Inverted Repeat Regions Research Articles

The complete chloroplast genome and phylogenetic analysis of Cyperus brevifolius (Rottb.) Hassk. 1844 (Cyperaceae)

The medicinal plant Cyperus brevifolius (Rottb.) Hassk. 1844 has a long history of use in traditional Chinese medicine. In this study, we determined and systematically analyzed the complete chloroplast (cp) genome of C. brevifolius. The genome is 183,717 bp in length with a GC content of 33.24%. It comprises four distinct regions: a large-single copy (LSC) region of 101,190 bp, a small-single copy (SSC) region of 10,366 bp, and two inverted repeat (IR) regions of 36,079 bp each. A total of 137 genes are present in the genome including 89 protein-coding genes, 40 tRNA genes, and eight rRNA genes. Phylogenetic analysis reveals that C. brevifolius belongs to the Cyperus genus. This newly sequenced cp genome provides valuable insights for future genetic and genomic studies on Cyperus.

The complete chloroplast genome of Durio zibethinus L. cultivar Ri6 (Helicteroideae, Malvaceae)

Durian, a member of the Malvaceae family, is famous for its delicious fruits, which have strong scents and are rich in nutrients. In this study, we sequenced and characterized the complete chloroplast genome of Durio zibethinus L. 1774 cultivar Ri6, a popular durian cultivar in Vietnam, using the Illumina Hiseq platform. The results showed a circular chloroplast genome composed of a large single copy of 96,115 bp, a small single copy of 20,819 bp, and two inverted repeat regions of 24,185 bp. This genome consisted of 79 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The overall GC content of this genome was 35.7%. Phylogenetic analysis inferred from 78 protein-coding regions revealed monophyly of Durio species and a close relationship between D. zibethinus cultivar Ri6 and cultivar Mongthong. This study provides essential information for further studies examining genetic population, breedings, and species identification among Durio taxa and cultivars.

The complete chloroplast genome sequence and phylogenetic analysis of the Bichetii grass Chlorophytum laxum (Asparagaceae)

Chlorophytum laxum of Asparagaceae is a valuable ornamental plant native to the tropical regions of Asia, Africa, and Australia. The plant also has medicinal properties and is used as source for folk medicine. Despite being commercially important, genetic studies of C. laxum are still limited. To expand the genomic information of this plant species, we sequenced, assembled, and characterized its complete chloroplast genome. The chloroplast genome was 153,678 bp in length, with a large single-copy region (83,225 bp) and a small single-copy region (18,031 bp) separated by a pair of inverted repeat regions (26,211 bp each). A total of 127 genes were predicted, including 81 protein-coding, 38 tRNA, and eight rRNA genes. The overall GC content was 37.3%. Based on current sampling size, phylogenetic analysis using the maximum likelihood based on the complete chloroplast genome sequence revealed that the relationship in Chlorophytum is well resolved; C. laxum was closely related to C. rhizopendulum.

The complete chloroplast genome assembly of Solidago altissima (Lineaus, 1753) (Astereae; Asteraceae)

This study aims to report the complete chloroplast genome of Solidago altissima L., a globally recognized invasive plant. The complete genome length of S. altissima is 152,961 bp; S. altissima has a typical quadripartite structure (including a large single copy of 84,829 bp, a small single copy of 18,084 bp, and two inverted repeat regions of 25,024 bp), which is commonly found in angiosperms. The genome contains 129 genes, consisting of 85 coding sequences, 36 tRNA genes, and 8 rRNA genes. To understand the phylogenetic relationship between S. altissima and its related species, maximum likelihood analysis was performed. The results revealed that S. altissima is closely related to Symphyotrichum subulatum. The findings of the present study could provide fundamental data for the future phylogenetic and evolutionary studies, while also research on species invasion and resolving complexity of S. altissima.

