Inverted Repeat Research Articles

The complete chloroplast genome of Calyptothecium philippinense Broth. (Pterobryaceae, Hypnales)

The genus Calyptothecium, currently comprising ca. 30 species worldwide, is the largest genus within the family Pterobryaceae. However, a comprehensive taxonomic revision of this genus is lacking. Calyptothecium philippinense Broth. 1899, a moss species widely found in the tropical regions of Asia, is characterized by the unique rugose leaves and large auriculate leaf bases. In this study, we sequenced the complete chloroplast genome (CPG) of C. philippinense using the Illumina NovaSeq 6000 platform. The length of the CPG of C. philippinense was determined to be 124,513 bp, with an AT content of 74%. The CPG of C. philippinense exhibited a standard quadripartite structure, consisting of one small single-copy (SSC) region (18,541 bp), one large single-copy region (LSC) (87,222 bp), and two inverted repeat (IR) regions (9375 bp each). A total of 126 genes from the CPG of C. philippinense were annotated, including 82 protein-coding genes, eight ribosomal RNA genes, and 36 transfer RNA genes. Phylogenetic analysis based on the CPGs of 25 bryophyte taxa revealed that the three Pterobryaceae species C. philippinense, Calyptothecium hookeri (Mitt.) Broth. and Pterobryopsis orientalis (Müll. Hal.) M. Fleisch. formed a robust clade. The findings could facilitate more accurate classification and help elucidate evolutionary relationships within Calyptothecium.

Characterization of the complete chloroplast genome sequence of Artemisia sylvatica Maximowicz 1859 (Asteraceae)

Artemisia sylvatica Maximowicz 1859 is one of the medicinal herbs in Artemisia. This study presents the complete chloroplast genome of A. sylvatica, sequenced using the Illumina NovaSeq platform. The genome is 151,161 bp in length, featuring a GC content of 38%. It consists of a large single-copy (LSC) region of 82,892 bp, a small single-copy (SSC) region of 18,353 bp, and two inverted repeat (IR) regions of 24,958 bp each. In total, the genome contains 132 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis positions A. sylvatica within the subgenus Artemisia, highlighting its evolutionary relationships within this diverse genus. The first chloroplast genome of A. sylvatica was reported in this work contributes to the enrichment of genomic data for the genus Artemisia.

Characterization of the complete chloroplast genome sequence of Schisandra propinqua subsp. sinensis (Oliv.) R.M.K.Saunders 1997 (Schisandraceae)

Schisandra propinqua subsp. sinensis (Oliv.) R.M.K. Saunders 1997, a woody vine plant esteemed for its medicinal properties, has garnered attention in botanical research. In this study, we elucidated the complete chloroplast genome sequence of S. propinqua. The genome spans 145,562 bp and comprises a large single-copy (LSC) region of 94,164 bp, a small single-copy region of 18,294 bp (SSC), and a pair of inverted repeats (IR) of 16,552 bp. Notably, S. propinqua exhibits an overall GC content of 36.2%. Annotation revealed a total of 116 genes, encompassing 81 protein-coding genes, 27 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Phylogenetic analysis unveiled a close relationship among Schisandraceae, indicating the evolutionary proximity. This comprehensive genomic dataset provides valuable insights into the genetic makeup and evolutionary dynamics within the Schisandra genus.

The complete chloroplast genome and phylogenetic analysis of Garcinia esculenta Y. H. Li. 1981 (Clusiaceae)

Garcinia esculenta Y. H. Li. 1981 (Clusiaceae) is an endemic tree species in China, primarily found in western and northwestern Yunnan Province. In this research, the complete chloroplast genome of G. esculenta was sequenced using the Illumina NovaSeq6000 platform. The result showed that the length of the complete chloroplast genome was 155,853 bp, which was composed of a large single-copy region (LSC) of 84,534 bp, a small single-copy region (SSC) of 17,175 bp, and a pair of inverted repeat (IR) regions of 27,072 bp. The overall GC content was 36.1%. The complete chloroplast genome encompassed 128 genes, comprising 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis of the complete chloroplast genome sequences of 22 species revealed that G. esculenta is most closely related to G. oblongifolia.

