Number Of Simple Sequence Repeats Research Articles

Comparison of the Distribution Patterns of Microsatellites Across the Genomes of Reptiles

ABSTRACTMicrosatellites or simple sequence repeats (SSRs) are prevalent across various organisms' genomes. However, their distribution patterns and evolutionary dynamics in reptile genomes are rarely studied systematically. We herein conducted a comprehensive analysis of SSRs in the genomes of 36 reptile species. Our findings revealed that the total number of SSRs ranged from 1,840,965 to 7,664,452, accounting for 2.16%–8.19% of the genomes analyzed. The relative density ranged from 21,567.82 to 81,889.41 bp per megabase (Mbp). The abundance of different SSR categories followed the pattern of imperfect SSR (I‐SSR) > perfect SSR (P‐SSR) > compound SSR (C‐SSR). A significant positive correlation was observed between the number of SSRs and genome size (p = 0.0034), whereas SSR frequency (p = 0.013) or density (p = 0.0099) showed a negative correlation with genome size. Furthermore, no correlation was found between SSR length and genome size. Mononucleotide repeats were the most common P‐SSRs in crocodilians and turtles, whereas mononucleotides, trinucleotides, or tetranucleotides were the most common P‐SSRs in snakes, lizards, and tuatara. P‐SSRs of varying motif sizes showed nonrandom distribution across different genic regions, with AT‐rich repeats being predominant. The genomic SSR content of the squamate lineage ranked the highest in abundance and variability, whereas crocodilians and turtles showed a slowly evolving and reduced microsatellite landscape. Gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that genes harboring P‐SSRs in the coding DNA sequence regions were primarily involved in the regulation of transcription and translation processes. The SSR dataset generated in this study provides potential candidates for functional analysis and calls for broader‐scale analyses across the evolutionary spectrum.

Conserved Plastid Genomes of Pourthiaea Trees: Comparative Analyses and Phylogenetic Relationship

The genus Pourthiaea Decne., a deciduous woody group with high ornamental value, belongs to the family Rosaceae. Here, we reported newly sequenced plastid genome sequences of Pourthiaea beauverdiana (C. K. Schneid.) Hatus., Pourthiaea parvifolia E. Pritz., Pourthiaea villosa (Thunb.) Decne., and Photinia glomerata Rehder & E. H. Wilson. The plastomes of these three Pourthiaea species shared the typical quadripartite structures, ranging in size from 159,903 bp (P. parvifolia) to 160,090 bp (P. beauverdiana). The three Pourthiaea plastomes contained a pair of inverted repeat regions (26,394–26,399 bp), separated by a small single-copy region (19,304–19,322 bp) and a large single-copy region (87,811–87,973 bp). A total of 113 unique genes were predicted for the three Pourthiaea plastomes, including four ribosomal RNA genes, 30 transfer RNA genes, and 79 protein-coding genes. Analyses of inverted repeat/single-copy boundary, mVISTA, nucleotide diversity, and genetic distance showed that the plastomes of 13 Pourthiaea species (including 10 published plastomes) are highly conserved. The number of simple sequence repeats and long repeat sequences is similar among 13 Pourthiaea species. The three non-coding regions (trnT-GGU-psbD, trnR-UCU-atpA, and trnH-GUG-psbA) were the most divergent. Only one plastid protein-coding gene, rbcL, was under positive selection. Phylogenetic analyses based on 78 shared plastid protein-coding sequences and 29 nrDNA sequences strongly supported the monophyly of Pourthiaea. As for the relationship with other genera in our phylogenies, Pourthiaea was sister to Malus in plastome phylogenies, while it was sister to the remaining genera in nrDNA phylogenies. Furthermore, significant cytonuclear discordance likely stems from hybridization events within Pourthiaea, reflecting complex evolutionary dynamics within the genus. Our study provides valuable genetic insights for further phylogenetic, taxonomic, and species delimitation studies in Pourthiaea, as well as essential support for horticultural improvement and conservation of the germplasm resources.