Insights into chloroplast genome evolution in Rutaceae through population genomics

Chloroplast genomes, pivotal for understanding plant evolution, remain unexplored in Rutaceae, a family with key perennial crops like citrus. Leveraging next-generation sequencing data from 509 Rutaceae accessions across 15 species, we conducted a de novo assembly of 343 chloroplast genomes, unveiling a chloroplast variation map highlighting the heterogeneous evolution rates across genome regions. Notably, differences in chloroplast genome size primarily originate from large single-copy and small single-copy regions. Structural variants predominantly occurred in the single-copy region, with two insertions located at the single-copy and inverted repeat region boundary. Phylogenetic analysis, principal component analysis, and population genetic statistics confirmed the cohesive clustering of different Citrus species, reflecting evolutionary dynamics in Citrus diversification. Furthermore, a close chloroplast genetic affinity was revealed among Atalantia (previously regarded as primitive citrus), Clausena, and Murraya. Zanthoxylum formed a distinct group with heightened genetic diversity. Through expanding our analysis to include 34 published chloroplast genomes, we explored chloroplast gene selection, revealing divergent evolutionary trends in photosynthetic pathways. While Photosystem I and Photosystem II exhibited robust negative selection, indicating stability, the Nicotinamide adenine dinucleotide (NADH) dehydrogenase pathway demonstrated rapid evolution, which was indicative of environmental adaptation. Finally, we discussed the effects of gene length and GC content on chloroplast gene evolution. In conclusion, our study reveals the genetic characterization of chloroplast genomes during Rutaceae diversification, providing insights into the evolutionary history of this family.

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

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. 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. 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. 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.

Solanum aculeatissimum and Solanum torvum chloroplast genome sequences: a comparative analysis with other Solanum chloroplast genomes

BackgroundSolanum aculeatissimum and Solanum torvum belong to the Solanum species, and they are essential plants known for their high resistance to diseases and adverse conditions. They are frequently used as rootstocks for grafting and are often crossbred with other Solanum species to leverage their resistance traits. However, the phylogenetic relationship between S. aculeatissimum and S. torvum within the Solanum genus remains unclear. Therefore, this paper aims to sequence the complete chloroplast genomes of S. aculeatissimum and S. torvum and analyze them in comparison with 29 other previously published chloroplast genomes of Solanum species.ResultsWe observed that the chloroplast genomes of S. aculeatissimum and S. torvum possess typical tetrameric structures, consisting of one Large Single Copy (LSC) region, two reverse-symmetric Inverted Repeats (IRs), and one Small Single Copy (SSC) region. The total length of these chloroplast genomes ranged from 154,942 to 156,004 bp, with minimal variation. The highest GC content was found in the IR region, while the lowest was in the SSC region. Regarding gene content, the total number of chloroplast genes and CDS genes remained relatively consistent, ranging from 128 to 134 and 83 to 91, respectively. Nevertheless, there was notable variability in the number of tRNA genes and rRNAs. Relative synonymous codon usage (RSCU) analysis revealed that both S. aculeatissimum and S. torvum preferred codons that utilized A and U bases. Analysis of the IR boundary regions indicated that contraction and expansion primarily occurred at the junction between SSC and IR regions. Nucleotide polymorphism analysis and structural variation analysis demonstrated that chloroplast variation in Solanum species mainly occurred in the LSC and SSC regions. Repeat sequence analysis revealed that A/T was the most frequent base pair in simple repeat sequences (SSR), while Palindromic and Forward repeats were more common in long sequence repeats (LSR), with Reverse and Complement repeats being less frequent. Phylogenetic analysis indicated that S. aculeatissimum and S. torvum belonged to the same meristem and were more closely related to Cultivated Eggplant.ConclusionThese findings enhance our comprehension of chloroplast genomes within the Solanum genus, offering valuable insights for plant classification, evolutionary studies, and potential molecular markers for species identification.

Insights into comparative genomics, structural features, and phylogenetic relationship of species from Eurasian Aster and its related genera (Asteraceae: Astereae) based on complete chloroplast genome.

