Inverted Repeat Regions Research Articles

Phylogeny of Leontopodium (Asteraceae) in China-with a reference to plastid genome and nuclear ribosomal DNA.

The infrageneric taxonomy system, species delimitation, and interspecies systematic relationships of Leontopodium remain controversial and complex. However, only a few studies have focused on the molecular phylogeny of this genus. In this study, the characteristics of 43 chloroplast genomes of Leontopodium and its closely related genera were analyzed. Phylogenetic relationships were inferred based on chloroplast genomes and nuclear ribosomal DNA (nrDNA). Finally, together with the morphological characteristics, the relationships within Leontopodium were identified and discussed. The results showed that the chloroplast genomes of Filago, Gamochaeta, and Leontopodium were well-conserved in terms of gene number, gene order, and GC content. The most remarkable differences among the three genera were the length of the complete chloroplast genome, large single-copy region, small single-copy region, and inverted repeat region. In addition, the chloroplast genome structure of Leontopodium exhibited high consistency and was obviously different from that of Filago and Gamochaeta in some regions, such as matk, trnK (UUU)-rps16, petN-psbM, and trnE (UUC)-rpoB. All the phylogenetic trees indicated that Leontopodium was monophyletic. Except for the subgeneric level, our molecular phylogenetic results were inconsistent with the previous taxonomic system, which was based on morphological characteristics. Nevertheless, we found that the characteristics of the leaf base, stem types, and carpopodium base were phylogenetically correlated and may have potential value in the taxonomic study of Leontopodium. In the phylogenetic trees inferred using complete chloroplast genomes, the subgen. Leontopodium was divided into two clades (Clades 1 and 2), with most species in Clade 1 having herbaceous stems, amplexicaul, or sheathed leaves, and constricted carpopodium; most species in Clade 2 had woody stems, not amplexicaul and sheathed leaves, and not constricted carpopodium.

Characteristics of the chloroplast genome of Dracaena marginata and phylogenetic analysis

Dracaena marginata is a widely cultivated horticultural plant in the world, which has high ornamental and medicinal value. In this study, the whole genome of leaves from D. marginata was sequenced by Illumina HiSeq 4000 platform. The chloroplast genome were assembled for functional annotation, sequence characteristics and phylogenetic analysis. The results showed that the chloroplast genome of D. marginata composed of four regions with a size of 154 926 bp, which was the smallest chloroplast genome reported for Dracaena species to date. A total of 132 genes were identified, including 86 coding genes, 38 tRNA genes and 8 rRNA genes. Codon bias analysis found that the codon usage bias was weak and there was a bias for using A/U base endings. 46 simple sequence repeat and 54 repeats loci were detected in the chloroplast genome, with the maximum detection rate in the large single copy region and inverted repeat region, respectively. The inverted repeats boundaries of D. marginata and Dracaena were highly conserved, whereas gene location differences occurred. Phylogenetic analysis revealed that D. serrulata and D. cinnabari form a monophyletic clade, which was the closest relationship and conformed to the morphological classification characteristics. The analysis of the chloroplast genome of D. marginata provides important data basis for species identification, genetic diversity and chloroplast genome engineering of Dracaena.

More than a spiny morphology: plastome variation in the prickly pear cacti (Opuntieae).