Genome-wide simple sequence repeat analysis and specific molecular marker development of rye

BackgroundRye (Secale cereale L.) is the most widely used related species in wheat genetic breeding, and the introduction of its chromosome fragments into the wheat genome through distant hybridization is essential for enriching the genetic diversity of wheat. Rapid and accurate detection of rye chromatin in the wheat genome is important for distant hybridization. Simple sequence repeats (SSRs) are widely distributed in the genome, and SSRs of different species often exhibit species-specific characteristics.ResultsIn this study, genome-wide SSRs in rye were identified, and their characteristics were outlined. A total of 997,027 SSRs were selected, with a density of 115.97 SSRs/Mb on average. There was no significant difference in the number of SSRs on each chromosome. The number of SSRs on 2R was the highest (15.29%), and the number of SSRs on 1R was the lowest (13.02%). The number of SSRs on each chromosome is significantly correlated with chromosome length. The types of SSR motifs were abundant, and each type of SSR was distributed on 7 chromosomes of rye. The numbers of mononucleotide simple sequence repeats (MNRs), dinucleotide simple sequence repeats (DNRs), and trinucleotide simple sequence repeats (TNRs) were the greatest, accounting for 46.90%, 18.37%, and 22.64% of the total number, respectively. Among the MNRs, the number of G/C repeats and the number of 10 bp motifs were the greatest, accounting for 26.24% and 31.32% of the MNRs, respectively. Based on the SSR sequences, a total of 657 pairs of primers were designed. The PCR results showed that 119 pairs of these primers were rye-specific and could effectively detect rye chromatin in the wheat genome. Moreover, 86 pairs of the primers could also detect one or more specific rye chromosomes.ConclusionThese results lay a foundation for both genomic evolution studies of rye and molecular breeding in wheat.

Complete chloroplast genomes and phylogenetic relationships of Pedicularis chinensis and Pedicularis kansuensis

The complete cp genomes of Pedicularis chinensis (GenBank accession number: OQ587614) and Pedicularis kansuensis (GenBank accession number: OQ587613) were sequenced, assembled, and annotated. Their chloroplast (cp) genome lengths were 146,452 bp, and 146,852 bp, respectively; 120 and 116 genes were identified, comprising 75 and 72 protein-coding genes (PCGs), 37 and 36 transfer RNA (tRNA) genes, and 8 and 8 ribosomal RNA (rRNA) genes, for P. chinensis and P. kansuensis, respectively. A simple sequence repeat (SSR) analysis revealed that the repetitive sequences were mainly composed of mononucleotide repeats (A/T motif) and dinucleotide repeats (AT/TA motif). Comparative genomics identified several variant genes (rpl22, rps19, rpl12, ycf1, trnH, psbA, and ndhH) and variant regions (trnS-GGA, trnV-UAC, ndhJ-trnV, ycf4-cemA, ndhE-nhdG, and rpl32-trnL) with a high Pi, indicating the potential to serve as deoxyribo nucleic acid (DNA) barcodes for Pedicularis species identification. The results show that the cp genomes of P. chinensis and P. kansuensis were the same as those of other plants in Pedicularis, with different degrees of AT preference for codons. Large differences in the number of SSRs and the expansion of the inverted repeat (IR) region showed strong variability and interspecific differentiation between these two species and other species represented in the genus Pedicularis. A phylogenetic analysis showed that P. kansuensis had the closest relationship with P. oliveriana, and P. chinensis had the closest relationship with P. aschistorhyncha. These results will facilitate the study of the phylogenetic classification and interspecific evolution of Pedicularis plants.

The chloroplast genomes of two medicinal species (Veronica anagallis-aquatica L. and Veronica undulata Wall.) and its comparative analysis with related Veronica species

