are relatively conserved with the same gene order, and three Sect. Palmata species remarkably showed high sequence similarities. Some hotspots could be used to discriminate the Rheum species, and 17 plastid genes were subject to positive selection. The phylogenetic analyses indicated that all the Polygonaceae species were clustered in the same group and showed that Rheum species, except for Rheum wittrockii, formed a monophyletic group with high maximum parsimony/maximum likelihood bootstrap support values and Bayesian posterior probabilities. The molecular dating based on plastomes indicated that the divergences within Polygonaceae species were dated to the Upper Cretaceous period [73.86-77.99 million years ago (Ma)]. The divergence of Sect. Palmata species was estimated to have occurred around 1.60 Ma, indicating that its diversification was affected by the repeated climatic fluctuation in the Quaternary.

Comprehensive genomic analyses with 115 plastomes from algae to seed plants: structure, gene contents, GC contents, and introns

BACKGROUND

Chloroplasts are a common character in plants. The chloroplasts in each plant lineage have shaped their own genomes, plastomes, by structural changes and transferring many genes to nuclear genomes during plant evolution. Some plastid genes have introns that are mostly group II introns.

OBJECTIVE

This study aimed to get genomic and evolutionary insights on the plastomes from green algae to flowering plants.

METHODS

Plastomes of 115 species from green algae, bryophytes, pteridophytes (spore bearing vascular plants), gymnosperms, and angiosperms were mined from NCBI organelle genome database. Plastome structure, gene contents and GC contents were analyzed by the in-house developed Phyton code. Intronic features including presence/absence, length, intron phases were analyzed by manually in the annotated information in NCBI.

RESULTS

The canonical quadripartite structures were retained in most plastomes except of a few plastomes that had lost an invert repeat (IR). Expansion or reduction or deletion of IRs resulted in the length variation of the plastomes. The number of protein coding genes ranged from 40 to 92 with an average 79.43 ± 5.84 per plastome and gene losses were apparent in specific lineages. The number of trn genes ranged from 13 to 33 with an average 21.19 ± 2.42 per plastome. Ribosomal RNA genes, rrn, were located in the IRs so that they were present in a duplicate except of the species that had lost one of the IR. GC contents were variable from 24.9 to 51.0% with an average 38.21 ± 3.27%, indicating bias to high AT contents. Plastid introns were present in 18 protein coding genes, six trn genes, and one rrn gene. Intron losses occurred among the orthologous genes in different plant lineages. The plastid introns were long compared with the nuclear introns, which might be related with the spliceosome nuclear introns and self-splicing group II plastid introns. The trnK-UUU intron contained the maturase encoding matK gene except in the chlorophyte algae and monilophyte ferns in which the trnK-UUU was lost, but matK retained. There were many annotation artefacts in the intron positions in the NCBI database. In the analysis of intron phases, phase 0 introns were more frequent than those of phase 2 and 3 introns. Phase polymorphism was observed in the introns of clpP which was derived from nucleotide insertion. Plastid trn introns were long compared to the archaeal or eukaryotic nuclear tRNA introns. Of the six plastid trn introns, one was at the D loop and other five were at the anticodon loop. The insertion sites were conserved among the trn genes in archaea, eukaryotic nuclear and plastid tRNA genes.

CONCLUSIONS

Current study refurbrished the previous findings of structural variations, gene contents, and GC contents of the chloroplast genomes from green algae to flowering plants. The study also included some noble findings and discussions on the plastome introns including their length variations and phase variation. We also presented and corrected some false annotations on the introns in protein coding and tRNA genes in the genome database, which might be confirmed by the chloroplast transcriptome analysis in the future.