The complete chloroplast genome sequence of Primula medogensis (Primulaceae) and its phylogeny

Primula medogensis W.B Ju, B. Xu & X.F. Gao 2023, a new species categorized under P. sect. Cordifoliae, was officially described in 2023. Given its recent classification, the genetic resources for this species are currently very limited. Here, we sequenced and assembled the first complete chloroplast genome of P. medogensis using Illumina sequencing technology. The complete chloroplast genome of P. medogensis is 151,486 bp in length, exhibiting a typical quadripartite structure. It consists of a large single-copy region (LSC; 83,407 bp) and a small single-copy region (SSC;17675 bp), separated by a pair of inverted repeat regions (IRs; 25202 bp). A total of 131 genes were annotated, including 86 protein-coding, 37 tRNA, and eight rRNA genes. The overall GC content was 37.1%. Phylogenetic analysis of 59 Primula species revealed a close relationship between P. medogensis and P. calliantha subsp. bryophila.

The complete chloroplast genome sequence and phylogenetic analysis of Hordeum pusillum Nutt., 1818 (Poaceae)

Hordeum pusillum (Hordeum pusillum Nutt., 1818) is an annual barley that is native to the west of the North America and widespread in southern United States and tropical America. In this study, we have provided the first complete characterization of the chloroplast genome of H. pusillum. Our research revealed that the circular chloroplast genome of H. pusillum consists of a large single-copy region (LSC: 80,853 bp), a small single-copy region (SSC: 12,745 bp), and a pair of inverted repeat regions (IRs: 21,587 bp), totaling 136,772 bp in length. Within the chloroplast genome of H. pusillum, 91 protein-coding genes, 38 tRNA genes, and ten rRNA genes were identified. To determine the evolutionary relationship of Hordeum species with reported chloroplast genome sequences, we constructed a phylogenetic tree using the entire chloroplast genome sequences. The evolutionary position of H. pusillum corresponds to its geographical location. The chloroplast genome of H. pusillum provided in this study may have significant implications for the phylogenetic study of Poaceae species.

The complete chloroplast genome of Camellia huulungensis Rosmann et Ninh, a golden Camellia species endemic to Vietnam

Camellia huulungensis Rosmann & Ninh 1997, belonging to the sect. Chrysantha, holds important ornamental value and medicinal value. In this study, the complete chloroplast genome sequence of C. huulungensis was assembled using high-throughput sequencing technology. The entire length of chloroplast genome is 156,546 bp and contains a small single-copy region (18,257 bp), a large single-copy region (86,219 bp), and a pair of inverted repeat regions (26,035 bp). A total of 133 genes were annotated, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content is 37.33%. The phylogenetic analysis showed that C. huulungensis is sister to C. aurea. The results can provide genetic data for further phylogenetic studies of Camellia.

Characterization of the complete chloroplast genome of Liparis gigantea (Orchidaceae)

Liparis gigantea is a Chinese traditional medicinal herb in the Orchidaceae family. It is a rare and special Liparis species that exhibits relatively large flowers. To illuminate its phylogenetic status and augment genomic resources, the complete chloroplast (cp) genome of L. gigantea was first sequenced and assembled using whole genome next-generation sequencing in this study. The cp genome size is 158,462 bp with a total GC content of 36.9%. Characterized by a quadripartite structure, the genome consists of a large single-copy (LSC) region of 86,032 bp, a small single-copy (SSC) region of 18,322 bp, which is separated by a pair of 27,054 bp inverted repeat regions (IRs). A total of 133 genes were annotated, including 87 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis strongly supported L. gigantea as the sister to two closely related terrestrial species, Liparis nervosa and L. vivipara. The results of this study provide genomic information for future research and application of this medicinal herb.

The complete chloroplast genome of Fuchsia standishii J. Harrison, 1840 (Onagraceae) from Yunnan, China

Fuchsia standishii J. Harrison, 1840, a perennial shrub, is renowned for its vividly colored and uniquely shaped blooms, which have an extended flowering season. Commonly cultivated as an ornamental potted plant, it is utilized in traditional Chinese medicine. In this study, we successfully sequenced and assembled the complete chloroplast genome of F. standishii using high-throughput Illumina sequencing technology. The assembled chloroplast genome displays a typical quadripartite structure, with a total length of 156,391 bp. It consists of a pair of inverted repeat regions (IRs), each measuring 25,069 bp, separated by a large single-copy region (LSC) of 87,754 bp and a small single-copy region (SSC) of 18,499 bp. The overall GC content of the genome is 37.60%. The genome includes a total of 129 genes, comprising 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis of 17 complete chloroplast genomes revealed that F. standishii forms a monophyletic group with the entire Circaea. This study provides a molecular foundation for future phylogenetic research on Fuchsia.

