New Insights Into the Plastome Evolution of the Millettioid/Phaseoloid Clade (Papilionoideae, Leguminosae)

The complete chloroplast genome of Flemingia stricta Roxb. ex Ait. 1812 (Phaseoleae, Fabaceae)

Flemingia stricta Roxb. ex Ait. 1812 belongs to the Phaseoleae tribe within the Fabaceae family and has significant pharmaceutical value. In this study, we reported the complete chloroplast genome of F. stricta using the Illumina DNA sequencing data. The chloroplast genome was 152,940 bp and encoded 111 unique genes, including 77 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. The phylogenetic analysis confirmed that F. stricta was closely related to Flemingia prostrata and Flemingia macrophylla. The chloroplast genome of F. stricta could provide critical information for the molecular breeding of F. stricta and be used as a reference genome for other species of Phaseoleae.

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

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

Campylotropis xinfeniae (Fabaceae, Papilionoideae), a new species from Yunnan, China, based on morphological and molecular evidence

Campylotropis xinfeniae, a new species from the dry-hot valley of the Jinsha River in the Yunnan province, China, is described and illustrated. It is morphologically similar to C. wilsonii and C. brevifolia in having glabrescent old branches, absent stipels, 3-foliolate leaves, and adaxially puberulent leaflets, while it differs from the latter two in having often paniculate inflorescences, obviously white standard, not incurved sickle keel, larger narrowly oblique legumes, and longer legume beak. The complete chloroplast genome of this new species is 149,073 bp in length and exhibits a typical quadripartite structure. Phylogenetic analyses based on the complete chloroplast genome also supported C. xinfeniae as a new species located at the basal distinct clade of the genus Campylotropis, clearly separated from the remaining members of the genus and its allied genera. A conservation assessment of data deficient (DD) is recommended for the new species without extensive exploring of similar habitats according to the IUCN Categories and Criteria.

Deciphering the Plastomic Code of Chinese Hog-Peanut (Amphicarpaea edgeworthii Benth., Leguminosae): Comparative Genomics and Evolutionary Insights within the Phaseoleae Tribe

The classification and phylogenetic relationships within the Phaseoleae tribe (Leguminosae) have consistently posed challenges to botanists. This study addresses these taxonomic intricacies, with a specific focus on the Glycininae subtribe, by conducting a comprehensive analysis of the highly conserved plastome in Amphicarpaea edgeworthii Benth., a critical species within this subtribe. Through meticulous genomic sequencing, we identified a plastome size of 148,650 bp, composed of 128 genes, including 84 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Comparative genomic analysis across seven Glycininae species illuminated a universally conserved circular and quadripartite structure, with nine genes exhibiting notable nucleotide diversity, signifying a remarkable genomic variability. Phylogenetic reconstruction of 35 Phaseoleae species underscores the affinity of Amphicarpaea with Glycine, placing Apios as a sister lineage to all other Phaseoleae species, excluding Clitorinae and Diocleinae subtribes. Intriguingly, Apios, Butea, Erythrina, and Spatholobus, traditionally clumped together in the Erythrininae subtribe, display paraphyletic divergence, thereby contesting their taxonomic coherence. The pronounced structural differences in the quadripartite boundary genes among taxa with unresolved subtribal affiliations demand a reevaluation of Erythrininae's taxonomic classification, potentially refining the phylogenetic contours of the tribe.

Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume

Sambucus L. is found in the family Viburnaceae (syn. Adoxaceae) and encompasses approximately 29 accepted species. The complex morphology of these species has caused continued confusion concerning their nomenclature, classification, and identification. Despite previous attempts to resolve taxonomic complexities in the Sambucus genus, there are still unclear phylogenetic relationships among several species. In this study, the newly obtained plastome of Sambucus williamsii Hance. as well as the populations of Sambucus canadensis L., Sambucus javanica Blume, and Sambucus adnata Wall. ex DC were sequenced, and their sizes, structural similarity, gene order, gene number, and guanine-cytosine (GC) contents were analyzed. The phylogenetic analyses were conducted using the whole chloroplast genomes and protein-coding genes (PCGs). The findings revealed that the chloroplast genomes of Sambucus species exhibited typical quadripartite double-stranded DNA molecules. Their lengths ranged from 158,012 base pairs (bp) (S. javanica) to 158,716 bp (S. canadensis L). Each genome comprised a pair of inverted repeats (IRs), which separated the large single-copy (LSC) and small single-copy (SSC) regions. In addition, the plastomes contained 132 genes, encompassing 87 protein-coding, 37 tRNA, and four rRNA genes. In the simple sequence repeat (SSR) analysis, A/T mononucleotides had the highest proportion, with the most repetitive sequences observed in S. williamsii. The comparative genome analyses showed high similarities in structure, order, and gene contents. The hypervariable regions in the studied chloroplast genomes were trnT-GGU, trnF-GAA, psaJ, trnL-UAG, ndhF, and ndhE, which may be used as candidate barcodes for species discrimination in Sambucus genus. Phylogenetic analyses supported the monophyly of Sambucus and revealed the separation of S. javanica and S. adnata populations. Sambucus chinensis Lindl. was nested within S. javanica in the same clade, collaborating their conspecific treatment. These outcomes indicate that the chloroplast genome of Sambucus plants is a valuable genetic resource for resolving taxonomic discrepancies at the lower taxonomic levels and can be applied in molecular evolutionary studies.

Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume

Sambucus L. is found in the family Viburnaceae (syn. Adoxaceae) and encompasses approximately 29 accepted species. The complex morphology of these species has caused continued confusion concerning their nomenclature, classification, and identification. Despite previous attempts to resolve taxonomic complexities in the Sambucus genus, there are still unclear phylogenetic relationships among several species. In this study, the newly obtained plastome of Sambucus williamsii Hance. as well as the populations of Sambucus canadensis L., Sambucus javanica Blume, and Sambucus adnata Wall. ex DC were sequenced, and their sizes, structural similarity, gene order, gene number, and guanine–cytosine (GC) contents were analyzed. The phylogenetic analyses were conducted using the whole chloroplast genomes and protein-coding genes (PCGs). The findings revealed that the chloroplast genomes of Sambucus species exhibited typical quadripartite double-stranded DNA molecules. Their lengths ranged from 158,012 base pairs (bp) (S. javanica) to 158,716 bp (S. canadensis L). Each genome comprised a pair of inverted repeats (IRs), which separated the large single-copy (LSC) and small single-copy (SSC) regions. In addition, the plastomes contained 132 genes, encompassing 87 protein-coding, 37 tRNA, and four rRNA genes. In the simple sequence repeat (SSR) analysis, A/T mononucleotides had the highest proportion, with the most repetitive sequences observed in S. williamsii. The comparative genome analyses showed high similarities in structure, order, and gene contents. The hypervariable regions in the studied chloroplast genomes were trnT-GGU, trnF-GAA, psaJ, trnL-UAG, ndhF, and ndhE, which may be used as candidate barcodes for species discrimination in Sambucus genus. Phylogenetic analyses supported the monophyly of Sambucus and revealed the separation of S. javanica and S. adnata populations. Sambucus chinensis Lindl. was nested within S. javanica in the same clade, collaborating their conspecific treatment. These outcomes indicate that the chloroplast genome of Sambucus plants is a valuable genetic resource for resolving taxonomic discrepancies at the lower taxonomic levels and can be applied in molecular evolutionary studies.

Phylogenomics and plastome evolution of Indigofera (Fabaceae)

Introduction

Indigofera L. is the third largest genus in Fabaceae and includes economically important species that are used for indigo dye-producing, medicinal, ornamental, and soil and water conservation. The genus is taxonomically difficult due to the high level of overlap in morphological characters of interspecies, fewer reliability states for classification, and extensive adaptive evolution. Previous characteristic-based taxonomy and nuclear ITS-based phylogenies have contributed to our understanding of Indigofera taxonomy and evolution. However, the lack of chloroplast genomic resources limits our comprehensive understanding of the phylogenetic relationships and evolutionary processes of Indigofera.

Methods

Here, we newly assembled 18 chloroplast genomes of Indigofera. We performed a series of analyses of genome structure, nucleotide diversity, phylogenetic analysis, species pairwise Ka/Ks ratios, and positive selection analysis by combining with allied species in Papilionoideae.

Results and discussion

The chloroplast genomes of Indigofera exhibited highly conserved structures and ranged in size from 157,918 to 160,040 bp, containing 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Thirteen highly variable regions were identified, of which trnK-rbcL, ndhF-trnL, and ycf1 were considered as candidate DNA barcodes for species identification of Indigofera. Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) methods based on complete chloroplast genome and protein-coding genes (PCGs) generated a well-resolved phylogeny of Indigofera and allied species. Indigofera monophyly was strongly supported, and four monophyletic lineages (i.e., the Pantropical, East Asian, Tethyan, and Palaeotropical clades) were resolved within the genus. The species pairwise Ka/Ks ratios showed values lower than 1, and 13 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis using the branch-site model, eight of which were associated with photosynthesis. Positive selection of accD suggested that Indigofera species have experienced adaptive evolution to selection pressures imposed by their herbivores and pathogens. Our study provided insight into the structural variation of chloroplast genomes, phylogenetic relationships, and adaptive evolution in Indigofera. These results will facilitate future studies on species identification, interspecific and intraspecific delimitation, adaptive evolution, and the phylogenetic relationships of the genus Indigofera.