Molecular evolution of chloroplast genomes in Monsteroideae (Araceae)

This study provides broad insight into the chloroplast genomes of the subfamily Monsteroideae. The identified polymorphic regions may be suitable for designing unique and robust molecular markers for phylogenetic inference. Monsteroideae is the third largest subfamily (comprises 369 species) and one of the early diverging lineages of the monocot plant family Araceae. The phylogeny of this important subfamily is not well resolved at the species level due to scarcity of genomic resources and suitable molecular markers. Here, we report annotated chloroplast genome sequences of four Monsteroideae species: Spathiphyllum patulinervum, Stenospermation multiovulatum, Monstera adansonii, and Rhaphidophora amplissima. The quadripartite chloroplast genomes (size range 163,335-164,751 bp) consist of a pair of inverted repeats (25,270-25,931 bp), separating a small single copy region (21,448-22,346 bp) from a large single copy region (89,714-91,841 bp). The genomes contain 114 unique genes, including four rRNA genes, 80 protein-coding genes, and 30 tRNA genes. Gene features, amino acid frequencies, codon usage, GC contents, oligonucleotide repeats, and inverted repeats dynamics exhibit similarities among the four genomes. Higher rate of synonymous substitutions was observed as compared to non-synonymous substitutions in 76 protein-coding genes. Positive selection was observed in seven protein-coding genes, including psbK, ndhK, ndhD, rbcL, accD, rps8, and ycf2. Our included species of Araceae showed the monophyly in Monsteroideae and other subfamilies. We report 30 suitable polymorphic regions. The polymorphic regions identified here might be suitable for designing unique and robust markers for inferring the phylogeny and phylogeography among closely related species within the genus Spathiphyllum and among distantly related species within the subfamily Monsteroideae. The chloroplast genomes presented here are a valuable contribution towards understanding the molecular evolutionary dynamics in the family Araceae.

Evolutionary dynamics of chloroplast genomes in subfamily Aroideae (Araceae)

Aroideae is the largest and most diverse subfamily of the plant family Araceae. Despite its agricultural and horticultural importance, the genomic resources are sparse for this subfamily. Here, we report de novo assembled and fully annotated chloroplast genomes of 13 Aroideae species. The quadripartite chloroplast genomes (size range of 158,177-170,037 bp) are comprised of a large single copy (LSC; 75,594-94,702 bp), a small single copy (SSC; 12,903-23,981 bp) and a pair of inverted repeats (IRs; 25,266-34,840 bp). Notable gene rearrangements and IRs contraction / expansions were found for Anchomanes hookeri and Zantedeschia aethiopica. Codon usage, amino acid frequencies, oligonucleotide repeats, GC contents, and gene features revealed similarities among the 13 species. The number of oligonucleotide repeats was uncorrelated with genome size or phylogenetic position of the species. Phylogenetic analyses corroborated the monophyly of Aroideae but were unable to resolve the positions of Calla and Schismatoglottis.

Plastid Genomes of Five Species of Riverweeds (Podostemaceae): Structural Organization and Comparative Analysis in Malpighiales

With the advent of next-generation sequencing technologies, whole-plastome data can be obtained as a byproduct of low-coverage sequencing of the plant genomic DNA. This provides an opportunity to study plastid evolution across groups, as well as testing phylogenetic relationships among taxa. Within the order Malpighiales (∼16,000 spp.), the Podostemaceae (∼300 spp.) stand out for their unique habit, living attached to rocks in fast-flowing aquatic habitats, and displaying highly modified morphologies that confound our understanding of their classification, biology, and evolution. In this study, we used genome skimming data to assemble the full plastid genome of 5 species within Podostemaceae. We analyzed our data in a comparative framework within Malpighiales to determine the structure, gene content, and rearrangements in the plastomes of the family. The Podostemaceae have one of the smallest plastid genomes reported so far for the Malpighiales, possibly due to variation in length of inverted repeat (IR) regions, gene loss, and intergenic region variation. We also detected a major inversion in the large single-copy region unique to the family. The uncommon loss or pseudogenization of ycf1 and ycf2 in angiosperms and in land plants in general is also found to be characteristic of Podostemaceae, but the compensatory mechanisms and implications of this and of the pseudogenization of accD, rpl22, and clpP and loss of rps16 remain to be explained in this group. In addition, we estimated a phylogenetic tree among selected species in Malpighiales. Our findings indicate that the Podostemaceae are a distinct lineage with long branches that suggest faster rates of evolution in the plastome of the group, compared with other taxa in the order. This study lays the foundations for future phylogenomic studies in the family.

