Cp Genome Sequence Research Articles

Chloroplast genome sequencing and divergence analysis of 18 Pyrus species: insights into intron length polymorphisms and evolutionary processes.

Pears constitute an essential temperate crop and are primarily produced through interspecific hybridization owing to self-incompatibility that complicates their breeding history. To address this, we sequenced the complete chloroplast (cp) genomes of 18 Pyrus and one Malus species using the Illumina HiSeq4000 platform. The cp genomes ranged from 159,885 bp to 160,153bp and exhibited a conserved circular DNA structure with an average GC content of 36.5%. Each cp genome contained 127 genes, including 83 protein-coding, 36 tRNA, and 8 rRNA genes. Divergence analysis with mVISTA showed high conservation in the coding regions and notable variations in the non-coding regions. All species shared 17 intron-containing genes, with ycf3 and clpP each having two introns. Five intron-containing genes (ndhB, rpl2, rps12, trnA-UGC, and trnE-UUC) were located in the inverted repeat regions, while trnL-UAA was located in the large single-copy region, with conserved intron lengths across Pomoideae. We identified polymorphic intron sequences in the rpl22, petB, clpP, ndhA, and rps16 genes and designed primers for these regions. Notably, the two Pyrus ussuriensis accessions Doonggeullebae and Cheongdangrori showed intron-length polymorphisms despite being classified as the same species. Phylogenetic analysis of the cp genome sequences revealed two major clusters, indicating distinct maternal lineages and evolutionary origins. This study underscores the importance of cp gene polymorphisms in P. fauriei, P. calleryana, P. ussuriensis, and P. pyrifolia, providing valuable insights into Pyrus evolution as well as aiding in the conservation and breeding of pear germplasm.

The adaptive evolution of Quercus section Ilex using the chloroplast genomes of two threatened species

Chloroplast (cp) genome sequences have been extensively used for phylogenetic and evolutionary analyses, as many have been sequenced in recent years. Identification of Quercus is challenging because many species overlap phenotypically owing to interspecific hybridization, introgression, and incomplete lineage sorting. Therefore, we wanted to gain a better understanding of this genus at the level of the maternally inherited chloroplast genome. Here, we sequenced, assembled, and annotated the cp genomes of the threatened Quercus marlipoensis (160,995 bp) and Q. kingiana (161,167 bp), and mined these genomes for repeat sequences and codon usage bias. Comparative genomic analyses, phylogenomics, and selection pressure analysis were also performed in these two threatened species along with other species of Quercus. We found that the guanine and cytosine content of the two cp genomes were similar. All 131 annotated genes, including 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes, had the same order in the two species. A strong A/T bias was detected in the base composition of simple sequence repeats. Among the 59 synonymous codons, the codon usage pattern of the cp genomes in these two species was more inclined toward the A/U ending. Comparative genomic analyses indicated that the cp genomes of Quercus section Ilex are highly conserved. We detected eight highly variable regions that could be used as molecular markers for species identification. The cp genome structure was consistent and different within and among the sections of Quercus. The phylogenetic analysis showed that section Ilex was not monophyletic and was divided into two groups, which were respectively nested with section Cerris and section Cyclobalanopsis. The two threatened species sequenced in this study were grouped into the section Cyclobalanopsis. In conclusion, the analyses of cp genomes of Q. marlipoensis and Q. kingiana promote further study of the taxonomy, phylogeny and evolution of these two threatened species and Quercus.

New Variants in the Chloroplast Genome Sequence of Two Colombian Individuals of the Cedar Timber Species (Cedrela odorata L.), Using Long-Read Oxford Nanopore Technology

The plant species Cedrela odorata has been largely exploited in the timber industry due to the high demand for its wood. Therefore, C. odorata has been considered a vulnerable species since 1994, under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). C. odorata is a key timber species included in the management and conservation plans for the Amazon and Central American rainforests. These plans include the development of genetic and genomic resources to study local populations of the species in Colombia. In this study, two novel chloroplast (cp) genomes were assembled and annotated using the MinION long-read sequencing technology. The new cp genomes were screened for sequence variants (SVs), and a total of 16 SNPs were identified, presumably unique to populations from the Amazon region in Colombia. Comparative genomics with other reported cp genomes from different populations of C. odorata support the hypothesis of intraspecific diversity associated with their place of origin. These cp genome sequences of C. odorata from Colombian individuals represent valuable genomic resources for the species, suitable for identifying novel DNA fingerprinting and barcoding applications.