Aster L. is an economically and phylogenetically important genus in the tribe Astereae. Here, the complete plastomes of the eight Aster species were assembled and characterized using next-generation sequencing datasets. The results indicated the complete plastomes of Aster had a quadripartite structure. These genomes were 152,045-152,729 bp in length and contained 132-133 genes, including 87 protein-coding genes, 37-38 tRNA genes, and eight rRNA genes. Expansion or contraction of inverted repeat regions and forward, palindromic, complement, and reverse repeats were detected in the eight Aster species. Additionally, our analyses showed the richest type of simple sequence repeats was A/T mononucleotides, and 14 highly variable regions were discovered by analyzing the border regions, sequence divergence, and hotspots. Phylogenetic analyses indicated that 27 species in Astereae were clustered into six clades, i.e., A to D, North American, and outgroup clades, and supported that the genera Heteropappus, Kalimeris, and Heteroplexis are nested within Aster. The results indicated the clades B to D might be considered as genera. Divergence time estimate showed the clades A, B, C, and D diverged at 23.15 Mya, 15.13 Mya, 24.29 Mya, and 21.66 Mya, respectively. These results shed light on the phylogenetic relationships of Aster and provided new information on species identification of Aster and its related genera.

Complete Chloroplast Genome of Alternanthera sessilis and Comparative Analysis with Its Congeneric Invasive Weed Alternanthera philoxeroides

Alternanthera sessilis is considered the closest relative to the invasive weed Alternanthera philoxeroides in China, making it an important native species for studying the invasive mechanisms and adaptations of A. philoxeroides. Chloroplasts play a crucial role in a plant’s environmental adaptation, with their genomes being pivotal in the evolution and adaptation of both invasive and related species. However, the chloroplast genome of A. sessilis has remained unknown until now. In this study, we sequenced and assembled the complete chloroplast genome of A. sessilis using high-throughput sequencing. The A. sessilis chloroplast genome is 151,935 base pairs long, comprising two inverted repeat regions, a large single copy region, and a small single copy region. This chloroplast genome contains 128 genes, including 8 rRNA-coding genes, 37 tRNA-coding genes, 4 pseudogenes, and 83 protein-coding genes. When compared to the chloroplast genome of the invasive weed A. philoxeroides and other Amaranthaceae species, we observed significant variations in the ccsA, ycf1, and ycf2 regions in the A. sessilis chloroplast genome. Moreover, two genes, ccsA and accD, were found to be undergoing rapid evolution due to positive selection pressure. The phylogenetic trees were constructed for the Amaranthaceae family, estimating the time of independent species formation between A. philoxeroides and A. sessilis to be approximately 3.5186–8.8242 million years ago. These findings provide a foundation for understanding the population variation within invasive species among the Alternanthera genus.

The complete chloroplast genome and phylogentic results support the species position of Swertia banzragczii and Swertia marginata (Gentianaceae) in Mongolia

BackgroundSwertia banzragczii and S. marginata are important medicinal species in Mongolia. However, their taxonomic positions and genetic backgrounds remain unknown. In this study, we explored the complete chloroplast genomes and DNA barcoding of these species and compared them with those of closely related species within the subgenus to determine their taxonomic positions and phylogenetic relationships.ResultThe chloroplast genomes of S. banzragczii and S. marginata encoded 114 genes, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Among them, 16 genes contained a single intron, and 2 genes had two introns. Closely related species had a conserved genome structure and gene content. Only differences in genome length were noticed, which were caused by the expansion and contraction of the inverted repeat (IR) region and loss of exons in some genes. The trnH-GUG–psbA and trnD-GUC–trnY-GUA intergenic regions had high genetic diversity within Swertia plastomes. Overall, S. banzragczii and S. marginata are true species and belong to the subgenus Swertia.ConclusionsThese results provide valuable genetic and morphological information on rare and subendemic Swertia species in Mongolia, which can be used for further advanced studies on the Swertia genus.

The size diversity of the Pteridaceae family chloroplast genome is caused by overlong intergenic spacers

BackgroundWhile the size of chloroplast genomes (cpDNAs) is often influenced by the expansion and contraction of inverted repeat regions and the enrichment of repeats, it is the intergenic spacers (IGSs) that appear to play a pivotal role in determining the size of Pteridaceae cpDNAs. This provides an opportunity to delve into the evolution of chloroplast genomic structures of the Pteridaceae family. This study added five Pteridaceae species, comparing them with 36 published counterparts.ResultsPoor alignment in the non-coding regions of the Pteridaceae family was observed, and this was attributed to the widespread presence of overlong IGSs in Pteridaceae cpDNAs. These overlong IGSs were identified as a major factor influencing variations in cpDNA size. In comparison to non-expanded IGSs, overlong IGSs exhibited significantly higher GC content and were rich in repetitive sequences. Species divergence time estimations suggest that these overlong IGSs may have already existed during the early radiation of the Pteridaceae family.ConclusionsThis study reveals new insights into the genetic variation, evolutionary history, and dynamic changes in the cpDNA structure of the Pteridaceae family, providing a fundamental resource for further exploring its evolutionary research.