Plastid genomes (plastomes) have long been recognized as highly conserved in their overall structure, size, gene arrangement and content among land plants. However, recent studies have shown that some lineages present unusual variations in some of these features. Members of the cactus family are one of these lineages, with distinct plastome structures reported across disparate lineages, including gene losses, inversions, boundary movements or loss of the canonical inverted repeat (IR) region. However, only a small fraction of cactus diversity has been analysed so far. Here, we investigated plastome features of the tribe Opuntieae, the remarkable prickly pear cacti, which represent one of the most diverse and important lineages of Cactaceae. We assembled de novo the plastome of 43 species, representing a comprehensive sampling of the tribe, including all seven genera, and analysed their evolution in a phylogenetic comparative framework. Phylogenomic analyses with different datasets (full plastome sequences and genes only) were performed, followed by congruence analyses to assess signals underlying contentious nodes. Plastomes varied considerably in length, from 121 to 162 kbp, with striking differences in the content and size of the IR region (contraction and expansion events), including a lack of the canonical IR in some lineages and the pseudogenization or loss of some genes. Overall, nine different types of plastomes were reported, deviating in the presence of the IR region or the genes contained in the IR. Overall, plastome sequences resolved phylogenetic relationships within major clades of Opuntieae with high bootstrap values but presented some contentious nodes depending on the dataset analysed (e.g. whole plastome vs. genes only). Congruence analyses revealed that most plastidial regions lack phylogenetic resolution, while few markers are supporting the most likely topology. Likewise, alternative topologies are driven by a handful of plastome markers, suggesting recalcitrant nodes in the phylogeny. Our study reveals a dynamic nature of plastome evolution across closely related lineages, shedding light on peculiar features of plastomes. Variation of plastome types across Opuntieae is remarkable in size, structure and content and can be important for the recognition of species in some major clades. Unravelling connections between the causes of plastome variation and the consequences for species biology, physiology, ecology, diversification and adaptation is a promising and ambitious endeavour in cactus research. Although plastome data resolved major phylogenetic relationships, the generation of nuclear genomic data is necessary to confront these hypotheses and assess the recalcitrant nodes further.

Plastid genome of Passiflora tripartita var. mollissima (poro-poro) from Huánuco, Peru

Passiflora tripartita var. mollissima, known locally as poro-poro, is an important native fruit used in traditional Peruvian medicine with relevant agro-industrial and pharmaceutical potential for its antioxidant capacity for human health. However, to date, only a few genetic data are available, which limits exploring its genetic diversity and developing new genetic studies for its improvement. We report the poro-poro plastid genome to expand the knowledge of its molecular markers, evolutionary studies, molecular pathways, and conservation genetics. Total genomic DNA was extracted from fresh leaves (herbarium voucher: USM:MHN331530). The DNA was sequenced using Illumina Novaseq 6000 platform providing 163,451 bp in length, with a large single-copy region of 85,525 bp and a small single-copy region of 13,518 bp, separated by a pair of inverted repeat regions (IR) of 32,204 bp, and the overall GC content was 36.87%. The chloroplast genome contains 129 genes (112 genes were unique and 17 genes were found duplicated in each IR region), including 85 protein-coding genes, 37 transfer RNA-coding genes, seven ribosomal RNA-coding genes, and 14 genes with introns (12 genes with one intron and two genes with two introns). The phylogenetic tree reconstructed based on single-copy orthologous genes and maximum likelihood analysis demonstrates poro-poro is most closely related to Passiflora menispermifolia and Passiflora oerstedii. In summary, our study provides the basis for developing new molecular markers that constitutes a valuable resource for studying molecular evolution and domestication. It also provides a powerful foundation for conservation genetics research and plant breeding programs. To our knowledge, this is the first report on the plastid genome of Passiflora tripartita var. mollissima from Peru.

Comparison of Biological and Genetic Characteristics between Two Most Common Broad-Leaved Weeds in Paddy Fields: Ammannia arenaria and A. multiflora (Lythraceae).

Ammannia arenaria and A. multifloras, morphologically similar at the seedling stage, are the most common broad-leaved weeds in paddy fields. Our study showed that A. arenaria occupied more space than A. multifloras when competing with rice. However, A. multifloras germination has lower temperature adaptability. No difference in sensitivity to common herbicides between two Ammannia species was observed. Chloroplast (cp) genomes could be conducive to clarify their genetic relationship. The complete cp genome sequences of A. arenaria (158,401 bp) and A. multiflora (157,900 bp) were assembled for the first time. In A. arenaria, there were 91 simple sequence repeats, 115 long repeats, and 86 protein-encoding genes, one, sixteen, and thirty more than those in A. multiflora. Inverted repeats regions expansion and contraction and the phylogenetic tree based on cp genomes demonstrated the closely relationship between the two species. However, in A. arenaria, 20 single nucleotide polymorphisms in the CDS region were detected compared to A. multiflora, which can be used to distinguish the two species. Moreover, there was one unique gene, infA, only in A. arenaria. This study provides reliable molecular resources for future research focusing on the infrageneric taxa identification, phylogenetic resolution, population structure, and biodiversity of Ammannia species.