Complete chloroplast genomes of two Ainsliaea species and the phylogenetic analysis in the tribe Pertyeae.

The genus Ainsliaea DC. is one of the major groups within the tribe Pertyeae (Asteraceae). It comprises several important Chinese medicinal species. However, the phylogenetic position has undergone a long process of exploration. The complete chloroplast (cp) genome sequences data has not been employed in species identification and phylogeny of Ainsliaea. In this study, the complete cp genomes of two Ainsliaea species (A. gracilis and A. henryi) were reported, followed by structural, comparative, and phylogenetic analyses within the tribe Peryteae. Both cp genomes displayed a typical quadripartite circular structure, with the LSC and SSC regions separated by the IR regions. The genomes were 152,959 (A. gracilis) and 152,805 (A. henryi) base pairs (bp) long, with a GC content of 37.6%. They were highly conserved, containing 134 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (rps19 and ycf1). Moreover, thirteen highly polymorphic regions (e.g., trnK-UUU, trnG-UCC, trnT-GGU, accD-psaI, and rpl22-rps19) were identified, indicating their potential as DNA barcodes. The phylogenetic analysis confirmed the placement of Ainsliaea in the tribe Pertyeae, revealing close relationships with the genera Myripnois and Pertya. In comparison with Ainsliaea, Myripnois was more closely related to Pertya. This study lays a theoretical foundation for future research on species identification, population genetics, resource conservation, and sustainable utilization within Ainsliaea and Pertyeae.

The Complete Chloroplast Genome of Syzygium syzygioides (Myrtaceae: Myrtales) and Phylogenetic Analysis

Abstract Background: Syzygium syzygioides (Miq.) Merr. and L. M. Perry is a common medicinal plant species known for its biologically active compounds. However, the chloroplast (cp) genome of S. syzygioides has not been previously reported. This study aimed to determine the complete cp genome sequence of S. syzygioides and investigate its phylogenetic relationships within the Syzygium genus. Methods: Leaf samples of S. syzygioides were collected from Vietnam, and the complete cp genome was sequenced and assembled. Phylogenetic analyses were then conducted to examine the evolutionary relationships between S. syzygioides and other Syzygium species. Results: The cp genome of S. syzygioides was found to be 158,172 base pairs in length, with a GC content of 37.0%. Phylogenetic reconstruction based on the cp genome data revealed that S. syzygioides is closely related to 10 other Syzygium species, including Syzygium buettnerianum, Syzygium bamagense, Syzygium grande, Syzygium megacarpum, Syzygium glomeratum, Syzygium claviflorum, Syzygium tsoongii, Syzygium fluviatile, Syzygium buxifolium, and Syzygium grijsii. Conclusions: This study provides the first report of the complete cp genome sequence of S. syzygioides, a medicinally important plant species in the Myrtaceae family. The phylogenetic analysis using the cp genome data sheds light on the evolutionary relationships within the Syzygium genus, which is the largest genus in the Myrtaceae. The new molecular data generated in this study can be used for the molecular identification and further phylogenetic investigations of Syzygium species, contributing to a better understanding of the diversity and evolutionary history of this economically and ecologically significant plant group.

The complete chloroplast genome sequence of Ampelopsis delavayana Planchon. ex Franch 1886 (Vitaceae)

Ampelopsis delavayana Planchon. ex Franch 1886 is a plant with significant pharmacological effects and ornamental importance. This research unveiled the complete chloroplast (cp) genome sequence of A. delavayana. The study highlights that the cp genome of A. delavayana possesses a distinct tetrameric structure spanning 162,497 base pairs, comprising a small single-copy (SSC) region of 18,902 base pairs, a large single-copy (LSC) region of 90,441 base pairs, and two inverted-repeat regions (IRs), each 26,577 base pairs in length. The GC content of the SSC, LSC, and IR regions of the genome was 31.80%, 35.16%, and 42.82%, respectively, culminating in an overall GC content of 37.27%. The genome comprised 130 genes, which included eight rRNAs, 36 tRNAs, and 86 protein-coding genes. Through phylogenetic analysis utilizing the maximum-likelihood method, it was established that A. delavayana was closely related to Ampelopsis glandulosa var. brevipedunculata, positioning it as a sister species. This report not only provides a scientific reference for understanding the phylogeny of the family Vitaceae but also enriches our genetic information of Ampelopsis.

