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

Comparative and phylogenetic analysis of chloroplast genomes from ten species in Quercus section Cyclobalanopsis

The genus Quercus L. is widely acknowledged as a significant assemblage within East Asia tropical and subtropical broadleaf evergreen forests, possessing considerable economic importance. Nevertheless, the differentiation of Quercus species is deemed arduous, and the interrelations among these species remain enigmatic. Leveraging Illumina sequencing, we undertook the sequencing and assembly of the chloroplast (cp) genomes of seven species belonging to Quercus section Cyclobalanopsis (Quercus argyrotricha, Q. augustinii, Q. bambusifolia, Q. bella, Q. edithiae, Q. jenseniana, and Q. poilanei). Furthermore, we collated three previously published cp genome sequences of Cyclobalanopsis species (Q. litseoides, Q. obovatifolia, and Q. saravanensis). Our primary objective was to conduct comparative genomics and phylogenetic analyses of the complete cp genomes of ten species from Quercus section Cyclobalanopsis. This investigation unveiled that Quercus species feature a characteristic circular tetrad structure, with genome sizes ranging from 160,707 to 160,999 base pairs. The genomic configuration, GC content, and boundaries of inverted repeats/single copy regions exhibited marked conservation. Notably, four highly variable hotspots were identified in the comparative analysis, namely trnK-rps16, psbC-trnS, rbcL-accD, and ycf1. Furthermore, three genes (atpF, rpoC1, and ycf2) displayed signals of positive selection pressure. Phylogenetic scrutiny revealed that the four sections of Cyclobalanopsis clustered together as sister taxa. The branch support values ranged from moderate to high, with most nodes garnering 100% support, underscoring the utility of cp genomic data in elucidating the relationships within the genus. Divergence time analysis revealed that Section Cyclobalanopsis represents the earliest type of Quercus genus. The outcomes of this investigation establish a foundation for forthcoming research endeavors in taxonomy and phylogenetics.

Camellia neriifolia and Camellia ilicifolia (Theaceae) as separate species: evidence from morphology, anatomy, palynology, molecular systematics

BACKGROUND

The systematic status of sect. Tuberculata and its taxonomy have recently attracted considerable attention. However, the different bases for defining the characteristics of sect. Tuberculata has led to many disagreements among the plants in this group. Camellia neriifolia and Camellia ilicifolia have been the subject of taxonomic controversy and have been treated as different species or varieties of the same species. Therefore, it is important to use multiple methods, i.e., integrative taxonomy, to determine the taxonomic status of C. neriifolia and C. ilicifolia. This is the first study to systematically explore the taxonomic position of these two plants on the basis of Morphology, Anatomy, Palynology and Molecular Systematics.

RESULTS

Extensive specimen reviews and field surveys showed that many differences exist in C. neriifolia and C. ilicifolia, such as the number of trunk (heavily debarked vs. slightly peeling), leaf type (smooth thin leathery, shiny vs. smooth leathery, obscure or slightly shiny), leaf margin (entire vs. serrate), flower type (subsessile vs. sessile), number of styles (3-4 vs. 3), and sepal (ovate vs. round). Moreover, C. neriifolia has a more distinctive faint yellow flower color, and trunk molting was more severe in C. neriifolia than that in C. ilicifolia. In addition, micromorphological analysis of the leaf epidermis showed that the two species differed in the anticlinal wall, stomatal apparatus, and stomatal cluster, and pollen morphology analyses based on pollen size, germination furrow, and polar and equatorial axes showed that they are both distinct from each other. The results of the phylogenetic tree constructed based on the whole chloroplast genome, protein-coding genes, and ITS2 showed that both C. ilicifolia and C. neriifolia were clustered in different branches and gained high support.

CONCLUSIONS

The results combine morphology, anatomy, palynology, and molecular systematics to treat both C. neriifolia and C. ilicifolia as separate species in the sect. Tuberculata, and the species names continue to be used as they were previously. In conclusion, clarifying the taxonomic status of C. neriifolia and C. ilicifolia deepens our understanding of the systematic classification of sect. Tuberculata.

