Inverted Repeat Contraction Research Articles

Complete Plastid Genomes of Nine Species of Ranunculeae (Ranunculaceae) and Their Phylogenetic Inferences.

The tribe Ranunculeae, Ranunculaceae, comprising 19 genera widely distributed all over the world. Although a large number of Sanger sequencing-based molecular phylogenetic studies have been published, very few studies have been performed on using genomic data to infer phylogenetic relationships within Ranunculeae. In this study, the complete plastid genomes of nine species (eleven samples) from Ceratocephala, Halerpestes, and Ranunculus were de novo assembled using a next-generation sequencing method. Previously published plastomes of Oxygraphis and other related genera of the family were downloaded from GenBank for comparative analysis. The complete plastome of each Ranunculeae species has 112 genes in total, including 78 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The plastome structure of Ranunculeae samples is conserved in gene order and arrangement. There are no inverted repeat (IR) region expansions and only one IR contraction was found in the tested samples. This study also compared plastome sequences across all the samples in gene collinearity, codon usage, RNA editing sites, nucleotide variability, simple sequence repeats, and positive selection sites. Phylogeny of the available Ranunculeae species was inferred by the plastome data using maximum-likelihood and Bayesian inference methods, and data partitioning strategies were tested. The phylogenetic relationships were better resolved compared to previous studies based on Sanger sequencing methods, showing the potential value of the plastome data in inferring the phylogeny of the tribe.

CPJSdraw: analysis and visualization of junction sites of chloroplast genomes.

Chloroplast genomes are usually circular molecules, and most of them are tetrad structures with two inverted repeat (IR) regions, a large single-copy region, and a small single-copy region. IR contraction and expansion are among the genetic diversities during the evolution of plant chloroplast genomes. The only previously released tool for the visualization of junction sites of the regions does not consider the diversity of the starting point of genomes, which leads to incorrect results or even no results for the examination of IR contraction and expansion. In this work, a new tool named CPJSdraw was developed for visualizing the junction sites of chloroplast genomes. CPJSdraw can format the starting point of the irregular linearized genome, correct the junction sites of IR and single-copy regions, display the tetrad structure, visualize the junction sites of any number (≥1) of chloroplast genomes, show the transcription direction of genes adjacent to junction sites, and indicate the IR expansion or contraction of chloroplast genomes. CPJSdraw is a software that is universal and reliable in analysis and visualization of IR expansion or contraction of chloroplast genomes. CPJSdraw has more accurate analysis and more complete functions when compared with previously released tool. CPJSdraw as a perl package and tested data are available at http://dx.doi.org/10.5281/zenodo.7669480 for English users. In addition, an online version with a Chinese interface is available at http://cloud.genepioneer.com:9929/#/tool/alltool/detail/335.

Characterization of the Dicranostigma leptopodum chloroplast genome and comparative analysis within subfamily Papaveroideae

BackgroundDicranostigma leptopodum (Maxim.) Fedde is a perennial herb with bright yellow flowers, well known as "Hongmao Cao" for its medicinal properties, and is an excellent early spring flower used in urban greening. However, its molecular genomic information remains largely unknown. Here, we sequenced and analyzed the chloroplast genome of D. leptopodum to discover its genome structure, organization, and phylogenomic position within the subfamily Papaveroideae.ResultsThe chloroplast genome size of D. leptopodum was 162,942 bp, and D. leptopodum exhibited a characteristic circular quadripartite structure, with a large single-copy (LSC) region (87,565 bp), a small single-copy (SSC) region (18,759 bp) and a pair of inverted repeat (IR) regions (28,309 bp). The D. leptopodum chloroplast genome encoded 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The dynamics of the genome structures, genes, IR contraction and expansion, long repeats, and single sequence repeats exhibited similarities, with slight differences observed among the eight Papaveroideae species. In addition, seven interspace regions and three coding genes displayed highly variable divergence, signifying their potential to serve as molecular markers for phylogenetic and species identification studies. Molecular evolution analyses indicated that most of the genes were undergoing purifying selection. Phylogenetic analyses revealed that D. leptopodum formed a clade with the tribe Chelidonieae.ConclusionsOur study provides detailed information on the D. leptopodum chloroplast genome, expanding the available genomic resources that may be used for future evolution and genetic diversity studies.

Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Leymus (Triticodae, Poaceae).