The complete chloroplast genome of Oxytropis ochrocephala Bunge 1874 (Fabaceae) and its phylogenetic analysis

This study presents the first-ever complete chloroplast (cp) genome sequence of Oxytropis ochrocephala Bunge 1874, a member of the Fabaceae family. The cp genome spans 126,996 base pairs and includes 109 genes, comprising 76 protein-coding genes, 29 tRNA genes, and four rRNA genes. Notably, the genome lacks an inverted repeat (IR) region. Additionally, we constructed phylogenetic trees for 34 species within Trib. Galegeae, employing both maximum likelihood (ML) and Bayesian inference (BI) methods. These analyses robustly support the monophyly of the Oxytropis species, evidenced by high bootstrap values (BP = 100) and posterior probabilities (PP = 1). Within this clade, O. ochrocephala exhibits a sister relationship with other Oxytropis species. Our findings provide valuable insights into the genetic makeup and evolutionary relationships of O. ochrocephala within the Galegeae tribe.

The complete chloroplast genome and characteristics analysis of Lonicera harae (Caprifoliaceae)

Herein, we determined and analyzed the chloroplast (cp) genome sequence of Lonicera harae for the first time. The chloroplast genome was 154,959 bp and contained a large single copy (LSC) of approximately 88,849 bp as well as a small single copy (SSC) of 18,832 bp separated by a pair of 23,639 bp inverted repeats (IRs). The overall G+C content in the L. harae chloroplast genome was 38.4%. A total of 114 unique genes were annotated, comprising 80 protein-coding genes (PCGs), 30 transfer RNAs (tRNAs), and four ribosomal RNAs (rRNAs). Of these, 17 contained one or two introns. Phylogenetic analysis of 54 accessions revealed that L. harae forms a clade with L. fragrantissima. This newly sequenced chloroplast genome provides valuable molecular phylogenomic information for future studies to determine the taxonomic position of L. harae and the phylogenetic relationships within the genus Lonicera.

TPMGD: A genomic database for the traditional medicines in Pakistan

ObjectiveIn Pakistan, traditional medicines are an important component of the medical system, with numerous varieties and great demands. However, due to the scattered resources and the lack of systematic collection and collation, adulteration of traditional Pakistani medicine (TPM) is common, which severely affects the safety of their medicinal use and the import and export trades. Therefore, it is urgent to systematically organize and unify the management of TPM and establish a set of standards and operable methods for the identification of TPM. MethodsWe collected and organized the information on 128 TPMs with regard to their medicinal parts, efficacy, usage, and genetic material, based on Pakistan Hamdard Pharmacopoeia of Eastern Medicine: Pharmaceutical Codex. The genetic information of TPM is summarized from national center for biotechnology information (NCBI) and global pharmacopoeia genome database (GPGD). Furthermore, we utilized bioinformatics technology to supplement the chloroplast genome (cp-genome) data of 12 TPMs. To build the web server, we used the Linux + Apache + MySQL + PHP (LAMP) system and constructed the webpage on a PHP: Hypertext Preprocessor (PHP) model view controller (MVC) framework. ResultsWe constructed a new genomic database, the traditional Pakistani medicine genomic database (TPMGD). This database comprises five entries, namely homepage, medicinal species, species identification, basic local alignment search tool (BLAST), and download. Currently, TPMGD contains basic profiles of 128 TPMs and genetic information of 102 TPMs, including 140 cytochrome c oxidase subunit I (COI) sequences and 119 mitochondrial genome sequences from Bombyx mori, 1 396 internal transcribed spacer 2 (ITS2) sequences and 1 074 intergenic region (psbA-trnH) sequences specific to 92 and 83 plant species, respectively. Additionally, TPMGD includes 199 cp-genome sequences of 82 TPMs. ConclusionTPMGD is a multifunctional database that integrates species description, functional information inquiry, genetic information storage, molecular identification of TPM, etc. The database not only provides convenience for TPM information queries but also establishes the scientific basis for the medication safety, species identification, and resource protection of TPM.