Chloroplast genome of Ecbolium viride: 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 and 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 P. 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, 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.

The complete chloroplast genome assembly of Commelina caroliniana Walter (Commelinaceae)

We sequenced and published the chloroplast genome of Commelina caroliniana Walter, which was previously misidentified as C. diffusa owing to their morphological similarities until 1989. The genome of C. caroliniana is 160,857 bp long [large single copy region: 88,064 bp; a small single copy region: 18,549 bp; two inverted repeat regions: 27,122 bp] and has a GC content of 35.7%. The genome comprises 133 genes, including 87 coding sequences (CDSs), 38 tRNAs, and eight rRNAs. The phylogenetic relationship between C. caroliniana and related species was analyzed using the maximum likelihood method based on the 79 CDSs of the chloroplast genome. Phylogenetic analysis revealed that C. caroliniana is closely related to C. communis. Our findings will contribute to studies on species identification and phylogenetic and evolutionary research. These results enhance our understanding of the Commelina genus.

Characterization of the complete chloroplast genome sequence of Agave durangensis (Asparagales: Asparagaceae: Agavoideae)

Agave durangensis commonly known as agave cenizo, is an endemic Agave species in Mexico used for mescal production, yet its taxonomic delimitation is still controversial. This study aimed to enhance taxonomic clarity by characterizing its chloroplast genome. Chloroplast DNA was isolated from 2-year-old A. durangensis leaves. The complete chloroplast genome size was 156,441 bp, comprising a large single-copy region (LSC), a pair of inverted repeat regions (IR), and a small single-copy region (SSC). Annotation revealed 87 protein-coding genes, 38 tRNAs, and 8 rRNAs, with notable gene inversions. Phylogenetic analysis suggests, A. durangensis forms a separate lineage within the Agave genus.

The complete chloroplast genome of the medicinally important plant Plumbago zeylanica L. (plumbaginaceae) and phylogenetic analysis

Plumbago zeylanica L. 1753 is a medicinally-important herb in family Plumbaginaceae. In this study, we assembled and reported the complete chloroplast genome of P. zeylanica. The plastome of P. zeylanica was 169,178 bp, including a large single-copy region of 92,135 bp, a small single-copy region (SSC) of 13,455 bp and a pair of inverted repeat regions (IRs) of 31,794 bp. It contained 124 genes, including 79 protein-coding genes, 37 tRNA genes and eight rRNA genes. Phylogenetic analysis showed that P. zeylanica formed a close relationship with P. auriculata in Plumbago. The first complete chloroplast genome report of P. zeylanica providing an opportunity to explore the genetic diversity, and would be also helpful in the species identification and conservation.

Characterization of the complete chloroplast genome of Eutrema deltoideum (Brassicaceae)

Eutrema deltoideum (Hook. f. et Thoms.) has been recognized as a potentially important vegetable and medicinal resource. In this study, we present the complete chloroplast genome of E. deltoideum and conduct a phylogenetic analysis. The chloroplast genome is 154,051 bp long and consists of a large single-copy (LSC) region of 84,149 bp, two inverted repeat (IR) regions of 26,065 bp each, and a small single-copy (SSC) region of 17,772 bp. It contains 132 complete genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 37 tRNA genes. Additionally, we identified 78 simple sequence repeats (SSRs). The phylogenetic tree reveals that E. deltoideum is closely related to E. heterophyllum, and the Eutrema genus is monophyletic. This study provides valuable information about E. deltoideum and enhances our understanding of its taxonomic classification.