The first complete chloroplast genome of Thalictrum fargesii: insights into phylogeny and species identification

Introduction

Thalictrum fargesii is a medicinal plant belonging to the genus Thalictrum of the Ranunculaceae family and has been used in herbal medicine in the Himalayan regions of China and India. This species is taxonomically challenging because of its morphological similarities to other species within the genus. Thus, herbal drugs from this species are frequently adulterated, substituted, or mixed with other species, thereby endangering consumer safety.

Methods

The present study aimed to sequence and assemble the entire chloroplast (cp) genome of T. fargesii using the Illumina HiSeq 2500 platform to better understand the genomic architecture, gene composition, and phylogenetic relationships within the Thalictrum.

Results and discussion

The cp genome was 155,929 bp long and contained large single-copy (85,395 bp) and small single-copy (17,576 bp) regions that were segregated by a pair of inverted repeat regions (26,479 bp) to form a quadripartite structure. The cp genome contains 133 genes, including 88 protein-coding genes (PCGs), 37 tRNA genes, and 8 rRNA genes. Additionally, this genome contains 64 codons that encode 20 amino acids, the most preferred of which are alanine and leucine. We identified 68 SSRs, 27 long repeats, and 242 high-confidence C-to-U RNA-editing sites in the cp genome. Moreover, we discovered seven divergent hotspot regions in the cp genome of T. fargesii, among which ndhD-psaC and rpl16-rps3 may be useful for developing molecular markers for identifying ethnodrug species and their contaminants. A comparative study with eight other species in the genus revealed that pafI and rps19 had highly variable sites in the cp genome of T. fargesii. Additionally, two special features, (i) the shortest length of the ycf1 gene at the IRA-SSC boundary and (ii) the distance between the rps19 fragment and trnH at the IRA-LSC junction, distinguish the cp genome of T. fargesii from those of other species within the genus. Furthermore, phylogenetic analysis revealed that T. fargesii was closely related to T. tenue and T. petaloidium.

Conclusion

Considering all these lines of evidence, our findings offer crucial molecular and evolutionary information that could play a significant role in further species identification, evolution, and phylogenetic studies on T. fargesii.

Pan-chloroplast genomes for accession-specific marker development in Hibiscus syriacus

Hibiscus syriacus L. is a renowned ornamental plant. We constructed 95 chloroplast genomes of H. syriacus L. cultivars using a short-read sequencing platform (Illumina) and a long-read sequencing platform (Oxford Nanopore Technology). The following genome assembly, we delineate quadripartite structures encompassing large single-copy, small single-copy, and inverted repeat (IRa and IRb) regions, from 160,231 bp to 161,041 bp. Our comprehensive analyses confirmed the presence of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes in the pan-chloroplast genome, consistent with prior research on the H. syriacus chloroplast genome. Subsequent pangenome analysis unveiled widespread genome sequence conservation alongside unique cultivar-specific variant patterns consisting of 193 single-nucleotide polymorphisms and 61 insertions or deletions. The region containing intra-species variant patterns, as identified in this study, has the potential to develop accession-specific molecular markers, enhancing precision in cultivar classification. These findings are anticipated to drive advancements in breeding strategies, augment biodiversity, and unlock the agricultural potential inherent in H. syriacus.

Comparative analysis and characterization of the chloroplast genome of Krascheninnikovia ceratoides (Amarathaceae): a xerophytic semi-shrub exhibiting drought resistance and high-quality traits

BACKGROUND

Krascheninnikovia ceratoides, a perennial halophytic semi-shrub belonging to the genus Krascheninnikovia (Amarathaceae), possesses noteworthy ecological, nutritional, and economic relevance. This species is primarily distributed across arid, semi-arid, and saline-alkaline regions of the Eurasian continent, encompassing Inner Mongolia, Xinjiang, Qinghai, Gansu, Ningxia, and Tibet.