Loss of a chloroplast encoded function could influence species range in kelp

Kelps are important providers and constituents of marine ecological niches, the coastal kelp forests. Kelp species have differing distribution ranges, but mainly thrive in temperate and arctic regions. Although the principal factors determining biogeographic distribution ranges are known, genomics could provide additional answers to this question. We sequenced DNA from two Laminaria species with contrasting distribution ranges, Laminaria digitata and Laminaria solidungula. Laminaria digitata is found in the Northern Atlantic with a southern boundary in Brittany (France) or Massachusetts (USA) and a northern boundary in the Arctic, whereas L. solidungula is endemic to the Arctic only. From the raw reads of DNA, we reconstructed both chloroplast genomes and annotated them. A concatenated data set of all available brown algae chloroplast sequences was used for the calculation of a robust phylogeny, and sequence variations were analyzed. The two Laminaria chloroplast genomes are collinear to previously analyzed kelp chloroplast genomes with important exceptions. Rearrangements at the inverted repeat regions led to the pseudogenization of ycf37 in L. solidungula, a gene possibly required under high light conditions. This defunct gene might be one of the reasons why the habitat range of L. solidungula is restricted to lowlight sublittoral sites in the Arctic. The inheritance pattern of single nucleotide polymorphisms suggests incomplete lineage sorting of chloroplast genomes in kelp species. Our analysis of kelp chloroplast genomes shows that not only evolutionary information could be gleaned from sequence data. Concomitantly, those sequences can also tell us something about the ecological conditions which are required for species well-being.

Extensive chloroplast genome rearrangement amongst three closely related Halamphora spp. (Bacillariophyceae), and evidence for rapid evolution as compared to land plants

Diatoms are the most diverse lineage of algae, but the diversity of their chloroplast genomes, particularly within a genus, has not been well documented. Herein, we present three chloroplast genomes from the genus Halamphora (H. americana, H. calidilacuna, and H. coffeaeformis), the first pennate diatom genus to be represented by more than one species. Halamphora chloroplast genomes ranged in size from ~120 to 150 kb, representing a 24% size difference within the genus. Differences in genome size were due to changes in the length of the inverted repeat region, length of intergenic regions, and the variable presence of ORFs that appear to encode as-yet-undescribed proteins. All three species shared a set of 161 core features but differed in the presence of two genes, serC and tyrC of foreign and unknown origin, respectively. A comparison of these data to three previously published chloroplast genomes in the non-pennate genus Cyclotella (Thalassiosirales) revealed that Halamphora has undergone extensive chloroplast genome rearrangement compared to other genera, as well as containing variation within the genus. Finally, a comparison of Halamphora chloroplast genomes to those of land plants indicates diatom chloroplast genomes within this genus may be evolving at least ~4–7 times faster than those of land plants. Studies such as these provide deeper insights into diatom chloroplast evolution and important genetic resources for future analyses.

Tension and Resolution: Dynamic, Evolving Populations of Organelle Genomes within Plant Cells

Mitochondria and plastids form dynamic, evolving populations physically embedded in the fluctuating environment of the plant cell. Their evolutionary heritage has shaped how the cell controls the genetic structure and the physical behavior of its organelle populations. While the specific genes involved in these processes are gradually being revealed, the governing principles underlying this controlled behavior remain poorly understood. As the genetic and physical dynamics of these organelles are central to bioenergetic performance and plant physiology, this challenges both fundamental biology and strategies to engineer better-performing plants. This article reviews current knowledge of the physical and genetic behavior of mitochondria and chloroplasts in plant cells. An overarching hypothesis is proposed whereby organelles face a tension between genetic robustness and individual control and responsiveness, and different species resolve this tension in different ways. As plants are immobile and thus subject to fluctuating environments, their organelles are proposed to favor individual responsiveness, sacrificing genetic robustness. Several notable features of plant organelles, including large genomes, mtDNA recombination, fragmented organelles, and plastid/mitochondrial differences may potentially be explained by this hypothesis. Finally, the ways that quantitative and systems biology can help shed light on the plethora of open questions in this field are highlighted.

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.