The complete chloroplast genome of Clematis serratifolia (Ranunculaceae) from Jilin province, China

Clematis serratifolia has high medicinal and ornamental value. In this study, we characterize and report, for the first time, the complete chloroplast genome sequence of C. serratifolia based on high-throughput sequence dates. The whole chloroplast genome of C. serratifolia is a circular molecule of 159,648 bp in length, consisting of a large single-copy (LSC) region of 79,394 bp, a small single-copy (SSC) region of 18,112 bp, and two inverted repeat (IR) regions of 31,071 bp. The overall GC content of the chloroplast genome is 38%, while that in the LSC, SSC, and IR regions is 36.3%, 31.3%, and 42.1%, respectively. The chloroplast genome of C. serratifolia contains 133 genes, including 89 coding genes, 8 ribosomal RNAs, and 36 transfer RNAs. Among them, 14 protein-coding genes have a single intron, and 2 genes have two introns. The phylogenetic analysis showed a close relationship between C. serratifolia and C. heracleifolia.

Complete chloroplast genome sequence of Artemisia littoricola (Asteraceae) from Dokdo Island Korea: genome structure, phylogenetic analysis, and biogeography study.

The Asteraceae family, particularly the Artemisia genus, presents taxonomic challenges due to limited morphological characteristics and frequent natural hybridization. Molecular tools, such as chloroplast genome analysis, offer solutions for accurate species identification. In this study, we sequenced and annotated the chloroplast genome of Artemisia littoricola sourced from Dokdo Island, employing comparative analyses across six diverse Artemisia species. Our findings reveal conserved genome structures with variations in repeat sequences and junction boundaries. Notably, the chloroplast genome of A. littoricola spans 150,985bp, consistent with other Artemisia species, and comprises 131 genes, including 86 protein-coding, 37 tRNA, and 8 rRNA genes. Among these genes, 16 possess a single intron, while clpP and ycf3 exhibit two introns each. Furthermore, 18 genes display duplicated copies within the IR regions. Moreover, the genome possesses 42 Simple Sequence Repeats (SSRs), predominantly abundant in A/T content and located within intergenic spacer regions. The analysis of codon usage revealed that the codons for leucine were the most frequent, with a preference for ending with A/U. While the chloroplast genome exhibited conservation overall, non-coding regions showed lower conservation compared to coding regions, with the Inverted Repeat (IR) region displaying higher conservation than single-copy regions. Phylogenetic analyses position A. littoricola within subgenus Dracunculus, indicating a close relationship with A. scoparia and A. desertorum. Additionally, biogeographic reconstructions suggest ancestral origins in East Asia, emphasizing Mongolia, China (North East and North Central and South Central China), and Korea. This study underscores the importance of chloroplast genomics in understanding Artemisia diversity and evolution, offering valuable insights into taxonomy, evolutionary patterns, and biogeographic history. These findings not only enhance our understanding of Artemisia's intricate biology but also contribute to conservation efforts and facilitate the development of molecular markers for further research and applications in medicine and agriculture.

Complete analysis of G-quadruplex forming sequences in the gapless assembly of human chromosome Y

Recent advancements have finally delivered a complete human genome assembly, including the elusive Y chromosome. This accomplishment closes a significant knowledge gap. Prior efforts were hampered by challenges in sequencing repetitive DNA structures such as direct and inverted repeats. We used the G4Hunter algorithm to analyze the presence of G-quadruplex forming sequences (G4s) within the current human reference genome (GRCh38) and the new telomere-to-telomere (T2T) Y chromosome assemblies. This analysis served a dual purpose: identifying the location of potential G4s within the genomes and exploring their association with functionally annotated sequences. Compared to GRCh38, the T2T assembly exhibited a significantly higher prevalence of G-quadruplex forming sequences. Notably, these repeats were abundantly located around precursor RNA, exons, genes, and within protein binding sites. This remarkable co-occurrence of G4-forming sequences with these critical regulatory regions suggests their role in fundamental DNA regulation processes. Our findings indicate that the current human reference genome significantly underestimated the number of G4s, potentially overlooking their functional importance.