The complete chloroplast genome of Ulmus mianzhuensis with insights into structural variations, adaptive evolution, and phylogenetic relationships of Ulmus (Ulmaceae)

BackgroundUlmus mianzhuensis is an endemic tree species in China with high ornamental and economic value. Currently, little is known regarding its genomic architecture, phylogenetic position, or adaptive evolution. Here, we sequenced the complete chloroplast genome (cp genome) of U. mianzhuensis and further compared the variations in gene organization and structure within Ulmus species to define their genomic evolution, then reconstructed the phylogenomic relationship of 31 related Ulmus species to explore the systematic position of U. mianzhuensis and the utility of cp genome for resolving phylogenetics among Ulmus species.ResultsOur results revealed that all the Ulmus species exhibited a typical quadripartite structure, with a large single copy (LSC) region of 87,170 − 88,408 bp, a small single copy (SSC) region of 18,650 − 19,038 bp and an inverted repeat (IR) region of 26,288 − 26,546 bp. Within Ulmus species, gene structure and content of cp genomes were highly conserved, although slight variations were found in the boundary of SC/IR regions. Moreover, genome-wide sliding window analysis uncovered the variability of ndhC-trnV-UAC, ndhF-rpl32, and psbI-trnS-GCU were higher among 31 Ulmus that may be useful for the population genetics and potential DNA barcodes. Two genes (rps15 and atpF) were further detected under a positive selection of Ulmus species. Comparative phylogenetic analysis based on the cp genome and protein-coding genes revealed consistent topology that U. mianzhuensis is a sister group to U. parvifolia (sect. Microptelea) with a relatively low-level nucleotide variation of the cp genome. Additionally, our analyses also found that the traditional taxonomic system of five sections in Ulmus is not supported by the current phylogenomic topology with a nested evolutionary relationship between sections.ConclusionsFeatures of the cp genome length, GC content, organization, and gene order were highly conserved within Ulmus. Furthermore, molecular evidence from the low variation of the cp genome suggested that U. mianzhuensis should be merged into U. parvifolia and regarded as a subspecies of U. parvifolia. Overall, we demonstrated that the cp genome provides valuable information for understanding the genetic variation and phylogenetic relationship in Ulmus.

A novel HRM-based gap-qRT-PCR for identification and quantitation of the vaccine and field strain(s) of lumpy skin disease virus

Lumpy skin disease (LSD) has become the most important animal health problem in India due to high morbidity, mortality and production losses caused by it. A homologous live-attenuated LSD vaccine (Lumpi-ProVacInd) was recently developed by using a local LSD virus (LSDV) strain (LSDV/2019/India/Ranchi) in India which is likely to replace the existing practice of vaccinating cattle with goatpox vaccine. It is essential to differentiate the vaccine and field strains, if a live-attenuated vaccine has been used for control and eradication of the disease. As compared to the prevailing vaccine and field/virulent strains, the Indian vaccine strain (Lumpi-ProVacInd) has a unique deletion of 801 nucleotides in its inverted terminal repeat (ITR) region. We exploited this unique feature and developed a novel high resolution melting-based gap quantitative real-time PCR (HRM-gap-qRT-PCR) for rapid identification and quantitation of the vaccine and field strain(s) of LSDV.

Complete chloroplast genome sequence of Camellia sinensis: genome structure, adaptive evolution, and phylogenetic relationships.