Leymus is a perennial genus that belongs to the tribe Triticeae (Poaceae) which has an adaptive capacity to ecological conditions and strong resistance to cold, drought, and salinity. Most Leymus species are fine herbs that can be used for agriculture, conservation, and landscaping. Due to confusion taxonomy within genera, the complete chloroplast (cp) genome of 13 Leymus species was sequenced, assembled, and compared with those of three other previously published Leymus species (Leymus condensatus, Leymus angustus, and Leymus mollis) to clarify the issue. Overall, the whole cp genome size ranged between 135,057 (L. condensatus) and 136,906 bp (Leymus coreanus) and showed a typical quadripartite structure. All studied species had 129 genes, including 83 protein-coding genes, 38 transfer RNAs, and 8 ribosomal RNAs. In total, 800 tandem repeats and 707 SSR loci were detected, most of which were distributed in the large single-copy region, followed by the inverted repeat (IR) and small single-copy regions. The sequence identity of all sequences was highly similar, especially concerning the protein-coding and IR regions; in particular, the protein-coding regions were significantly similar to those in the IR regions, regardless of small sequence differences in the whole cp genome. Moreover, the coding regions were more conserved than the non-coding regions. Comparisons of the IR boundaries showed that IR contraction and expansion events were reflected in different locations of rpl22, rps19, ndhH, and psbA genes. The close phylogenetic relationship of Leymus and Psathyrostachys indicated that Psathyrostachys possibly is the donor of the Ns genome sequence identified in Leymus. Altogether, the complete cp genome sequence of Leymus will lay a solid foundation for future population genetics and phylogeography studies, as well as for the analysis of the evolution of economically valuable plants.

Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae.

The genus Blumea (Asteroideae, Asteraceae) comprises about 100 species, including herbs, shrubs, and small trees. Previous studies have been unable to resolve taxonomic issues and the phylogeny of the genus Blumea due to the low polymorphism of molecular markers. Therefore, suitable polymorphic regions need to be identified. Here, we de novo assembled plastomes of the three Blumea species B. oxyodonta, B. tenella, and B. balsamifera and compared them with 26 other species of Asteroideae after correction of annotations. These species have quadripartite plastomes with similar gene content, genome organization, and inverted repeat contraction and expansion comprising 113 genes, including 80 protein‐coding, 29 transfer RNA, and 4 ribosomal RNA genes. The comparative analysis of codon usage, amino acid frequency, microsatellite repeats, oligonucleotide repeats, and transition and transversion substitutions has revealed high resemblance among the newly assembled species of Blumea. We identified 10 highly polymorphic regions with nucleotide diversity above 0.02, including rps16‐trnQ, ycf1, ndhF‐rpl32, petN‐psbM, and rpl32‐trnL, and they may be suitable for the development of robust, authentic, and cost‐effective markers for barcoding and inference of the phylogeny of the genus Blumea. Among these highly polymorphic regions, five regions also co‐occurred with oligonucleotide repeats and support use of repeats as a proxy for the identification of polymorphic loci. The phylogenetic analysis revealed a close relationship between Blumea and Pluchea within the tribe Inuleae. At tribe level, our phylogeny supports a sister relationship between Astereae and Anthemideae rooted as Gnaphalieae, Calenduleae, and Senecioneae. These results are contradictory to recent studies which reported a sister relationship between “Senecioneae and Anthemideae” and “Astereae and Gnaphalieae” or a sister relationship between Astereae and Gnaphalieae rooted as Calenduleae, Anthemideae, and then Senecioneae using nuclear genome sequences. The conflicting phylogenetic signals observed at the tribal level between plastidt and nuclear genome data require further investigation.

Peculiarities of the inverted repeats in the complete chloroplast genome of Strobilanthes bantonensis Lindau

Strobilanthes bantonensis Lindau belongs to the family Acanthaceae. It is an antiviral herb that can be used to prevent Influenza virus infections in the border areas between China and Vietnam. Local people call it ‘Purple Ban-lan-gen’ because its root is very similar to that of Strobilanthes cusia (Nees) Kuntze, which is called ‘Southern Ban-lan-gen’ and is listed in Chinese Pharmacopeia. The two species have been used interchangeably locally. However, their pharmacological equivalence has caused concern for years. We have sequenced the chloroplast genome of S. cusia previously. In this study, we sequenced the complete chloroplast genome sequence of S. bantonensis to preform in-depth comparative genetic analysis of the two Strobilanthes species. The chloroplast genome of S. bantonensis is a circular DNA molecule with a total length of 144,591 bp and encodes 84 protein-coding, 8 ribosomes, and 37 transfer RNA genes. The chloroplast genome has a conservative quadripartite structure, including a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeat (IR) regions, with lengths of 92,068 bp, 17,767 bp, and 17,378 bp, respectively. Phylogenetic analysis confirmed that S. bantonensis is closely related to the S. cusia. Compared with other species from Acanthaceae, S. bantonensis has a significantly shortened IR region, suggesting the occurrence of IR contraction events. This study will help future taxonomic, evolutionary, phylogenetic, and bioprospecting studies of the sizeable Strobilanthes genus, which contains over 400 species.