The complete chloroplast genome of Buxus sinica var. parvifolia (Buxaceae) and its phylogenetic analysis

Buxus sinica var. parvifolia is a shrub or small arbor of the Buxaceae family, rich in various medicinal alkaloids and of great horticultural value. In this study, we sequenced, assembled, and annotated the complete chloroplast genome of B. sinica var. parvifolia for the first time. The length of the chloroplast genome is 158,995 bp with 38.1% overall GC content. It includes a large single-copy (LSC) region of 88,140 bp, a small single-copy (SSC) region of 17,761 bp, and two inverted repeat regions of 26,547 bp. Additionally, 132 functional genes in the genome are identified, including 87 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. Phylogenetic analysis showed that B. sinica var. parvifolia is closely related to Buxus microphylla. The complete chloroplast genome sequence of B. sinica var. parvifolia and its phylogenetic analysis provides useful genomic information for the further study of B. sinica var. parvifolia and other Buxus species.

Characterization and phylogenetic analysis of the chloroplast genome of Solanum pseudocapsicum (Solanaceae)

Solanum pseudocapsicum Linnaeus 1753, a popular indoor potted plant known for its ornamental fruits, had its chloroplast genome sequenced in this study to determine its phylogenetic relationship with other related species and to construct a phylogenetic analysis tree. The research findings are as follows: 1. The chloroplast genome of S. pseudocapsicum comprises a large single-copy (LSC) region of 86,260 base pairs, a small single-copy (SSC) region of 18,325 base pairs, and two inverted repeat (IR) regions, each measuring 25,390 base pairs in length. 2. The G + C content of the entire chloroplast genome is 37.59%, with the highest G + C content found in the IR regions, reaching 43.03%; followed by the LSC region, which has a G + C content of 35.68%; and the lowest in the SSC region, with a G + C content of 31.53%. 3. The genome contains 127 genes, including 82 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, with 18 genes duplicated in the IR regions. 4. Phylogenetic analysis revealed that S. pseudocapsicum, Solanum betaceum, Solanum laciniatum, and Solanum nitidum are genetically closely related and are located on the same branch of the phylogenetic tree, indicating a close relationship among them. This study provides a foundation for the identification, classification, and exploration of genetic diversity within the Solanum genus.

The complete chloroplast genome sequence of Begonia pedatifida

Begonia pedatifida has persistently been utilized as a traditional folk herbal medicine. This study has sequenced the chloroplast genome of B. pedatifida to establish its genomic characteristics and to discern its phylogenetic relationships with other closely related species. The chloroplast genome structure of B. pedatifida reveals a circular molecule with a length of 169,606 bp, including a large single copy (LSC) region of 76,086 bp, a small single copy (SSC) region of 18,314 bp, and a pair of inverted repeats (IRS) region of 37,603 bp. The entire genome contains 138 genes, which consist of 88 protein-coding genes, 42 tRNA genes, and 8 rRNA genes. Phylogenetic analysis suggests that B. pedatifida is closely related to Begonia emeiensis, Begonia jinyunensis, and Begonia pulchrifolia, sharing a common ancestor and forming sister lineages. This research provides genetic information for further study on B. pedatifida.

Characterization and phylogenetic analysis of the chloroplast genome in Elaeocarpus duclouxii

Elaeocarpus duclouxii, an evergreen tree species, is renowned for its fruits rich in flavonoids exhibiting potent antioxidant properties. Despite its significance, the chloroplast genome of this plant has remained unexplored until now. Our study presents the first comprehensive sequencing and analysis of the E. duclouxii chloroplast genome, revealing a circular DNA molecule of 158,148 base pairs. This genome comprises a large single-copy region of 85,700 base pairs, a small single-copy region of 17,672 base pairs, and a pair of inverted repeat regions totaling 27,388 base pairs. The genome encodes 132 genes, including 87 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. Phylogenetic analyses indicate a close evolutionary relationship between E. duclouxii and E. sylvestris. This study not only represents the first phylogenetic investigation of E. duclouxii but also establishes a crucial genomic foundation for future research area such as conservation genetics, evolutionary biology, and potential biotechnological applications.

The complete chloroplast genome of Psydrax latifolia: evolutionary dynamics, comparative genomics and phylogeny