The complete chloroplast genome of Mussaenda pubescens and phylogenetic analysis

The chloroplast (cp) genome sequence of Mussaenda pubescens, a promising resource that is used as a traditional medicine and drink, is important for understanding the phylogenetic relationships among the Mussaenda family and genetic improvement and reservation. This research represented the first comprehensive description of the morphological characteristics of M. pubescens, as well as an analysis of the complete cp genome and phylogenetic relationship. The results indicated a close relationship between M. pubescens and M. hirsutula based on the morphological characteristics of the flower and leaves. The cp was sequenced using the Illumina NovaSeq 6000 platform. The results indicated the cp genome of M. pubescens spanned a total length of 155,122 bp, including a pair of inverted repeats (IRA and IRB) with a length of 25,871 bp for each region, as well as a large single-copy (LSC) region and a small single-copy (SSC) region with lengths of 85,370 bp and 18,010 bp, respectively. The results of phylogenetic analyses demonstrated that species within the same genus displayed a tendency to group closely together. It was suggested that Antirhea, Cinchona, Mitragyna, Neolamarckia, and Uncaria might have experienced an early divergence. Furthermore, M. hirsutula showed a close genetic connection to M. pubescens, with the two species having partially overlapping distributions in China. This study presents crucial findings regarding the identification, evolution, and phylogenetic research on Mussaenda plants, specifically targeting M. pubescens.

Characterization of the complete chloroplast genome sequence of <i>Hypericum petiolulatum</i> (Hypericaceae)

<i>Hypericum</i> L. (Hypericaceae) is one of the best-selling herbal medicines in the world comprising ca. 500 species of herbs, shrubs, and small trees. <i>Hypericum petiolulatum</i> Hook. f. & Thomson ex Dyer is widely distributed in China, Vietnam, Myanmar, Nepal, India, Malaysia, and Bhutan and is used as a traditional herb to treat hemoptysis and inflammation. In this study, we sequenced and assembled the complete chloroplast (cp) genome of <i>H. petiolulatum</i>. The complete plastome of <i>H. petiolulatum</i> was 136,105 bp in length, with a large single copy region (LSC) of 93,709 bp, a small single copy region (SSC) of 11088 bp and two identical inverted repeats (IRs) of 15,654 bp. The overall GC content of the plastome was 37.0%, while GC contents of the LSC, SSC, and each IR were 35.5%, 31.0%, and 43.8%, respectively. In addition, 116 genes consisting of 76 protein-coding genes, six ribosomal RNA genes, and 34 transfer RNA genes were identified. A phylogenetic analysis of 14 taxa inferred based on cp genome sequences revealed a close relationship between <i>H. petiolulatum</i> and <i>H. perforatum</i>. The complete cp genome sequence of <i>H. petiolulatum</i> reported in this paper will facilitate population and phylogenomics studies of this medicinal plant group.

The first complete chloroplast genome of <i>Polygonatum hirtellum</i>: Genome features and phylogenetic relationships

<i>Polygonatum hirtellum</i> is a perennial herb within the family Asparagaceae. In the present study, the chloroplast (cp) genome of <i>P. hirtellum</i> is reported for the first time, and its phylogenetic relationships are also investigated. The findings revealed that the cp genome was 155,697 bp and exhibited a typical quadripartite structure, consisting of a large single copy (84,468 bp), a small single copy (18,491 bp), and a pair of invert repeat sequences (26,369 bp). The GC content of the cp genomes amounted to 37.7%; 130 genes were identified, consisting of 84 protein-coding genes, 38 transfer RNA genes, and eight ribosomal RNA genes. A phylogenetic analysis based on the cp genome and coding sequence showed that <i>P. hirtellum</i> was a member of section <i>Verticillata</i> and could be distinguished from other species of the genus <i>Polygonatum</i> used in the analysis.

Comparative and phylogenetic analysis of the complete chloroplast genomes of ten Pittosporum species from East Asia.

Pittosporum (Pittosporaceae) is famous as the ornamental and medical values, which is distributed tropical and subtropical regions of Eastern Hemisphere. The few phylogenetic studies have included samples from the Pacific Island, but the phylogenetic relationships of Asian species has not been studied. Here, the complete chloroplast (cp) genomes of ten Pittosporum species from East Asia were first sequenced and compared with those of the published species of this genus. Our results indicated that cp genomes of these species had a typical and conserved quadripartite structure. 131 genes were identical in order and orientation and no changes of inverted repeat (IR) occurred. However, the comparative analysis of cp genomes suggested that sequence divergence mainly appeared in non-coding or intergenic regions, in which several divergence hotspots were identified. By contrast, protein-coding genes showed the lowest variance under strong purifying selection. Phylogenetic analysis based on the cp genome sequences showed that the tested Pittosporum species were clustered into two major clades, in which the Asian species formed Clade I and the remaining species from Australia and New Zealand formed Clade II with high support values, which was consistent with the results of ITS data with low support values. These results suggested that cp genome is a robust phylogenetic indicator for deep nodes in the phylogeny of Pittosporum. Meanwhile, these results will provide the valuable information to better understand the phylogeny and biogeography of Pittosporum.