Complete chloroplast genome of Jasminum sambac L. (Oleaceae)

Jasmine [Jasminum sambac (L.) Aiton] is an important cultivated plant species that is valued for its ornamental, medicinal and edible values. However, the genomic information available for jasmine is limited. In this study, the complete chloroplast (cp) genomes of single-petal (SP) and double-petal (DP) cultivars of jasmine were investigated. An entire cp genome comparison, inverted repeat contraction and expansion were analyzed among several species, including the two jasmine cultivars, and phylogenetic analysis was performed. The results showed that the complete cp genomes were 163,315 bp (SP) and 163,281 bp (DP) long, respectively. Both genomes exhibited a single circular molecule with quadripartite structure consisting of a pair of inverted repeats separated by the large and small single-copy regions. Both SP and DP cultivars contained 114 unique genes. Sequence analysis identified 31 tandem repeats, 15 forward repeats, 14 palindrome repeats and five complement repeats in both cp genomes. A total of 118 and 117 simple sequence repeats (SSRs) were detected in the cp genomes of SP and DP cultivars, respectively. Phylogenetic analysis strongly supported that the SP cultivar was close to DP, and J. sambac belonged to the family Oleaceae, order Contortae. The complete cp genome sequences presented in this report may contribute to genetic and phylogenetic studies of this species.

Plastid phylogenomic insights into the evolution of subfamily Dialioideae (Leguminosae)

The subfamily Dialioideae (Leguminosae) consists of 17 genera and about 85 species. Previous studies have detected significant plastid genome (plastome) structure variations in legumes, particularly in subfamilies Papilionoideae and Caesalpinioideae. Hence it is important to investigate plastomes from the newly recognized Dialioideae to better understand the plastome variation across the whole family. Here, we used nine plastomes representing nine genera of Dialioideae to explore plastome structural variation and intergeneric relationships in this subfamily. All plastomes of Dialioideae exhibited a typical quadripartite structure, and had relatively conserved structure compared with other legume subfamilies. However, the genome size ranged from 154,124 bp to 165,973 bp and gene numbers ranged from 129 to 132, mainly due to the expansion and contraction of the inverted repeat (IR) regions. The IR of Distemonanthusbenthamianus has experienced two separate expansions into the large single copy (LSC) region and the small single copy (SSC) region, and one contraction from SSC. Poeppigiaprocera has experienced two separate IR expansions into LSC, while Dicoryniaparaensis has experienced an IR contraction from LSC. Highly divergent regions or genes (ndhC−trnVUAC,psbK−trnQUUG,rps19−rps3,rpl33−rps18,accD−psaI,trnGUCC−trnSGCU,psbI−trnSGCU,5′rps16−trnQUUG and ycf1) were identified as potential molecular markers for further species delimitation and population genetics analysis in legumes. Phylogenetic analysis based on 77 protein-coding sequences fully resolved the intergeneric relationships among nine genera except a moderately supported sister relationship between Petalostylislabicheoides and Labichealanceolata. Our study reveals new insights into the structural variations of plastomes in subfamily Dialioideae and advances our understanding of the evolutionary trajectories of legume plastomes.

Comparison of Chloroplast Genomes among Species of Unisexual and Bisexual Clades of the Monocot Family Araceae.

The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of four genera representing three subfamilies of Araceae: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using these chloroplast genomes. The sizes of the chloroplast genomes ranged from 163,770 bp to 169,982 bp. These genomes comprise 113 unique genes, including 79 protein-coding, 4 rRNA, and 30 tRNA genes. Among these genes, 17–18 genes are duplicated in the inverted repeat (IR) regions, comprising 6–7 protein-coding (including trans-splicing gene rps12), 4 rRNA, and 7 tRNA genes. The total number of genes ranged between 130 and 131. The infA gene was found to be a pseudogene in all four genomes reported here. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The oligonucleotide repeats and junctions JSB (IRb/SSC) and JSA (SSC/IRa) were highly variable among the genomes. The patterns of IR contraction and expansion were shown to be homoplasious, and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were seen in three genes in S. bogneri, including ycf2, clpP, and rpl36. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae.

Complete chloroplast genome of Castanopsis sclerophylla (Lindl.) Schott: Genome structure and comparative and phylogenetic analysis.