RESULTS

We reported the comprehensive chloroplast (cp) genome of K. ceratoides, characterized by a circular conformation spanning 151,968 bp with a GC content of 36.60%. The cp genome encompassed a large single copy (LSC, 84,029 bp), a small single copy (SSC, 19,043 bp), and a pair of inverted repeats (IRs) regions (24,448 bp each). This genome harbored 128 genes and encompassed 150 simple sequence repeats (SSRs). Through comparative analyses involving cp genomes from other Cyclolobeae (Amarathaceae) taxa, we observed that the K. ceratoides cp genome exhibited high conservation, with minor divergence events in protein-coding genes (PCGs) accD, matK, ndhF, ndhK, ycf1, and ycf2. Phylogenetic reconstructions delineated K. ceratoides as the sister taxon to Atriplex, Chenopodium, Dysphania, and Suaeda, thus constituting a robust clade. Intriguingly, nucleotide substitution ratios (Ka/Ks) between K. ceratoides and Dysphania species for ycf1 and ycf2 genes surpassed 1.0, indicating the presence of positive selection pressure on these loci.

CONCLUSIONS

The findings of this study augment the genomic repository for the Amarathaceae family and furnish crucial molecular instruments for subsequent investigations into the ecological adaptation mechanisms of K. ceratoides within desert ecosystems.

Complete chloroplast genome assembly and phylogenetic analysis of blackcurrant (Ribes nigrum), red and white currant (Ribes rubrum), and gooseberry (Ribes uva-crispa) provide new insights into the phylogeny of Grossulariaceae

Background

Blackcurrant (Ribes nigrum), red currant (R. rubrum), white currant (R. rubrum), and gooseberry (R. uva-crispa) belong to Grossulariaceae and are popular small-berry crops worldwide. The lack of genomic data has severely limited their systematic classification and molecular breeding.

Methods

The complete chloroplast (cp) genomes of these four taxa were assembled for the first time using MGI-DNBSEQ reads, and their genome structures, repeat elements and protein-coding genes were annotated. By genomic comparison of the present four and previous released five Ribes cp genomes, the genomic variations were identified. By phylogenetic analysis based on maximum-likelihood and Bayesian methods, the phylogeny of Grossulariaceae and the infrageneric relationships of the Ribes were revealed.

Results

The four cp genomes have lengths ranging from 157,450 to 157,802 bp and 131 shared genes. A total of 3,322 SNPs and 485 Indels were identified from the nine released Ribes cp genomes. Red currant and white currant have 100% identical cp genomes partially supporting the hypothesis that white currant (R. rubrum) is a fruit color variant of red currant (R. rubrum). The most polymorphic genic and intergenic region is ycf1 and trnT-psbD, respectively. The phylogenetic analysis demonstrated the monophyly of Grossulariaceae in Saxifragales and the paraphyletic relationship between Saxifragaceae and Grossulariaceae. Notably, the Grossularia subgenus is well nested within the Ribes subgenus and shows a paraphyletic relationship with the co-ancestor of Calobotrya and Coreosma sections, which challenges the dichotomous subclassification of the Ribes genus based on morphology (subgenus Ribes and subgenus Grossularia). These data, results, and insights lay a foundation for the phylogenetic research and breeding of Ribes species.

Comparative analysis of the medicinal plant Polygonatum kingianum (Asparagaceae) with related verticillate leaf types of the Polygonatum species based on chloroplast genomes

Background

Polygonatum kingianum has been widely used as a traditional Chinese medicine as well as a healthy food. Because of its highly variable morphology, this medicinal plant is often difficult to distinguish from other related verticillate leaf types of the Polygonatum species. The contaminants in P. kingianum products not only decrease the products' quality but also threaten consumer safety, seriously inhibiting the industrial application of P. kingianum.

Methods

Nine complete chloroplast (cp) genomes of six verticillate leaf types of the Polygonatum species were de novo assembled and systematically analyzed.