Veronica anagallis-aquatica L. and Veronica undulata Wall. are widely used ethnomedicinal plants in China. The two species have different clinical efficacies, while their extremely similar morphology and unclear interspecific relationship make it difficult to accurately identify them, leading to increased instances of mixed usage. This article reports on the complete chloroplast genomes sequence of these two species and their related Veronica species to conduct a comparative genomics analysis and phylogenetic construction. The results showed that the chloroplast (cp) genomes of Veronica exhibited typical circular quadripartite structures, with total lengths of 149,386 to 152,319 base pairs (bp), and GC content of 37.9 to 38.1%, and the number of genes was between 129–134. The total number of simple sequence repeats (SSRs) in V. anagallis-aquatica and V. undulata is 37 and 36, while V. arvensis had the highest total number of 56, predominantly characterized by A/T single bases. The vast majority of long repeat sequence types are forward repeats and palindromic repeats. Selective Ka/Ks values showed that three genes were under positive selection. Sequence differences often occur in the non-coding regions of the large single-copy region (LSC) and small single-copy region (SSC), with the lowest sequence variation in the inverted repeat regions (IR). Seven highly variable regions (trnT-GGU-psbD, rps8-rpl16, trnQ-UUG, trnN-GUU-ndhF, petL, ycf3, and ycf1) were detected, which may be potential molecular markers for identifying V. anagallis-aquatica and V. undulata. The phylogenetic tree indicates that there is a close genetic relationship between the genera Veronica and Neopicrorhiza, and V. anagallis-aquatica and V. undulata are sister groups. The molecular clock analysis results indicate that the divergence time of Veronica may occur at ∼ 9.09 Ma, and the divergence time of these two species occurs at ∼ 0.48 Ma. It is speculated that climate change may be the cause of Veronica species diversity and promote the radiation of the genus. The chloroplast genome data of nine Veronica specie provides important insights into the characteristics and evolution of the chloroplast genome of this genus, as well as the phylogenetic relationships of the genus Veronica.

Plastomes of Nothofagus reflect a shared biogeographic history in Patagonia.

Plastomes are used in phylogenetic reconstructions because of their relatively conserved nature. Nonetheless, some limitations arise, particularly at lower taxonomic levels due to reduced interspecific polymorphisms and frequent hybridization events that result in unsolved phylogenies including polytomies and reticulate evolutionary patterns. Next-generation sequencing technologies allow access to genomic data and strongly supported phylogenies, yet biased topologies may be obtained due to insufficient taxon sampling. We analyze the hypothesis that intraspecific plastome diversity reflects biogeographic history and hybridization cycles among taxa. We generated 12 new plastome sequences covering distinct latitudinal locations of all species of subgenus Nothofagus from North Patagonia. Chloroplast genomes were assembled, annotated, and searched for simple sequence repeats (SSRs). Phylogenetic reconstructions included species and sampled locations. The six Nothofagus species analyzed were of similar size and structure; only Nothofagus obliqua of subgenus Lophozonia, used as an outgroup, presented slight differences in size. We detected a variable number of SSRs in distinct species and locations. Phylogenetic analyses of plastomes confirmed that subgenus Nothofagus organizes into two monophyletic clades each consisting of individuals of different species. We detected a geographic structure within subgenus Nothofagus and found evidence of local chloroplast sharing due to past hybridization, followed by adaptive introgression and ecological divergence. These contributions enrich the comprehension of transversal evolutionary mechanisms such as chloroplast capture and its implications for phylogenetic and phylogenomic analyses.

In silico analysis on frequency and distribution of microsatellites in genes associated with spinal cord astrocytoma

Microsatellites, also called short tandem repeats (STRs) or simple sequence repeats (SSRs) are short DNA sequence segments consisting of tandemly repeated motifs. SSRs are regarded as one of the most effective tools for genetic research. In this study, we conducted an in silico analysis to investigate the presence, distribution, and characteristics of SSRs within the genes associated with spinal cord astrocytoma. The aim of this study was to identify SSRs in coding and non-coding regions, analyze their correlation with gene parameters, and determine the GC content in the gene sequences. The results revealed that the widespread presence of SSRs within the genes is associated with spinal cord astrocytoma (SCA). The distribution of SSR motifs varied among the analyzed genes, and certain motifs were common across multiple genes. Additionally, we observed a strong positive correlation between the total number of SSRs and gene size, indicating that larger genes tend to have a higher number of microsatellites. Furthermore, we identified SSRs in both coding and non-coding regions of the genes. The incidence of SSRs and cSSRs differed among genes, suggesting potential functional implications for gene expression and regulation. Our study provides valuable insights into the genetic diversity within the astrocytoma genes and highlights the potential significance of SSRs in gene regulation. In conclusion, this study contributes to a better understanding of the role of microsatellites within the genes associated with spinal cord astrocytoma. The observed patterns of SSR distribution and characteristics suggest their potential functional relevance in the development and progression of astrocytoma.