Castanopsis sclerophylla (Lindl.) Schott is an important species of evergreen broad-leaved tree in subtropical areas and has high ecological and economic value. However, there are few studies on its chloroplast genome. In this study, the complete chloroplast genome sequence of C. sclerophylla was determined using the Illumina HiSeq 2500 platform. The complete chloroplast genome of C. sclerophylla is 160,497 bp long, including a pair of inverted repeat (IR) regions (25,675 bp) separated by a large single-copy (LSC) region of 90,255 bp and a small single-copy (SSC) region of 18,892 bp. The overall GC content of the chloroplast genome is 36.82%. A total of 131 genes were found; of these, 111 genes are unique and annotated, including 79 protein-coding genes, 27 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). Twenty-one genes were found to be duplicated in the IR regions. Comparative analysis indicated that IR contraction might be the reason for the smaller chloroplast genome of C. sclerophylla compared to three congeneric species. Sequence analysis indicated that the LSC and SSC regions are more divergent than IR regions within Castanopsis; furthermore, greater divergence was found in noncoding regions than in coding regions. The maximum likelihood phylogenetic analysis showed that four species of the genus Castanopsis form a monophyletic clade and that C. sclerophylla is closely related to Castanopsis hainanensis with strong bootstrap values. These results not only provide a basic understanding of Castanopsis chloroplast genomes, but also illuminate Castanopsis species evolution within the Fagaceae family. Furthermore, these findings will be valuable for future studies of genetic diversity and enhance our understanding of the phylogenetic evolution of Castanopsis.

Complete Chloroplast Genome of Fokienia hodginsii (Dunn) Henry et Thomas: Insights into Repeat Regions Variation and Phylogenetic Relationships in Cupressophyta

Fokienia hodginsii (Dunn) Henry et Thomas is a relic gymnosperm with broad application value. It is a fit candidate when choosing species for the construction of artificial forests. We determined the complete chloroplast genome sequence of F. hodginsii, which is 129,534 bp in length and encodes 83 protein genes, 33 transfer RNA (tRNA) genes, as well as four ribosomal RNA genes. The GC content of the complete sequence and protein coding regions is 34.8% and 36.2%, respectively. We identified 11 tandem repeats, 11 forward repeats, and three palindromic repeats and classified them by size. Following our microsatellite analysis, a total number of 73 simple sequence repeats were detected, preferentially within the intergenic space. Being a member of Cupressophyta, F. hodginsii owns several common characters; the trnR-CCG gene has been deleted, while the trnI-CAU and trnQ-UUG genes have been duplicated. Moreover, the accD gene, which encodes acetyl-CoA carboxylase, contains 771 codons in F. hodginsii, similar to Cryptomeria japonica (L. F.) D. Don, further supporting the diversity of accD and its size expansion in Cupressophyta. Concerning the loss of inverted repeat (IR) regions, the 86-bp sequence with the duplicated trnI-CAU gene is inferred to be the footprint of IR contraction. Phylogenetically, F. hodginsii is placed as a sister taxon to Chamaecyparis hodginsii (Dunn) Rushforth. This work offers meaningful guidance as well as reference value to the breeding research and improvement of F. hodginsii. Moreover, it gives us a better understanding of the genomic structure and evolutionary history of gymnosperms, especially coniferales.

Plastome characteristics of Cannabaceae

Cannabaceae is an economically important family that includes ten genera and ca. 117 accepted species. To explore the structure and size variation of their plastomes, we sequenced ten plastomes representing all ten genera of Cannabaceae. Each plastome possessed the typical angiosperm quadripartite structure and contained a total of 128 genes. The Inverted Repeat (IR) regions in five plastomes had experienced small expansions (330–983 bp) into the Large Single-Copy (LSC) region. The plastome of Chaetachme aristata has experienced a 942-bp IR contraction and lost rpl22 and rps19 in its IRs. The substitution rates of rps19 and rpl22 decreased after they shifted from the LSC to IR. A 270-bp inversion was detected in the Parasponia rugosa plastome, which might have been mediated by 18-bp inverted repeats. Repeat sequences, simple sequence repeats, and nucleotide substitution rates varied among these plastomes. Molecular markers with more than 13% variable sites and 5% parsimony-informative sites were identified, which may be useful for further phylogenetic analysis and species identification. Our results show strong support for a sister relationship between Gironniera and Lozanell (BS = 100). Celtis, Cannabis-Humulus, Chaetachme-Pteroceltis, and Trema-Parasponia formed a strongly supported clade, and their relationships were well resolved with strong support (BS = 100). The availability of these ten plastomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the intergeneric phylogeny of Cannabaceae.