The Complete Chloroplast Genome of An Ophiorrhiza baviensis Drake Species Reveals Its Molecular Structure, Comparative, and Phylogenetic Relationships

Ophiorrhiza baviensis Drake, a flowering medical plant in the Rubiaceae, exists uncertainly within the Ophiorrhiza genus' evolutionary relationships. For the first time, the whole chloroplast (cp) genome of an O. baviensis Drake species was sequenced and annotated. Our findings demonstrate that the complete cp genome of O. baviensis is 154,770 bp in size, encoding a total of 128 genes, including 87 protein-coding genes, 8 rRNAs, and 33 tRNAs. A total of 59 SSRs were screened in the studied cp genome, along with six highly variable loci, which can be applied to generate significant molecular markers for the Ophiorrhiza genus. The comparative analysis of the O. baviensis cp genome with two published others of the Ophiorrhiza genus revealed a high similarity; however, there were some notable gene rearrangements in the O. densa plastome. The maximum likelihood phylogenetic trees were constructed based on the concatenation of the rps16 gene and the trnL-trnF intergenic spacer sequence, indicating a close relationship between the studied O. baviensis and other Ophiorrhiza. This study will provide a theoretical molecular basis for identifying O. baviensis Drake, as well as species of the Ophiorrhiza genus, and contribute to shedding light on the chloroplast genome evolution of Rubiaceae.

Interplay of Ecological Opportunities and Functional Traits Drives the Evolution and Diversification of Millettiod Legumes (Fabaceae)

Understanding the striking diversity of the angiosperms is a paramount issue in biology and of interest to biologists. The Millettiod legumes is one of the most hyper-diverse groups of the legume family, containing many economically important medicine, furniture and craft species. In the present study, we explore how the interplay of past climate change, ecological opportunities and functional traits' evolution may have triggered diversification of the Millettiod legumes. Using a comprehensive species-level phylogeny from three plastid markers, we estimate divergence times, infer habit shifts, test the phylogenetic and temporal diversification heterogeneity, and reconstruct ancestral biogeographical ranges. We found that three dramatic accumulations of the Millettiod legumes occurred during the Miocene. The rapid diversification of the Millettiod legumes in the Miocene was driven by ecological opportunities created by the emergence of new niches and range expansion. Additionally, habit shifts and the switch between biomes might have facilitated the rapid diversification of the Millettiod legumes. The Millettiod legumes provide an excellent case for supporting the idea that the interplay of functional traits, biomes, and climatic and geographic factors drives evolutionary success.

Characterization of the plastome of Physaliscordata and comparative analysis of eight species of Physalis sensu stricto

In this study, we sequenced, assembled, and annotated the plastome of Physaliscordata Mill. and compared it with seven species of the genus Physalis sensu stricto. Sequencing, annotating, and comparing plastomes allow us to understand the evolutionary mechanisms associated with physiological functions, select possible molecular markers, and identify the types of selection that have acted in different regions of the genome. The plastome of P.cordata is 157,000 bp long and presents the typical quadripartite structure with a large single-copy (LSC) region of 87,267 bp and a small single-copy (SSC) region of 18,501 bp, which are separated by two inverted repeat (IRs) regions of 25,616 bp each. These values are similar to those found in the other species, except for P.angulata L. and P.pruinosa L., which presented an expansion of the LSC region and a contraction of the IR regions. The plastome in all Physalis species studied shows variation in the boundary of the regions with three distinct types, the percentage of the sequence identity between coding and non-coding regions, and the number of repetitive regions and microsatellites. Four genes and 10 intergenic regions show promise as molecular markers and eight genes were under positive selection. The maximum likelihood analysis showed that the plastome is a good source of information for phylogenetic inference in the genus, given the high support values and absence of polytomies. In the Physalis plastomes analyzed here, the differences found, the positive selection of genes, and the phylogenetic relationships do not show trends that correspond to the biological or ecological characteristics of the species studied.

Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae)

Urticeae s.l., a tribe of Urticaceae well-known for their stinging trichomes, consists of more than 10 genera and approximately 220 species. Relationships within this tribe remain poorly known due to the limited molecular and taxonomic sampling in previous studies, and chloroplast genome (CP genome/plastome) evolution is still largely unaddressed. To address these concerns, we used genome skimming data-CP genome and nuclear ribosomal DNA (18S-ITS1-5.8S-ITS2-26S); 106 accessions-for the very first time to attempt resolving the recalcitrant relationships and to explore chloroplast structural evolution across the group. Furthermore, we assembled a taxon rich two-locus dataset of trnL-F spacer and ITS sequences across 291 accessions to complement our genome skimming dataset. We found that Urticeae plastomes exhibit the tetrad structure typical of angiosperms, with sizes ranging from 145 to 161 kb and encoding a set of 110-112 unique genes. The studied plastomes have also undergone several structural variations, including inverted repeat (IR) expansions and contractions, inversion of the trnN-GUU gene, losses of the rps19 gene, and the rpl2 intron, and the proliferation of multiple repeat types; 11 hypervariable regions were also identified. Our phylogenomic analyses largely resolved major relationships across tribe Urticeae, supporting the monophyly of the tribe and most of its genera except for Laportea, Urera, and Urtica, which were recovered as polyphyletic with strong support. Our analyses also resolved with strong support several previously contentious branches: (1) Girardinia as a sister to the Dendrocnide-Discocnide-Laportea-Nanocnide-Zhengyia-Urtica-Hesperocnide clade and (2) Poikilospermum as sister to the recently transcribed Urera sensu stricto. Analyses of the taxon-rich, two-locus dataset showed lower support but was largely congruent with results from the CP genome and nuclear ribosomal DNA dataset. Collectively, our study highlights the power of genome skimming data to ameliorate phylogenetic resolution and provides new insights into phylogenetic relationships and chloroplast structural evolution in Urticeae.

Complete Chloroplast Genomes Provide Insights Into Evolution and Phylogeny of Campylotropis (Fabaceae)

The genus Campylotropis Bunge (Desmodieae, Papilionoideae) comprises about 37 species distributed in temperate and tropical Asia. Despite the great potential in soil conservation, horticulture, and medicine usage, little is known about the evolutionary history and phylogenetic relationships of Campylotropis due to insufficient genetic resources. Here, we sequenced and assembled 21 complete chloroplast genomes of Campylotropis species. In combination with the previously published chloroplast genomes of C. macrocarpa and closely related species, we conducted comparative genomics and phylogenomic analysis on these data. Comparative analysis of the genome size, structure, expansion and contraction of inverted repeat (IR) boundaries, number of genes, GC content, and pattern of simple sequence repeats (SSRs) revealed high similarities among the Campylotropis chloroplast genomes. The activities of long sequence repeats contributed to the variation in genome size and gene content in Campylotropis chloroplast genomes. The Campylotropis chloroplast genomes showed moderate sequence variation, and 13 highly variable regions were identified for species identification and further phylogenetic studies. We also reported one more case of matK pseudogene in the legume family. The phylogenetic analysis confirmed the monophyly of Campylotropis and the sister relationship between Lespedeza and Kummerowia, the latter two genera were then sister to Campylotropis. The intrageneric relationships of Campylotropis based on genomic scale data were firstly reported in this study. The two positively selected genes (atpF and rps19) and eight fast-evolving genes identified in this study may help us to understand the adaptation of Campylotropis species. Overall, this study enhances our understanding of the chloroplast genome evolution and phylogenetic relationships of Campylotropis.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics

Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.

Comparative Chloroplast Genomics of Sophora Species: Evolution and Phylogenetic Relationships in the Early-Diverging Legume Subfamily Papilionoideae (Fabaceae)

The taxonomy and evolutionary history of Sophora L., a genus with high economic and medicinal value, remain uncertain due to the absence of genetic resource (especially in China) and low polymorphism of molecular markers. Our aim was to elucidate the molecular evolution and phylogenetic relationships in chloroplast genomes of Sophora species in the early-diverging legume subfamily Papilionoideae (Fabaceae). We reported nine Sophora chloroplast genome from China using Illumina sequencing. We performed a series of analyses with previously published genomes of Sophora species to investigate their genomic characteristics, identified simple sequence repeats, large repeat sequences, tandem repeats, and highly polymorphic loci. The genomes were 152,953-158,087 bp in length, and contained 111-113 unique genes, including 76-78 protein coding, 31 tRNA, and 4 rRNA. The expansion of inverted repeat boundary of Sophora resulted in rps12 entering into the LSC region and loss of trnT-CGU gene in some species. Also, we found an approximately 23 kb inversion between trnC-GCA and trnF-GAA within the genus. In addition, we identified seven highly polymorphic loci (pi (π) > 0.035) suitable for inferring the phylogeny of Sophora species. Among these, three regions also co-occurred with large repeat sequences and support use of repeats as a proxy for the identification of polymorphic loci. Based on whole chloroplast genome and protein-coding sequences data-set, a well-supported phylogenetic tree of Sophora and related taxa showed that this genus is monophyletic, but sect. Disamaea and sect. Sophora, are incongruent with traditional taxonomic classifications based on fruit morphology. Our finding provides significant genetic resources to support further investigation into the phylogenetic relationship and evolution of the genus Sophora.