Phylogenetic placement of the monotypic Baolia (Amaranthaceae s.l.) based on morphological and molecular evidence

BackgroundBaolia H.W.Kung & G.L.Chu is a monotypic genus only known in Diebu County, Gansu Province, China. Its systematic position is contradictory, and its morphoanatomical characters deviate from all other Chenopodiaceae. Recent study has regarded Baolia as a sister group to Corispermoideae. We therefore sequenced and compared the chloroplast genomes of this species, and resolved its phylogenetic position based on both chloroplast genomes and marker sequences.ResultsWe sequenced 18 chloroplast genomes of 16 samples from two populations of Baolia bracteata and two Corispermum species. These genomes of Baolia ranged in size from 152,499 to 152,508 bp. Simple sequence repeats (SSRs) were primarily located in the LSC region of Baolia chloroplast genomes, and most of them consisted of single nucleotide A/T repeat sequences. Notably, there were differences in the types and numbers of SSRs between the two populations of B. bracteata. Our phylogenetic analysis, based on both complete chloroplast genomes from 33 species and a combination of three markers (ITS, rbcL, and matK) from 91 species, revealed that Baolia and Corispermoideae (Agriophyllum, Anthochlamys, and Corispermum) form a well-supported clade and sister to Acroglochin. According to our molecular dating results, a major divergence event between Acroglochin, Baolia, and Corispermeae occurred during the Middle Eocene, approximately 44.49 mya. Ancestral state reconstruction analysis showed that Baolia exhibited symplesiomorphies with those found in core Corispermoideae characteristics including pericarp and seed coat.ConclusionsComparing the chloroplast genomes of B. bracteata with those of eleven typical Chenopodioideae and Corispermoideae species, we observed a high overall similarity and a one notable noteworthy case of inversion of approximately 3,100 bp. of DNA segments only in two Atriplex and four Chenopodium species. We suggest that Corispermoideae should be considered in a broader sense, it includes Corispermeae (core Corispermoideae: Agriophyllum, Anthochlamys, and Corispermum), as well as two new monotypic tribes, Acroglochineae (Acroglochin) and Baolieae (Baolia).

Comparative genomics on chloroplasts of Rubus (Rosaceae)

Rubus, the largest genus in Rosaceae, contains over 1400 species that distributed in multiple habitats across the world, with high species diversity in the temperate regions of Northern Hemisphere. Multiple Rubus species are cultivated for their valuable fruits. However, the intrageneric classification and phylogenetic relationships are still poorly understood. In this study, we sequenced, assembled, and characterized 17 plastomes of Rubus, and conducted comparative genomics integrating with 47 previously issued plastomes of this genus. The 64 plastomes of Rubus exhibited typical quadripartite structure with sizes ranging from 155,144 to 156,700 bp, and contained 132 genes including 87 protein-coding genes, 37 tRNA genes and eight rRNA genes. All plastomes are conservative in the gene order, the frequency of different types of long repeats and simple sequence repeats (SSRs), the codon usage, and the selection pressure of protein-coding genes. However, there are also some differences in the Rubus plastomes, including slight contraction and expansion of the IRs, a variation in the numbers of SSRs and long repeats, and some genes in certain clades undergoing intensified or relaxed purifying selection. Phylogenetic analysis based on whole plastomes showed that the monophyly of Rubus was strongly supported and resolved it into six clades corresponding to six subgenera. Moreover, we identified 12 highly variable regions that could be potential molecular markers for phylogenetic, population genetic, and barcoding studies. Overall, our study provided insight into plastomic structure and sequence diversification of Rubus, which could be beneficial for future studies on identification, evolution, and phylogeny in this genus.