Sequencing and Comparative Analysis of the Chloroplast Genome of Angelica polymorpha and the Development of a Novel Indel Marker for Species Identification

The genus Angelica (Apiaceae) comprises valuable herbal medicines. In this study, we determined the complete chloroplast (CP) genome sequence of A. polymorpha and compared it with that of Ligusticum officinale (GenBank accession no. NC039760). The CP genomes of A. polymorpha and L. officinale were 148,430 and 147,127 bp in length, respectively, with 37.6% GC content. Both CP genomes harbored 113 unique functional genes, including 79 protein-coding, four rRNA, and 30 tRNA genes. Comparative analysis of the two CP genomes revealed conserved genome structure, gene content, and gene order. However, highly variable regions, sufficient to distinguish between A. polymorpha and L. officinale, were identified in hypothetical chloroplast open reading frame1 (ycf1) and ycf2 genic regions. Nucleotide diversity (Pi) analysis indicated that ycf4⁻chloroplast envelope membrane protein (cemA) intergenic region was highly variable between the two species. Phylogenetic analysis revealed that A. polymorpha and L. officinale were well clustered at family Apiaceae. The ycf4-cemA intergenic region in A. polymorpha carried a 418 bp deletion compared with L. officinale. This region was used for the development of a novel indel marker, LYCE, which successfully discriminated between A. polymorpha and L. officinale accessions. Our results provide important taxonomic and phylogenetic information on herbal medicines and facilitate their authentication using the indel marker.

Full plastome sequence of the fern Vandenboschia speciosa (Hymenophyllales): structural singularities and evolutionary insights

We provide here the first full chloroplast genome sequence, i.e., the plastome, for a species belonging to the fern order Hymenophyllales. The phylogenetic position of this order within leptosporangiate ferns, together with the general scarcity of information about fern plastomes, places this research as a valuable study on the analysis of the diversity of plastomes throughout fern evolution. Gene content of V. speciosa plastome was similar to that in most ferns, although there were some characteristic gene losses and lineage-specific differences. In addition, an important number of genes required U to C RNA editing for proper protein translation and two genes showed start codons alternative to the canonical AUG (AUA). Concerning gene order, V. speciosa shared the specific 30-kb inversion of euphyllophytes plastomes and the 3.3-kb inversion of fern plastomes, keeping the ancestral gene order shared by eusporangiate and early leptosporangiate ferns. Conversely, V. speciosa has expanded IR regions comprising the rps7, rps12, ndhB and trnL genes in addition to rRNA and other tRNA genes, a condition shared with several eusporangiate ferns, lycophytes and hornworts, as well as most seed plants.

Comparative chloroplast genomes of Paris Sect. Marmorata: insights into repeat regions and evolutionary implications

Background

Species of Paris Sect. Marmorata are valuable medicinal plants to synthesize steroidal saponins with effective pharmacological therapy. However, the wild resources of the species are threatened by plundering exploitation before the molecular genetics studies uncover the genomes and evolutionary significance. Thus, the availability of complete chloroplast genome sequences of Sect. Marmorata is necessary and crucial to the understanding the plastome evolution of this section and facilitating future population genetics studies. Here, we determined chloroplast genomes of Sect. Marmorata, and conducted the whole chloroplast genome comparison.

Results

This study presented detailed sequences and structural variations of chloroplast genomes of Sect. Marmorata. Over 40 large repeats and approximately 130 simple sequence repeats as well as a group of genomic hotspots were detected. Inverted repeat contraction of this section was inferred via comparing the chloroplast genomes with the one of P. verticillata. Additionally, almost all the plastid protein coding genes were found to prefer ending with A/U. Mutation bias and selection pressure predominately shaped the codon bias of most genes. And most of the genes underwent purifying selection, whereas photosynthetic genes experienced a relatively relaxed purifying selection.

Conclusions

Repeat sequences and hotspot regions can be scanned to detect the intraspecific and interspecific variability, and selected to infer the phylogenetic relationships of Sect. Marmorata and other species in subgenus Daiswa. Mutation and natural selection were the main forces to drive the codon bias pattern of most plastid protein coding genes. Therefore, this study enhances the understanding about evolution of Sect. Marmorata from the chloroplast genome, and provide genomic insights into genetic analyses of Sect. Marmorata.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5281-x) contains supplementary material, which is available to authorized users.