The chloroplast (cp) genome holds immense potential for a variety of applications including species identification, phylogenetic analysis, and evolutionary studies. In this study, we utilized Illumina NovaSeq 6000 to sequence the DNA of Camellia sinensis L. cultivar 'Zhuyeqi', followed by the assembly of its chloroplast genome using SPAdes v3.10.1, with subsequent analysis of its features and phylogenetic placement. The results showed that the cp genome of 'Zhuyeqi' was 157,072 bp, with a large single-copy region (LSC, 86,628 bp), a small single-copy region (SSC,18,282 bp), and two inverted repeat regions (IR, 26,081 bp). The total AT and GC contents of the cp genome of 'Zhuyeqi' were observed to be 62.21% and 37.29%, respectively. The cp genome encoded 135 unique genes, including 90 protein-coding genes (CDS), 37 tRNA genes, and 8 rRNA genes. Moreover, 31 codons and 247 simple sequence repeats (SSRs) were identified. The cp genomes of 'Zhuyeqi' were found to be relatively conserved, with conservation observed in the IR region, which showed no evidence of inversions or rearrangements. The five regions with the largest variations were identified, with four regions (rps12, rps19, rps16, and rpl33) located in the LSC region and one divergent region (trnI-GAU) in the IR region. Phylogenetic analysis revealed that Camellia sinensis (KJ996106.1) was closely related to 'Zhuyeqi', indicating a close phylogenetic relationship between these two species. These findings could provide important genetic information for further research into breeding of tea tree, phylogeny, and evolution of Camellia sinensis.

The Complete Chloroplast Genome Sequence of Staphylea holocarpa (Staphyleaceae).

Staphylea holocarpa (Hemsley 1895) is an ornamental deciduous shrub or tree in the family Staphyleaceae. As the shortage of the wild resources, S. holocarpa is also a rare plant. The revelation of the species origin and evolution progress and the relation. Therefore, the S. holocarpa complete chloroplast genome sequence was completed and characterized by de novo assembly. The cp genome length of S. holocarpa was 160,461bp and it has a typical quadripartite structure, consisted of an 89,760bp large single-copy region and a 18,639bp small single-copy region, which were divided by two inverted repeat regions of 26,031bp. After genome annotation, it comes to 130 genes that were predicted, which includes 85, 8, and 37 encoded proteins, rRNA, and tRNA, respectively. A phylogenetic analysis has shown that the S. holocarpa cp genome is related to the Staphylea trifolia. This work will be useful for further population genomic and phylogenetic studies of S. holocarpa.

Complete chloroplast genomes of five Cuscuta species and their evolutionary significance in the Cuscuta genus

BackgroundCuscuta, a parasitic plant species in the Convolvulaceae family, grows in many countries and regions. However, the relationship between some species is still unclear. Therefore, more studies are needed to assess the variation of the chloroplast (cp) genome in Cuscuta species and their relationship with subgenera or sections, thus, providing important information on the evolution of Cuscuta species.ResultsIn the present study, we identified the whole cp genomes of C. epithymum, C. europaea, C. gronovii, C. chinensis and C. japonica, and then constructed a phylogenetic tree of 23 Cuscuta species based on the complete genome sequences and protein-coding genes. The complete cp genome sequences of C. epithymum and C. europaea were 96,292 and 97,661 bp long, respectively, and lacked an inverted repeat region. Most cp genomes of Cuscuta spp. have tetragonal and circular structures except for C. epithymum, C. europaea, C. pedicellata and C. approximata. Based on the number of genes and the structure of cp genome and the patterns of gene reduction, we found that C. epithymum and C. europaea belonged to subgenus Cuscuta. Most of the cp genomes of the 23 Cuscuta species had single nucleotide repeats of A and T. The inverted repeat region boundaries among species were similar in the same subgenera. Several cp genes were lost. In addition, the numbers and types of the lost genes in the same subgenus were similar. Most of the lost genes were related to photosynthesis (ndh, rpo, psa, psb, pet, and rbcL), which could have gradually caused the plants to lose the ability to photosynthesize.ConclusionOur results enrich the data on cp. genomes of genus Cuscuta. This study provides new insights into understanding the phylogenetic relationships and variations in the cp genome of Cuscuta species.