Draft genome and SSR data mining of a Peruvian landrace of Capsicum chinense, the arnaucho chili pepper

The Arnaucho chili pepper (ACP) is a traditional vegetable used in Peru because of its gastronomic properties. Due to its importance in the Peruvian diet and economy, this species is a resource that can be a candidate to plant breeding programs. In this study, the complete genome nucleotide sequence of this chili pepper was generated using the Illumina Hiseq 2500 sequencing technology. We sequenced the whole genome of the ACP using a paired-end 150 strategy, obtaining 330.46 GB of sequencing data. The genome size of the ACP was 2.98 Gb with a contig N50 of 237 Mb and 95.39% complete BUSCOs. Also, we identified 71.96% of repetitive DNA of the genome assembly, of which retroelements occupy 37.95% of the total genome. We downloaded genomes of the Solanoideae subfamily and conducted a comparative analysis of simple sequence repeats (SSRs) with our draft genome, and we identified lower number of SSRs in the ACP genome compared to other pepper species. This first ACP genome is expected to contribute to a better understanding of its genetics to adapt to the arid conditions of the Peruvian coastal ecosystem and evolution.

The first complete chloroplast genome sequences of Pistacia eurycarpa Yalt, a horticultural important rootstock and industrial tree

AbstractPistacia genus is botanically classified in the Sapindales order and the Anacardiaceae family, and the member of this genus P. eurycarpa is used as a rootstock for pistachio. Due to its rich oil content, various soaps are produced from the green peels of P. eurycarpa nuts and are used in the cosmetic industry as soap. In the current study, we aimed to release the complete chloroplast genome of P. eurycarpa to detect the relationship of the members of the Sapindales and also Pistacia genus. The length of the chloroplast genome of P. eurycarpa was identified 160,693 (bp) and consisted of the distinct parts of the genomic fragments such as LSC, SSC, and IR regions. The length of the LSC was 88,410 (bp), and SSC genomic range represented a total of 19,087 (bp). Inverted regions length was 26,598 (bp). A total of 125 genes were determined within the whole chloroplast genome of P. eurycarpa. The number of simple sequence repeats (SSRs) in the chloroplast genome was computed as 74. Three main clusters defined the dendrogram of all accessions. The closest pairs of species were identified among the P. eurycarpa and P. vera species. The farthest genetic relationship was calculated among the members of the Sapindales species Mangifera indica and the Fagales species Castanea mollissima. The sequences of the chloroplast genome of P. eurycarpa species can be evaluated for the construction of the basis of the complete evolution of the order, genera, and the development of the SSRs for species-specific markers for revealing the evolution of Pistacia species for future breeding research.

Characterization of Simple Sequence Repeat (SSR) Markers Mined in Whole Grape Genomes.

SSR (simple sequence repeat) DNA markers are widely used for genotype DNA identification, QTL mapping, and analyzing genetic biodiversity. However, SSRs in grapes are still in their early stages, with a few primer pairs accessible. With the whole-genome sequencing (WGS) of several grape varieties, characterization of grape SSR changed to be necessary not only to genomics but to also help SSR development and utility. Based on this, we identified the whole-genome SSR of nine grape cultivars ('PN40024', 'Cabernet Sauvignon', 'Carménère', 'Chardonnay', 'Merlot', 'Riesling', 'Zinfandel', 'Shine Muscat', and 'Muscat Hamburg') with whole-genome sequences released publicly and found that there are great differences in the distribution of SSR loci in different varieties. According to the difference in genome size, the number of SSRs ranged from 267,385 (Cabernet Sauvignon) to 627,429 (Carménère), the density of the SSR locus in the genome of nine cultivars was generally 1 per Kb. SSR motif distribution characteristic analysis of these grape cultivars showed that the distribution patterns among grape cultivars were conservative, mainly enriched in A/T. However, there are some differences in motif types (especially tetranucleotides, pentanucleotides, and hexanucleotides), quantity, total length, and average length in different varieties, which might be related to the size of the assembled genome or the specificity of variety domestication. The distribution characteristics of SSRs were revealed by whole-genome analysis of simple repeats of grape varieties. In this study, 32 pairs of primers with lower polymorphism have been screened, which provided an important research foundation for the development of molecular markers of grape variety identification and the construction of linkage maps of important agronomic traits for crop improvement.