The complete chloroplast genome of Lagochilus ilicifolius Bunge ex Bentham, Labiat. Gen. 1834 (Lamiaceae) and its phylogenetic analysis

Lagochilus ilicifolius Bunge ex Bentham, Labiat. Gen is a perennial herb with much-branched stems native to Nei Mongol, Ningxia, Gansu, N Shaanxi. It can be used clinically as a hemostatic agent. The chloroplast genome length is 151,466 bp. It contained two inverted repeat regions of 25,660 bp each, a large single-copy region of length 82,504 bp, and a small single-copy region of length 17,642 bp. Also, the GC content is 38.6%. There were 133 genes annotated, including 88 known protein-coding genes, 37 tRNAs, and eight rRNAs. The phylogenetic tree was constructed using Bayesian method for plastome data of 29 species. The entire chloroplast genome of L. ilicifolius within the Lamiaceae is the first to reveal genetic taxonomy at the molecular level, and the new phylogenetic tree data can be used for future evolutionary studies.

Characterization of the complete chloroplast genome sequence of Camellia tetracocca (Theaceae)

Camellia tetracocca H.T. Chang 1981 is an important wild relative of cultivated tea plants. Its leaves are widely used by local people to make tea, showing great economic and breeding values. We here report the complete chloroplast genome of C. tetracocca using Illumina sequencing technology. The complete chloroplast genome of C. tetracocca is 157,026 bp in length, and structurally contains a pair of inverted repeat regions (IRa and IRb, 26,052 bp) separated by a large single-copy region (LSC, 86,669 bp) and a small single-copy region (SSC, 18,253 bp). It is composed of 131 predicted genes, including 86 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. The overall GC content is 37.31%. Phylogenetic analysis among four Camellia species and 11 other close species reveals a close relationship between C. tetracocca and C. gymnogyna.

Complete chloroplast genome of two Arabis L. species from Korea and assessment of their phylogenetic relationship in plastome based phylogeny

Arabis stelleri DC. and A. takesimana Nakai belong to the family Brassicaceae. Arabis stelleri is widely distributed in East Asia and A. takesimana is a Korean endemic plant. In this study, we report the complete chloroplast genomes of both species, measuring 153,577 bp for A. stelleri and 153,557 bp for A. takesimana. The plastome of A. stelleri comprises two inverted repeats (IRs) of 26,421 bp, a large single-copy (LSC) region measuring 82,705 bp, and a small single-copy (SSC) region of 18,030 bp. Whereas, A. takesimana has IR regions of 26,426 bp, LSC of 82,694 bp and SSC of 18,011 bp. Both the plastomes contain 131 total genes, 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes and 36.4% GC. The organization and gene content of both the plastomes were found to be similar to previously reported Arabis plastomes. In addition, we have tested the phylogenetic position of both the Arabis species and the relationship of genus Arabis with other Brassicaceae members in comprehensive family level plastome based phylogeny. Arabis stelleri and A. takesimana are phylogenetically placed within the Arabis clade and show close relationship to A. flagellosa, A. nipponica, A. paniculata and A. hirsuta.

Two chloroplast genomes with reduced inverted repeat regions in Mammillaria series Stylothelae (Cactaceae)

Background: The chloroplast genomes of Cactaceae exhibit boundary modifications in the inverted repeat regions (IRs), gene inversions, and deletions. Among nine Mammillaria species, three distinct chloroplast structures have been identified, although not all of these correspond to the morphology-based classification of the genus.
 Question: Is there a distinct chloroplast genome structure in the species of Mammillaria series Stylothelae?
 Studied species: Mammillaria bocasana and M. erythrosperma.
 Study site and dates: Mexico from 2019 to 2023.
 Methods: Chloroplast DNA was sequenced, and chloroplast genomes were de novo assembled using the Fast-Plast program. Complete plastome sequences were annotated and verified. The sequences were aligned in MAUVE program to detect possible structural changes. A maximum likelihood phylogeny was executed to evaluate the relationships of the studied species.
 Results: The plastomes ranged from 107,368 bp in Mammillaria bocasana to 108,069 bp in M. erythrosperma. Both presented a quadripartite structure and contained 108 genes. The IRs were ~ 1,600 bp long and included the genes rpl2, rpl23 (pseudo), and trnI-CAU. MAUVE identified a ~ 21 kb inversion in the large single copy containing a block of genes related to photosynthesis. The phylogenetic analysis placed both species in a single clade separated from the other species within Mammillaria subg. Mammillaria.
 Conclusions: The studied species of Mammillaria series Stylothelae exhibited a different and synapomorphic chloroplast genome structure. Other Mammillaria chloroplast genome structures have evolved independently in different lineages.