Chloroplast Genome Structure and Phylogenetic Analysis of 13 Lamiaceae Plants in Tibet.

The chloroplast (cp) genome has unique and highly conserved characteristics and is therefore widely used in species identification and classification, as well as to improve the in-depth understanding of plant evolution. In this study, the cp genomes of 13 Lamiaceae plants in the Tibet Autonomous Region of China were sequenced, assembled and annotated using bioinformatics methods. Phylogenetic trees were constructed to reveal the phylogenetic relationship of related species in the Lamiaceae. The results showed that all 13 cp genomes had a typical four-segment structure, including one large single-copy (LSC) region, one pair of inverted repeat (IR) regions and one small single-copy (SSC) region. The sequence lengths of the 13 cp genomes were between 149,081 bp and 152,312 bp, and the average GC content was 37.6%. These genomes contained 131-133 annotated genes, including 86-88 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. A total of 542 SSR loci were detected using MISA software. The repeat types were mostly single-nucleotide repeats, accounting for 61% of simple repeats. A total of 26,328-26,887 codons were detected in 13 cp genomes. According to the RSCU value analysis, the codons mostly ended with A/T. Analysis of IR boundaries showed that the other species were relatively conserved, except for Nepeta laevigata (D. Don) Hand.-Mazz., which differed in gene type and location on both sides of the boundary. By analysing nucleotide diversity, two highly mutated regions located in the LSC and SSC regions were identified in the 13 cp genomes. Using the cp genome of Lycium ruthenicum Murray as the outgroup, 97 cp genomes of the Lamiaceae were used to construct an Maximum Likehood (ML) phylogenetic tree, in which these species were divided into eight major clades, corresponding to eight subfamilies based on morphological classification. The phylogenetic results based on monophyletic relationships were consistent with the morphological classification status at the tribe level.

The complete chloroplast genome sequence of Aconitum tschangbaischanense (Ranunculaceae)

The perennial herbal medicine species Aconitum tschangbaischanense, is endemic to Changhai Mountain, Jilin province. In this study, we attempted to uncover the complete chloroplast (cp) genome of A. tschangbaischanense based on sequencing data using the Illumina sequencing technology. As per the results: (1) the length of its complete cp genome is 155,881 bp with a typical tetrad structure; (2) the structure of its cp genome contains large single-copy and small single-copy (LSC and SSC) regions of 86,351 and 16,9444 bp, respectively, isolated by two inverted repeat regions (IRs) of 26,293 bp; (3) we annotated a total 131 genes, consisting of 86 protein-coding genes, eight rRNA genes, and 37 tRNA genes. According to the maximum-likelihood phylogenetic tree based on complete cp genomes, A. tschangbaischanense, showed close association with A. carmichaelii, which belongs to clade I. Finally, this study provides the characteristics of the cp genome of A. tschangbaischanense, and its phylogenetic position.

The complete chloroplast genome sequence of Zingiber teres S. Q. Tong & Y. M. Xia (Zingiberaceae)

Here, the complete chloroplast genome sequence of Zingiber teres is described using MGI paired-end sequencing. The genome is 163,428 bp in length and contains a small single-copy region (SSC) of 15,782 bp, a large single-copy region (LSC) of 88,142 bp, and two inverted repeat (IR) regions of 29,752 bp. The overall GC content is 36.1%, and the GC content of the IR regions is 41.1%, which is higher than that of both the LSC region (33.8%) and SSC region (29.5%). The genome of Z. teres contains 133 complete genes, including 88 protein-coding genes (79 protein-coding gene species), 38 tRNA genes (28 tRNA species), and 8 rRNA genes (four rRNA species). Maximum likelihood phylogenetic analysis yielded a well-resolved tree of the genus Zingiber, and Z. teres and Zingiber mioga were sister species in this tree. The development of DNA barcodes could aid the identification of Zingiber species.