Insights into taxonomy and phylogenetic relationships of eleven Aristolochia species based on chloroplast genome.

The Aristolochia, as an important genus comprised of over 400 species, has attracted much interest because of its unique chemical and pharmacological properties. However, the intrageneric taxonomy and species identification within Aristolochia have long been difficult because of the complexity of their morphological variations and lack of high-resolution molecular markers. In this study, we sampled 11 species of Aristolochia collected from distinct habitats in China, and sequenced their complete chloroplast (cp) genomes. The 11 cp genomes of Aristolochia ranged in size from 159,375bp (A. tagala) to 160,626 bp (A. tubiflora), each containing a large single-copy (LSC) region (88,914-90,251 bp), a small single-copy (SSC) region (19,311-19,917 bp), and a pair of inverted repeats (IR) (25,175-25,698 bp). These cp genomes contained 130-131 genes each, including 85 protein-coding genes (CDS), 8 ribosomal RNA genes, and 37-38 transfer RNA genes. In addition, the four types of repeats (forward, palindromic, reverse, and complement repeats) were examined in Aristolochia species. A. littoralis had the highest number of repeats (168), while A. tagala had the lowest number (42). The total number of simple sequence repeats (SSRs) is at least 99 in A. kwangsiensis, and, at most, 161 in A. gigantea. Interestingly, we detected eleven highly mutational hotspot regions, including six gene regions (clpP, matK, ndhF, psbT, rps16, trnK-UUU) and five intergenic spacer regions (ccsA-ndhD, psbZ-trnG-GCC, rpl33-rps18, rps16-trnQ-UUG, trnS-GCU-trnG-UCC). The phylogenetic analysis based on the 72 protein-coding genes showed that 11 Aristolochia species were divided into two clades which strongly supported the generic segregates of the subgenus Aristolochia and Siphisia. This research will provide the basis for the classification, identification, and phylogeny of medicinal plants of Aristolochiaceae.

Complete mitochondrial genome of Thuja sutchuenensis and its implications on evolutionary analysis of complex mitogenome architecture in Cupressaceae

BackgroundThe complex physical structure and abundant repeat sequences make it difficult to assemble the mitogenomes of seed plants, especially gymnosperms. Only approximately 33 mitogenomes of gymnosperms have been reported. However, as the most widely distributed and the second largest family among gymnosperms, Cupressaceae has only six assembled mitogenomes, including five draft mitogenomes and one complete mitogenome, which has greatly hindered the understanding of mitogenome evolution within this large family, even gymnosperms.ResultsIn this study, we assembled and validated the complete mitogenome of Thuja sutchuenensis, with a size of 2.4 Mb. Multiple sequence units constituted its complex structure, which can be reduced to three linear contigs and one small circular contig. The analysis of repeat sequences indicated that the numbers of simple sequence repeats increased during the evolutionary history of gymnosperms, and the mitogenome of Thuja sutchuenensis harboured abundant extra-long repeats (more than 5 kb). Additionally, the longest repeat sequence identified in these seven gymnosperms also came from the mitogenome of Thuja sutchuenensis, with a length of up to 47 kb. The analysis of colinear blocks and gene clusters both revealed that the orders of mitochondrial genes within gymnosperms was not conserved. The comparative analysis showed that only four tRNAs were shared by seven gymnosperms, namely, trnD-GUC, trnE-UUC, trnI-CAU and trnY-GUA. Furthermore, four genes have undergone potential positive selection in most gymnosperm species, namely, atp8, ccmB, mttB and sdh4.ConclusionWe successfully assembled the second complete mitogenome within Cupressaceae and verified that it consisted of multiple sequence units. Our study also indicated that abundant long repeats may contribute to the generation of the complex conformation of the mitogenome of Thuja sutchuenensis. The investigation of Thuja sutchuenensis’s mitogenome in our study provides new insight into further understanding the complex mitogenome architecture within gymnosperms.