Interspecific Sharing of Closely Related Chloroplast Genome Haplotypes among Sclerophyllous Oaks in the Hot-Dry Valley of the Jinsha River, Southwestern China

Evergreen sclerophyllous oak forests (ESOFs) in southwestern China are a special vegetation type developed in response to the expansion of arid habitats after the uplift of the Himalayas. Here, we used chloroplast (cp) DNA and nuclear ribosomal (nr) DNA to investigate the fine-scale genetic variation patterns of six sympatric oaks (Quercus, Fagaceae) in the hot-dry valley ESOFs of the Jinsha River, southwestern China. Three cp genomes were assembled for each species. Nine cp genome haplotypes and 16 nrDNA haplotypes were identified based on single-nucleotide variants and indels. Our results demonstrated that discordance existed between the cpDNA and nrDNA phylogenies of the sclerophyllous oaks in section Ilex. The nrDNA phylogeny was consistent with species boundaries, while the cpDNA phylogeny was decoupled from taxonomy. Interspecific sharing of closely related cp genome haplotypes was detected between Quercus cocciferoides and the other two sclerophyllous oaks, Q. longispica and Q. franchetii. Specifically, Q. cocciferoides and Q. longispica sampled in a mixed stand exhibited two haplotypes that differed by a 9 bp indel. The local distribution of the two highly similar haplotypes suggested that they may have arisen from ancient introgression. Given that the two species have diverged for a long time, it is possible that the ancestral cp genome of one species was captured by another species through asymmetric introgression in early times, and an indel event occurred subsequently. Phylogenetic analyses using more previously published cp genome sequences indicated that Q. cocciferoides and Q. franchetii shared multiple cpDNA lineages of Ilex oaks, which may be caused by shared ancestral polymorphism and/or ancient introgression. Our study showed that at least three highly variable regions (ψycf1, ndhF-rpl32, and trnKUUU-rps16 or rpl32-trnLUAG) can distinguish the nine haplotypes identified by whole-cp genome sequences. These markers are useful for the evolutionary studies of the maternal lineages of oaks in hot-dry valley ESOFs.

Complete chloroplast genomes of three copal trees (Bursera: Bullockia): comparative analysis and phylogenetic relationships.

Bursera trees are conspicuous elements of the tropical dry forests in the Neotropics that have significant cultural value due to their fragrant resins (incense), wood sources (handcrafts), and ecological benefits. Despite their relevance, genetic resources developed for the genus are scarce. We obtained the complete chloroplast (Cp) genome sequence, analyzed the genome structure, and performed functional annotation of three Bursera species of the Bullockia section: Bursera cuneata, B. palmeri, and B. bipinnata. The Cp genome sizes ranged from 159,824 to 159,872bp in length, including a large single-copy (LSC) region from 87,668 to 87,656bp, a small single-copy (SSC) from 18,581 to 18,571bp, and two inverted repeats regions (IRa and IRb) of 26,814bp each. The three Cp genomes consisted of 135 genes, of which 90 were protein-coding, 37 tRNAs, and 8 rRNAs. The Cp genomes were relatively conserved, with the LSC region exhibiting the greatest nucleotide divergence (psbJ, trnQ-UCC, trnG-UCC, and petL genes), whereas few changes were observed in the IR border regions. Between 589 and 591 simple sequence repeats were identified. Analysis of phylogenetic relationships using our data for each Cp region (LSC, SSC, IRa, and IRb) and of seven species within Burseraceae confirmed that Commiphora is the sister genus of Bursera. Only the phylogenetic trees based on the SSC and LSC regions resolved the close relationship between B. bipinnata and B. palmeri. Our work contributes to the development of Bursera's genomic resources for taxonomic, evolutionary, and ecological-genetic studies.