The first chloroplast sequence of Rosa davurica Pall. var. Davurica

Rosa davurica Pall. var. davurica is a member of the plant family Rosaceae. Although R. davurica has high application value, its chloroplast genome sequence has not been reported. This study aims to reveal the genetic characteristics of the chloroplast genome of Rosa roxburghii. The length of its total chloroplast DNA is 156,971 bp, with 37.22% G/C content. Its chloroplast genome has two inverted repeat (IRa and IRb) regions totaling 26,051 bp which are separated by a large single copy (LSC) region of 86,032 bp and a small single copy (SSC) region of 18,837 bp. The genome contains 131 independent genes (86 protein-coding, 37 tRNA, and 8 rRNA), and there are 18 repeated genes within the IR region. Among these genes, 17 genes contained one or two introns. The phylogenetic analysis showed that R. davurica was relatively close to other Rosa species, such as the Rosa hybrid.

Complete chloroplast genome sequence of the liverwort, Porella grandiloba Lindb. (Porellaceae)

Porella grandiloba Lindb. is a liverwort species of Porellaceae, primarily distributed in East Asia. Here, we determined the complete chloroplast (cp) genome sequence of P. grandiloba. The complete cp genome was 121,433 bp in length with a typical quadripartite structure consisting of a large single-copy region (83,039 bp), a small single-copy region (19,586 bp), and two copies of inverted repeat regions (9,404 bp, each). Genome annotation predicted 131 genes, including 84 protein-coding, 36 tRNA, and eight rRNA genes. The maximum likelihood tree indicated that P. grandiloba was sister to P. perrottetiana, which species formed a clade with Radula japonica (Radulaceae).

The complete chloroplast genome sequence of Chrysojasminum subhumile and its phylogenetic position within Oleaceae

We assembled and characterized the complete chloroplast genome sequence of Chrysojasminum subhumile (W.W.Sm.) Banfi & Galasso 2014, a valuable horticultural and medicinal plant species. The total genome size was 159,918 bp in length and the GC content was 37.4%. It displayed a circular structure and could be divided into a large single-copy region, a small single-copy region, and a pair of inverted repeat regions. The genome encoded a total of 131 unique genes, including 82 protein-coding genes, 41 tRNA genes, and eight rRNA genes. Among these genes, 17 contained a single intron, and two genes had two introns. Phylogenetic analysis results showed that C. subhumile was closely related to Jasminum.

The complete plastid genome and characteristics analysis of Achillea millefolium.

Achillea is a crop with Chinese herbal characteristics and horticultural values. Its leaves and flowers contain aromatic oil, and the ripe herb can also be used as medicine to induce sweat and relieve rheumatic pains. It is seen cultivated in gardens all over China. Currently, the most comprehensive chloroplast genome sample involved in the study refers to New World clades of Achillea, which are used for marker selection and phylogenetic research. We completely sequenced the chloroplast genomes of Achillea millefolium. These sequencing results showed that the plastid genome is 149,078 bp in size and possesses a typical quadripartite structure containing one large single copy (LSC) with 82,352 bp, one small single copy (SSC) with 18,426 bp, and a pair of inverted repeat (IR) regions with 24,150 bp in Achillea millefolium. The chloroplast genome encodes a common number of genes, of which 88 are protein-coding genes, 37 transfer ribonucleic acid genes, and 8 ribosomal ribonucleic acid genes, which are highly similar in overall size, genome structure, gene content, and sequence. The exact similarity was observed when compared to other Asteraceae species. However, there were structural differences due to the restriction or extension of the inverted repeat (IR) regions-the palindromic repeats being the most prevalent form. Based on 12 whole-plastomes, 3 hypervariable regions (rpoB, rbcL, and petL-trnP-UGG) were discovered, which could be used as potential molecular markers.