Plastome evolution and phylogenomics of Impatiens (Balsaminaceae)

This study reported seven new plastomes from Impatiens and observed three highly variable regions for phylogeny and DNA barcoding, which resolved the relationships among sections of subgenus Impatiens. Impatiens L. (Balsaminaceae, Ericales) is one of the largest and most diverse genera of angiosperms, widely known for its taxonomic difficulty. In this study, we reevaluated the infrageneric relationships within the genus Impatiens, using complete plastome sequence data. Seven complete plastomes of Impatiens (representing 6 species) were newly sequenced and characterized along with 20 previously published plastomes of other Impatiens species, plus 2 plastomes of outgroups (Hydrocera triflora, Balsaminaceae; Marcgravia coriacea, Marcgraviaceae). The total size of these 29 plastomes ranged from 151,538bp to 152,917bp, except 2 samples of Impatiens morsei, which exhibited a shorter length and lost some genes encoding NADH dehydrogenase subunits. Moreover, the number of simple sequence repeats (SSRs) ranged from 51 to 113, and the number of long repeats from 17 to 26. In addition, three highly variable regions were identified (trnG-GCC (The previous one), ndhF-rpl32-trnL-UGA-ccsA, and ycf1). Our phylogenomic analysis based on 80 plastome-derived protein-coding genes strongly supported the monophyly of Impatiens and its two subgenera (Clavicarpa and Impatiens), and fully resolved relationships among the six (out of seven) sampled sections of subgenus Impatiens. Overall, the plastome DNA markers and phylogenetic results reported in this study will facilitate future identification, taxonomic and DNA barcoding studies in Impatiens as well as evolutionary studies in Balsaminaceae.

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.

The Complete Chloroplast Genome Sequence of Eupatorium fortunei: Genome Organization and Comparison with Related Species.

Eupatorium fortunei Turcz, a perennial herb of the Asteraceae family, is one of the horticultural and medicinal plants used for curing various diseases and is widely distributed in China and other Asian countries. It possesses antibacterial, antimetastatic, antiangiogenic, and antioxidant properties along with anticancer potential. However, the intrageneric classification and phylogenetic relationships within Eupatorium have long been controversial due to the lack of high-resolution molecular markers, and the complete chloroplast (cp) genome sequencing has not been reported with new evolutionary insights. In the present study, E. fortunei was used as an experimental material, and its genome was sequenced using high-throughput sequencing technology. We assembled the complete cp genome, and a systematic analysis was conducted for E. fortunei, acquiring the correspondence of its NCBI accession number (OK545755). The results showed that the cp genome of E. fortunei is a typical tetrad structure with a total length of 152,401 bp, and the genome encodes 133 genes. Analysis of the complete cp genomes of 20 Eupatorieae shows that the number of simple sequence repeats (SSRs) ranged from 19 to 36 while the number of long sequence repeats was 50 in all cases. Eleven highly divergent regions were identified and are potentially useful for the DNA barcoding of Eupatorieae. Phylogenetic analysis among 22 species based on protein-coding genes strongly supported that E. fortunei is more closely related to Praxelis clematidea and belongs to the same branch. The genome assembly and analysis of the cp genome of E. fortunei will facilitate the identification, taxonomy, and utilization of E. fortunei as well as provide more accurate evidence for the taxonomic identification and localization of Asteraceae plants.

Plastid Phylogenomics of Paeonia and the Evolution of Ten Flower Types in Tree Peony.

Paeonia suffruticosa Andr., a member of Paeoniaceae, is native to China. In its 1600 years' cultivation, more than 2000 cultivars for different purposes (ornamental, medicinal and oil use) have been inbred. However, there are still some controversies regarding the provenance of tree peony cultivars and the phylogenetic relationships between and within different cultivar groups. In this study, plastid genome sequencing was performed on 10 representative tree peony cultivars corresponding to 10 different flower types. Structure and comparative analyses of the plastid genomes showed that the total lengths of the chloroplast genome of the 10 cultivars ranged from 152,153 to 152,385 bp and encoded 84-88 protein-coding genes, 8 rRNAs and 31-40 tRNAs. The number of simple sequence repeats and interspersed repeat sequences of the 10 cultivars ranged from 65-68 and 40-42, respectively. Plastid phylogenetic relationships of Paeonia species/cultivars were reconstructed incorporating data from our newly sequenced plastid genomes and 15 published species, and results showed that subsect. Vaginatae was the closest relative to the central plains cultivar group with robust support, and that it may be involved in the formation of the group. Paeonia ostii was recovered as a successive sister group to this lineage. Additionally, eleven morphological characteristics of flowers were mapped to the phylogenetic skeleton to reconstruct the evolutionary trajectory of flower architecture in Paeoniaceae.