Results

The total lengths of newly sequenced cp genomes ranged from 155,437 to 155,977 bp, including 86/87 protein-coding, 38 tRNA, and 8 rRNA genes, which all exhibited well-conserved genomic structures and gene orders. The differences in the IR/SC (inverted repeats/single-copy) boundary regions and simple sequence repeats were detected among the verticillate leaf types of the Polygonatum cp genomes. Comparative cp genomes analyses revealed that a higher similarity was conserved in the IR regions than in the SC regions. In addition, 11 divergent hotspot regions were selected, providing potential molecular markers for the identification of the Polygonatum species with verticillate leaf types. Phylogenetic analysis indicated that, as a super barcode, plastids realized a fast and efficient identification that clearly characterized the relationships within the verticillate leaf types of the Polygonatum species. In brief, our results not only enrich the data on the cp genomes of the genus Polygonatum but also provide references for the P. kingianum germplasm resource protection, herbal cultivation, and drug production.

Conclusion

This study not only accurately identifies P. kingianum species, but also provides valuable information for the development of molecular markers and phylogenetic analyses of the Polygonatum species with verticillate leaf types.

Analysis of the Chloroplast Genome of Ficus simplicissima Lour Collected in Vietnam and Proposed Barcodes for Identifying Ficus Plants

Ficus simplicissima Lour. is an Asian species of fig tree in the family Moraceae. The chloroplast (cp) genome of F. simplicissima m3 was sequenced using the Pacbio sequel platform. The F. simplicissima cpDNA has a size of 160,321 bp in length, of which GC content accounts for 36.13%. The cp genome of F. simplicissima consists of a single large copy (LSC) with a size of 91,346 bp, a single small copy (SSC) with a size of 20,131 bp, and a pair of inverted repeats with a size of 24,421 to 24,423 bp. The cp genome of F. simplicissima has 127 genes, including 85 protein-coding genes, eight rRNA genes, and 34 tRNA genes; 92 simple sequence repeats and 39 long repeats were detected in the cpDNA of F. simplicissim. A comparative cp genome analysis among six species in the Ficus genus indicated that the genome structure and gene content were highly conserved. The non-coding regions show more differentiation than the coding regions, and the LSC and SSC regions show more differences than the inverted repeat regions. Phylogenetic analysis supported that F. simplicissima m3 had a close relationship with F. hirta. The complete cp genome of F. simplicissima was proposed as a chloroplast DNA barcoding for genus-level in the Moraceae family and the psbA-trnH gene region for species-level identification.

The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution

BACKGROUND

The Ferula genus encompasses 180-185 species and is one of the largest genera in Apiaceae, with many of Ferula species possessing important medical value. The previous studies provided more information for Ferula, but its infrageneric relationships are still confusing. In addition, its genetic basis of its adaptive evolution remains poorly understood. Plastid genomes with more variable sites have the potential to reconstruct robust phylogeny in plants and investigate the adaptive evolution of plants. Although chloroplast genomes have been reported within the Ferula genus, few studies have been conducted using chloroplast genomes, especially for endemic species in China.

RESULTS

Comprehensively comparative analyses of 22 newly sequenced and assembled plastomes indicated that these plastomes had highly conserved genome structure, gene number, codon usage, and repeats type and distribution, but varied in plastomes size, GC content, and the SC/IR boundaries. Thirteen mutation hotspot regions were detected and they would serve as the promising DNA barcodes candidates for species identification in Ferula and related genera. Phylogenomic analyses with high supports and resolutions showed that Talassia transiliensis and Soranthus meyeri were nested in the Ferula genus, and thus they should be transferred into the Ferula genus. Our phylogenies also indicated the monophyly of subgenera Sinoferula and subgenera Narthex in Ferula genus. Twelve genes with significant posterior probabilities for codon sites were identified in the positively selective analysis, and their function may relate to the photosystem II, ATP subunit, and NADH dehydrogenase. Most of them might play an important role to help Ferula species adapt to high-temperatures, strong-light, and drought habitats.

CONCLUSION

Plastome data is powerful and efficient to improve the support and resolution of the complicated Ferula phylogeny. Twelve genes with significant posterior probabilities for codon sites were helpful for Ferula to adapt to the harsh environment. Overall, our study supplies a new perspective for comprehending the phylogeny and evolution of Ferula.