Chloroplast genome characteristics and phylogeny of the sinodielsia clade (apiaceae: apioideae)

BackgroundThe Sinodielsia clade of the subfamily Apioideae (Apiacieae) was established in 2008, and it is composed of 37 species from 17 genera. Its circumscription is still poorly delimited and unstable, and interspecific relationships in the clade lack comprehensive analysis. Chloroplast (cp.) genomes provide valuable and informative data sources for evolutionary biology and have been widely used in studies on plant phylogeny. To infer the phylogenetic history of the Sinodielsia clade, we assembled complete cp. genomes of 39 species and then performed phylogenetic analysis based on these cp. genome sequence data combined with 66 published cp. genomes from 16 genera relative to the Sinodielsia clade.ResultsThese 39 newly assembled genomes had a typical quadripartite structure with two inverted repeat regions (IRs: 17,599–31,486 bp) separated by a large single-copy region (LSC: 82,048–94,046 bp) and a small single-copy region (SSC: 16,343–17,917 bp). The phylogenetic analysis showed that 19 species were clustered into the Sinodielsia clade, and they were divided into two subclades. Six mutation hotspot regions were detected from the whole cp. genomes among the Sinodielsia clade, namely, rbcL–accD, ycf4–cemA, petA–psbJ, ycf1–ndhF, ndhF–rpl32 and ycf1, and it was found that ndhF–rpl32 and ycf1 were highly variable in the 105 sampled cp. genomes.ConclusionThe Sinodielsia clade was subdivided into two subclades relevant to geographical distributions, except for cultivated and introduced species. Six mutation hotspot regions, especially ndhF–rpl32 and ycf1, could be used as potential DNA markers in the identification and phylogenetic analyses of the Sinodielsia clade and Apioideae. Our study provided new insights into the phylogeny of the Sinodielsia clade and valuable information on cp. genome evolution in Apioideae.

Structural Characterization of Trivalvaria costata Chloroplast Genome and Molecular Evolution of rps12 Gene in Magnoliids

Chloroplasts (cp) are important organelles in plant cells that have been widely used in phylogenetic, molecular evolution, and gene expression studies due to their conserved molecular structure. In this study, we obtained the complete cp genome of Trivalvaria costata (Annonaceae) and analyzed its structural characteristics. Additionally, we analyzed the rps12 gene in the phylogenetic framework of magnoliids. The T. costata cp genome comprises 162,002 bp and contains 132 genes. We detected 48 simple sequence repeats (SSRs) and identified 29 high-frequency codons as well as 8 optimal codons. Our multiple analyses show that codon usage bias is mainly influenced by natural selection. For the first time, we found the rps12 gene to be entirely located in the IR region (in Annona). In groups with exon 1 located in the single-copy (SC) region and exons 2–3 located in the inverted repeat (IR) region, the transition rate and synonymous substitution rate of exon 1 were higher than those of exons 2–3. Adaptive evolution identified a positive selection site (116) located in the 310-helix region, suggesting that the rps12 gene may undergo adaptive changes during the evolutionary history of magnoliids. This study enhances our knowledge regarding genetic information on T. costata and provides support for reduced substitution rates in the IR region.

Chloroplast markers for the Malvaceae and the plastome of Henderson’s checkermallow (Sidalcea hendersonii S.Wats.), a rare plant from the Pacific Northwest

ObjectiveSidalcea is a genus of flowering plants restricted to the west coast of North America, commonly known as checkermallows. Remarkably, of the ~ 30 recognized species, 16 are of conservation concern (vulnerable, imperilled or critically imperilled). To facilitate biological studies in this genus, and in the wider Malvaceae, we have sequenced the whole plastid genome of Sidalcea hendersonii. This will allow us both to check those regions already developed as general Malvaceae markers in a previous study, and to search for new regions.ResultsBy comparing the Sidalcea genome to that of Althaea, we have identified a hypervariable circa 1 kb region in the short single copy region. This region shows promise for examining phylogeographic pattern, hybridization and haplotype diversity. Remarkably, considering the conservation of plastome architecture between Sidalcea and Althaea, the former has a 237 bp deletion in the otherwise highly conserved inverted repeat region. Newly designed primers provide a PCR assay to determine presence of this indel across the Malvaceae. Screening of previously designed chloroplast microsatellite markers indicates two markers with variation within S. hendersonii that would be useful in future population conservation genetics.