Comprehensive Comparative Analysis and Development of Molecular Markers for Dianthus Species Based on Complete Chloroplast Genome Sequences

Dianthus spp. is a genus with high economic and ornamental value in the Caryophyllaceae, which include the famous fresh-cut carnation and the traditional Chinese herbal medicine, D. superbus. Despite the Dianthus species being seen everywhere in our daily lives, its genome information and phylogenetic relationships remain elusive. Thus, we performed the assembly and annotation of chloroplast genomes for 12 individuals from seven Dianthus species. On this basis, we carried out the first comprehensive and systematic analysis of the chloroplast genome sequence characteristics and the phylogenetic evolution of Dianthus. The chloroplast genome of 12 Dianthus individuals ranged from 149,192 bp to 149,800 bp, containing 124 to 126 functional genes. Sequence repetition analysis showed the number of simple sequence repeats (SSRs) ranged from 75 to 80, tandem repeats ranged from 23 to 41, and pair-dispersed repeats ranged from 28 to 43. Next, we calculated the synonymous nucleotide substitution rates (Ks) of all 76 protein coding genes to obtain the evolution rate of these coding genes in Dianthus species; rpl22 showed the highest Ks (0.0471), which suggested that it evolved the swiftest. By reconstructing the phylogenetic relationships within Dianthus and other species of Caryophyllales, 16 Dianthus individuals (12 individuals reported in this study and four individuals downloaded from NCBI) were divided into two strongly supported sister clades (Clade A and Clade B). The Clade A contained five species, namely D. caryophyllus, D. barbatus, D. gratianopolitanus, and two cultivars (‘HY’ and ‘WC’). The Clade B included four species, in which D. superbus was a sister branch with D. chinensis, D. longicalyx, and F1 ‘87M’ (the hybrid offspring F1 from D. chinensis and ‘HY’). Further, based on sequence divergence analysis and hypervariable region analysis, we selected several regions that had more divergent sequences, to develop DNA markers. Additionally, we found that one DNA marker can be used to differentiate Clade A and Clade B in Dianthus. Taken together, our results provide useful information for our understanding of Dianthus classification and chloroplast genome evolution.

Complete chloroplast genome sequencing and comparative analysis of threatened dragon trees Dracaena serrulata and Dracaena cinnabari

Dracaena (Asparagaceae family) tree is famous for producing "dragon blood"—a bioactive red-colored resin. Despite its long history of use in traditional medicine, little knowledge exists on the genomic architecture, phylogenetic position, or evolution. Hence, in this study, we sequenced the whole chloroplast (cp) genomes of D. serrulata and D. cinnabari and performed comparative genomics of nine genomes of the genus Dracaena. The results showed that the genome sizes range from 155,055 (D. elliptica) to 155,449 (D. cochinchinensis). The cp genomes of D. serrulata and D. cinnabari encode 131 genes, each including 85 and 84 protein-coding genes, respectively. However, the D. hokouensis had the highest number of genes (133), with 85 protein coding genes. Similarly, about 80 and 82 repeats were identified in the cp genomes of D. serrulata and D. cinnabari, respectively, while the highest repeats (103) were detected in the cp genome of D. terniflora. The number of simple sequence repeats (SSRs) was 176 and 159 in D. serrulata and D. cinnabari cp genomes, respectively. Furthermore, the comparative analysis of complete cp genomes revealed high sequence similarity. However, some sequence divergences were observed in accD, matK, rpl16, rpoC2, and ycf1 genes and some intergenic spacers. The phylogenomic analysis revealed that D. serrulata and D. cinnabari form a monophyletic clade, sister to the remaining Dracaena species sampled in this study, with high bootstrap values. In conclusion, this study provides valuable genetic information for studying the evolutionary relationships and population genetics of Dracaena, which is threatened in its conservation status.