Chloroplast Genome-Wide Analysis Reveals New Single-Nucleotide Polymorphism Resources for the ARMS-qPCR Identification of Dendrobium brymerianum

Dendrobium brymerianum Rchb. f. is a species of orchid with pharmacological interest for its potential to inhibit the growth of human lung cancer cells. The identification of the Dendrobium species is a notable problem due to morphological similarities and the limitations of universal DNA barcodes. To overcome these difficulties, this study employed complete chloroplast (cp) genome sequences as useful resources for the identification of D. brymerianum. Based on Illumina sequencing, the complete cp genomes of five D. brymerianum individuals were assembled. These genomes were in the quadripartite structure, diverse in length between 151,832 and 152,189 bp, and comprised 126 genes. Moreover, significant differences were found in the Small Single-Copy (SSC) and Large Single-Copy (LSC) regions in comparison to the Inverted Repeat (IR) regions. This study recognized hotspot regions and simple sequence repeat (SSR) loci, providing valuable insights into genetic markers. The phylogenetic relationship of Dendrobium species was discovered, highlighting the need for more precise differentiation practices. To address this, ARMS-specific primers, mainly AAob1/AAob2, confirmed strong specificity, permitting the accurate identification of D. brymerianum from other species through ARMS-qPCR. Overall, this study of D. brymerianum chloroplast genomes has generated valuable data about sequence variations, phylogenetics, and mutation dynamics. These perceptions will be valuable in future research on population genetics, taxonomy, and species identification within the Dendrobium genus.

The Complete Chloroplast Genomes of Bulbophyllum (Orchidaceae) Species: Insight into Genome Structure Divergence and Phylogenetic Analysis.

Bulbophyllum is one of the largest genera and presents some of the most intricate taxonomic problems in the family Orchidaceae, including species of ornamental and medical importance. The lack of knowledge regarding the characterization of Bulbophyllum chloroplast (cp) genomes has imposed current limitations on our study. Here, we report the complete cp genomes of seven Bulbophyllum species, including B. ambrosia, B. crassipes, B. farreri, B. hamatum, B. shanicum, B. triste, and B. violaceolabellum, and compared with related taxa to provide a better understanding of their genomic information on taxonomy and phylogeny. A total of 28 Bulbophyllum cp genomes exhibit typical quadripartite structures with lengths ranging from 145,092 bp to 165,812 bp and a GC content of 36.60% to 38.04%. Each genome contained 125-132 genes, encompassing 74-86 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The genome arrangements, gene contents, and length were similar, with differences observed in ndh gene composition. It is worth noting that there were exogenous fragment insertions in the IR regions of B. crassipes. A total of 18-49 long repeats and 38-80 simple sequence repeats (SSRs) were detected and the single nucleotide (A/T) was dominant in Bulbophyllum cp genomes, with an obvious A/T preference. An analysis of relative synonymous codon usage (RSCU) revealed that leucine (Leu) was the most frequently used codon, while cysteine (Cys) was the least used. Six highly variable regions (rpl32-trnLUAG > trnTUGU-trnLUAA > trnFGAA-ndhJ > rps15-ycf1 > rbcL-accD > psbI-trnSGCU) and five coding sequences (ycf1 > rps12 > matK > psbK > rps15) were identified as potential DNA markers based on nucleotide diversity. Additionally, 31,641 molecular diagnostic characters (MDCs) were identified in complete cp genomes. A phylogenetic analysis based on the complete cp genome sequences and 68 protein-coding genes strongly supported that 28 Bulbophyllum species can be divided into four branches, sects. Brachyantha, Cirrhopetalum, and Leopardinae, defined by morphology, were non-monophyly. Our results enriched the genetic resources of Bulbophyllum, providing valuable information to illustrate the complicated taxonomy, phylogeny, and evolution process of the genus.

Assembly and characterization of the complete mitochondrial genome of Ventilago leiocarpa.