Comparison of chloroplast genomes and phylogenomics in the Ficus sarmentosa complex (Moraceae)

Due to maternal inheritance and minimal rearrangement, the chloroplast genome is an important genetic resource for evolutionary studies. However, the evolutionary dynamics and phylogenetic performance of chloroplast genomes in closely related species are poorly characterized, particularly in taxonomically complex and species-rich groups. The taxonomically unresolved Ficus sarmentosa species complex (Moraceae) comprises approximately 20 taxa with unclear genetic background. In this study, we explored the evolutionary dynamics, hotspot loci, and phylogenetic performance of thirteen chloroplast genomes (including eleven newly obtained and two downloaded from NCBI) representing the F. sarmentosa complex. Their sequence lengths, IR boundaries, repeat sequences, and codon usage were compared. Both sequence length and IR boundaries were found to be highly conserved. All four categories of long repeat sequences were found across all 13 chloroplast genomes, with palindromic and forward sequences being the most common. The number of simple sequence repeat (SSR) loci varied from 175 (F. dinganensis and F. howii) to 190 (F. polynervis), with the dinucleotide motif appearing the most frequently. Relative synonymous codon usage (RSCU) analysis indicated that codons ending with A/T were prior to those ending with C/T. The majority of coding sequence regions were found to have undergone negative selection with the exception of ten genes (accD, clpP, ndhK, rbcL, rpl20, rpl22, rpl23, rpoC1, rps15, and rps4) which exhibited potential positive selective signatures. Five hypervariable genic regions (rps15, ycf1, rpoA, ndhF, and rpl22) and five hypervariable intergenic regions (trnH-GUG-psbA, rpl32-trnL-UAG, psbZ-trnG-GCC, trnK-UUU-rps16 and ndhF-rpl32) were identified. Overall, phylogenomic analysis based on 123 Ficus chloroplast genomes showed promise for studying the evolutionary relationships in Ficus, despite cyto-nuclear discordance. Furthermore, based on the phylogenetic performance of the F. sarmentosa complex and F. auriculata complex, the chloroplast genome also exhibited a promising phylogenetic resolution in closely related species.

Genome sequencing and comparative analysis of Ficus benghalensis and Ficus religiosa species reveal evolutionary mechanisms of longevity

Ficus benghalensis and Ficus religiosa are large woody trees well known for their long lifespan, ecological and traditional significance, and medicinal properties. To understand the genomic and evolutionary aspects of these characteristics, the whole genomes of these Ficus species were sequenced using 10x Genomics linked reads and Oxford Nanopore long reads. The draft genomes of F. benghalensis and F. religiosa comprised of 392.89 Mbp and 332.97 Mbp, respectively. We established the genome-wide phylogenetic positions of the two Ficus species with respect to 50 other Angiosperm species. Comparative evolutionary analyses with other phylogenetically closer Eudicot species revealed adaptive evolution in genes involved in key cellular mechanisms associated with prolonged survival including phytohormones signaling, senescence, disease resistance, and abiotic stress tolerance, which provide genomic insights into the mechanisms conferring longevity and suggest that longevity is a multifaceted phenomenon. This study also provides clues on the existence of CAM pathway in these Ficus species.

The complete chloroplast genome sequence of Ficus pandurata Hance var. angustifolia W.C. Cheng (Moraceae)

Ficus pandurata var. angustifolia is an edible plant popular throughout China where it has a long history of use in traditional She medicine. Using Illumina sequencing, we assembled and annotated the complete chloroplast (cp) genome of F. pandurata var. angustifolia which is 160,526 bp and encodes 130 genes, comprised of 85 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Phylogenetic analysis resolved F. pandurata var. angustifolia as sister to F. deltoidea which together formed a clade with F. heteromorpha. This complete cp genome sequences is a valuable resource for future studies of evolution and species delimitation in genus Ficus as well as variety breeding and conservation for this species.