IntroductionThis study presents the first complete plastome (cpDNA) sequence of Psydrax latifolia, a member of the Rubiaceae family, which includes small trees, smooth shrubs, and occasionally lianas. This specimen was collected near the Red Sea coast in Jazan province, Saudi Arabia, specifically in the paleotropical Fifa Mountains. The research aimed to characterize and compare the plastome of Psydrax latifolia with other species in the Rubiaceae family to enhance our understanding of its evolutionary dynamics and phylogenetic relationships.MethodsThe plastome of P. latifolia was sequenced and reconstructed using whole-genome next-generation sequencing (NGS) techniques. Comparative analyses were performed between the plastome of P. latifolia and 16 other species within the Rubiaceae family to identify genomic features and evolutionary patterns. The plastome structure, gene content, and codon usage were analyzed, with a focus on the Relative Synonymous Codon Usage (RSCU) in different regions of the plastome.ResultsThe plastome of P. latifolia was found to be 153,242 base pairs (bp) in length, including a large single copy (LSC) region of 83,603 bp, a small single copy (SSC) region of 18,115 bp, and a pair of inverted repeats (IRs) of 25,762 bp each. It contained 87 protein-coding genes, 8 rRNA genes, and 33 tRNA genes, with an overall GC content of 37.30%. The RSCU analysis revealed regional variation, with the protein-coding region being more conserved than the intergenic spacer.DiscussionThis study provides the first complete plastome sequence of Psydrax latifolia, offering insights into its genomic structure and phylogenetic position within the Rubiaceae family. Comparative analyses with 16 Rubiaceae species highlighted distinct genomic features and evolutionary patterns. These findings contribute to the understanding of plastome evolution in the Rubiaceae family and provide a valuable resource for future phylogenetic and evolutionary studies.

Flagellar switch inverted repeat impacts flagellar invertibility and varies Clostridioides difficile RT027/MLST1 virulence.

Clostridioides difficile RT027 strains cause infections that vary in severity from asymptomatic to lethal, but the molecular basis for this variability is poorly understood. Through comparative analyses of RT027 clinical isolates, we determined that isolates that exhibit greater variability in their flagellar gene expression exhibit greater virulence in vivo. C. difficile flagellar genes are phase-variably expressed due to the site-specific inversion of the flgB 5'UTR region, which reversibly generates ON vs. OFF orientations for the flagellar switch. We found that longer inverted repeat (IR) sequences in this switch region correlate with greater disease severity, with RT027 strains carrying 6A/6T IR sequences exhibiting greater phenotypic heterogeneity in flagellar gene expression (60%-75% ON) and causing more severe disease than those with shorter IRs (> 99% ON or OFF). Taken together, our results reveal that phenotypic heterogeneity in flagellar gene expression may contribute to the variable disease severity observed in C. difficile patients.

Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability.

Transcriptional factors (TFs) in bacteria play a crucial role in gene regulation by binding to specific DNA sequences, thereby assisting in the activation or repression of genes. Despite their central role, deciphering shape recognition of bacterial TFs-DNA interactions remains an intricate challenge. A deeper understanding of DNA secondary structures could greatly enhance our knowledge of how TFs recognize and interact with DNA, thereby elucidating their biological function. In this study, we employed machine learning algorithms to predict transcription factor binding sites (TFBS) and classify them as directed-repeat (DR) or inverted-repeat (IR). To accomplish this, we divided the set of TFBS nucleotide sequences by size, ranging from 8 to 20 base pairs, and converted them into thermodynamic data known as DNA duplex stability (DDS). Our results demonstrate that the Random Forest algorithm accurately predicts TFBS with an average accuracy of over 82% and effectively distinguishes between IR and DR with an accuracy of 89%. Interestingly, upon converting the base pairs of several TFBS-IR into DDS values, we observed a symmetric profile typical of the palindromic structure associated with these architectures. This study presents a novel TFBS prediction model based on a DDS characteristic that may indicate how respective proteins interact with base pairs, thus providing insights into molecular mechanisms underlying bacterial TFs-DNA interaction.

Transposon-mediated genic rearrangements underlie variation in small RNA pathways

Transposable elements (TEs) can alter host gene structure and expression, whereas host organisms develop mechanisms to repress TE activities. In the nematode Caenorhabditis elegans , a small interfering RNA pathway dependent on the helicase ERI-6/7 primarily silences retrotransposons and recent genes of likely viral origin. By studying gene expression variation among wild C. elegans strains, we found that structural variants and transposon remnants likely underlie expression variation in eri-6/7 and the pathway targets. We further found that multiple insertions of the DNA transposons, Polintons, reshuffled the eri-6/7 locus and induced inversion of eri-6 in some wild strains. In the inverted configuration, gene function was previously shown to be repaired by unusual trans-splicing mediated by direct repeats. We identified that these direct repeats originated from terminal inverted repeats of Polintons . Our findings highlight the role of host-transposon interactions in driving rapid host genome diversification among natural populations and shed light on evolutionary novelty in genes and splicing mechanisms.