We reported the mitochondrial genome of Ventilago leiocarpa for the first time. Two and one sites lead to the generation of stop and stat codon through editing were verified. Ventilago leiocarpa, a member of the Rhamnaceae family, is frequently utilized in traditional medicine due to the medicinal properties of its roots. In this study, we successfully assembled the mitogenome of V. leiocarpa using both BGI short reads and Nanopore long reads. This mitogenome has a total length of 331,839bp. The annotated results showed 36 unique protein-coding, 16 tRNA and 3 rRNA genes in this mitogenome. Furthermore, we confirmed the presence of a branched structure through the utilization of long reads mapping, PCR amplification, and Sanger sequencing. Specifically, the ctg1 can form a single circular molecule or combine with ctg4 to form a linear molecule. Likewise, ctg2 can form a single circular molecule or can be connected to ctg4 to form a linear molecule. Subsequently, through a comparative analysis of the mitogenome and cpgenome sequences, we identified ten mitochondrial plastid sequences (MTPTs), including two complete protein-coding genes and five complete tRNA genes. The existence of MTPTs was verified by long reads. Colinear analysis showed that the mitogenomes of Rosales were highly divergent in structure. Finally, we identified 545 RNA editing sites involving 36 protein-coding genes by Deepred-mt. To validate our findings, we conducted PCR amplification and Sanger sequencing, which confirmed the generation of stop codons in atp9-223 and rps10-391, as well as the generation of a start codon in nad4L-2. This project reported the complex structure and RNA editing event of the V. Leiocarpa mitogenome, which will provide valuable information for the study of mitochondrial gene expression.

Molecular Characterization and Phylogenetic Analysis of Centipedegrass [Eremochloa ophiuroides (Munro) Hack.] Based on the Complete Chloroplast Genome Sequence.

Centipedegrass (Eremochloa ophiuroides) is an important warm-season grass plant used as a turfgrass as well as pasture grass in tropical and subtropical regions, with wide application in land surface greening and soil conservation in South China and southern United States. In this study, the complete cp genome of E. ophiuroides was assembled using high-throughput Illumina sequencing technology. The circle pseudomolecule for E. ophiuroides cp genome is 139,107 bp in length, with a quadripartite structure consisting of a large single copyregion of 82,081 bp and a small single copy region of 12,566 bp separated by a pair of inverted repeat regions of 22,230 bp each. The overall A + T content of the whole genome is 61.60%, showing an asymmetric nucleotide composition. The genome encodes a total of 131 gene species, composed of 20 duplicated genes within the IR regions and 111 unique genes comprising 77 protein-coding genes, 30 transfer RNA genes, and 4 ribosome RNA genes. The complete cp genome sequence contains 51 long repeats and 197 simple sequence repeats, and a high degree of collinearity among E. ophiuroide and other Gramineae plants was disclosed. Phylogenetic analysis showed E. ophiuroides, together with the other two Eremochloa species, is closely related to Mnesithea helferi within the subtribe Rottboelliinae. These findings will be beneficial for the classification and identification of the Eremochloa taxa, phylogenetic resolution, novel gene discovery, and functional genomic studies for the genus Eremochloa.

Comparative and phylogenetic analysis of chloroplast genomes from ten species in Quercus section Cyclobalanopsis.

The genus Quercus L. is widely acknowledged as a significant assemblage within East Asia tropical and subtropical broadleaf evergreen forests, possessing considerable economic importance. Nevertheless, the differentiation of Quercus species is deemed arduous, and the interrelations among these species remain enigmatic. Leveraging Illumina sequencing, we undertook the sequencing and assembly of the chloroplast (cp) genomes of seven species belonging to Quercus section Cyclobalanopsis (Quercus argyrotricha, Q. augustinii, Q. bambusifolia, Q. bella, Q. edithiae, Q. jenseniana, and Q. poilanei). Furthermore, we collated three previously published cp genome sequences of Cyclobalanopsis species (Q. litseoides, Q. obovatifolia, and Q. saravanensis). Our primary objective was to conduct comparative genomics and phylogenetic analyses of the complete cp genomes of ten species from Quercus section Cyclobalanopsis. This investigation unveiled that Quercus species feature a characteristic circular tetrad structure, with genome sizes ranging from 160,707 to 160,999 base pairs. The genomic configuration, GC content, and boundaries of inverted repeats/single copy regions exhibited marked conservation. Notably, four highly variable hotspots were identified in the comparative analysis, namely trnK-rps16, psbC-trnS, rbcL-accD, and ycf1. Furthermore, three genes (atpF, rpoC1, and ycf2) displayed signals of positive selection pressure. Phylogenetic scrutiny revealed that the four sections of Cyclobalanopsis clustered together as sister taxa. The branch support values ranged from moderate to high, with most nodes garnering 100% support, underscoring the utility of cp genomic data in elucidating the relationships within the genus. Divergence time analysis revealed that Section Cyclobalanopsis represents the earliest type of Quercus genus. The outcomes of this investigation establish a foundation for forthcoming research endeavors in taxonomy and phylogenetics.