Comparative Analysis Of Chloroplast Genomes Research Articles

Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China.

Uncaria, a perennial vine from the Rubiaceae family, is a typical Chinese traditional medicine. Currently, uncertainty exists over the Uncaria genus’ evolutionary relationships and germplasm identification. The complete chloroplast genomes of four Uncaria species mentioned in the Chinese Pharmacopoeia and Uncaria scandens (an easily confused counterfeit) were sequenced and annotated. The findings demonstrated that the whole chloroplast genome of Uncaria genus is 153,780–155,138 bp in full length, encoding a total of 128–131 genes, containing 83–86 protein-coding genes, eight rRNAs and 37 tRNAs. These regions, which include eleven highly variable loci and 31–49 SSRs, can be used to create significant molecular markers for the Uncaria genus. The phylogenetic tree was constructed according to protein-coding genes and the whole chloroplast genome sequences of five Uncaria species using four methods. The topology of the two phylogenetic trees showed no difference. The sequences of U. rhynchophylla and U. scandens are clustered in one group, while the U. hirsuta and U. macrophylla are clustered in another group. U. sessilifructus is clustered together with the above two small clades. New insights on the relationship were revealed via phylogenetic research in five Uncaria species. This study will provide a theoretical basis for identifying U. rhynchophylla and its counterfeits, as well as the species of the Uncaria genus. This research provides the initial chloroplast genome report of Uncaria, contributes to elucidating the chloroplast genome evolution of Uncaria in China.

Comparative Analysis of Chloroplast Genomes within Saxifraga (Saxifragaceae) Takes Insights into Their Genomic Evolution and Adaption to the High-Elevation Environment

Saxifraga species are widely distributed in alpine and arctic regions in the Northern hemisphere. Highly morphological diversity within this genus brings great difficulties for species identification, and their typical highland living properties make it interesting how they adapt to the extreme environment. Here, we newly generated the chloroplast (cp) genomes of two Saxifraga species and compared them with another five Saxifraga cp genomes to understand the characteristics of cp genomes and their potential roles in highland adaptation. The genome size, structure, gene content, GC content, and codon usage pattern were found to be highly similar. Cp genomes ranged from 146,549 bp to 151,066 bp in length, most of which comprised 130 predicted genes. Yet, due to the expansion of IR regions, the second copy of rps19 in Saxifraga stolonifera was uniquely kept. Through sequence divergence analysis, we identified seven hypervariable regions and detected some signatures of regularity associated with genetic distance. We also identified 52 to 89 SSRs and some long repeats among seven Saxifraga species. Both ML and BI phylogenetic analyses confirmed that seven Saxifraga species formed a monophyletic clade in the Saxifragaceae family, and their intragenus relationship was also well supported. Additionally, the ndhI and ycf1 genes were considered under positive selection in species inhabiting relatively high altitudes. Given the conditions of intense light and low CO2 concentration in the highland, the products of these two genes might participate in the adaptation to the extreme environment.

Comparative chloroplast genome analysis of Ficus (Moraceae): Insight into adaptive evolution and mutational hotspot regions.

As the largest genus in Moraceae, Ficus is widely distributed across tropical and subtropical regions and exhibits a high degree of adaptability to different environments. At present, however, the phylogenetic relationships of this genus are not well resolved, and chloroplast evolution in Ficus remains poorly understood. Here, we sequenced, assembled, and annotated the chloroplast genomes of 10 species of Ficus, downloaded and assembled 13 additional species based on next-generation sequencing data, and compared them to 46 previously published chloroplast genomes. We found a highly conserved genomic structure across the genus, with plastid genome sizes ranging from 159,929 bp (Ficus langkokensis) to 160,657 bp (Ficus religiosa). Most chloroplasts encoded 113 unique genes, including a set of 78 protein-coding genes, 30 transfer RNA (tRNA) genes, four ribosomal RNA (rRNA) genes, and one pseudogene (infA). The number of simple sequence repeats (SSRs) ranged from 67 (Ficus sagittata) to 89 (Ficus microdictya) and generally increased linearly with plastid size. Among the plastomes, comparative analysis revealed eight intergenic spacers that were hotspot regions for divergence. Additionally, the clpP, rbcL, and ccsA genes showed evidence of positive selection. Phylogenetic analysis indicated that none of the six traditionally recognized subgenera of Ficus were monophyletic. Divergence time analysis based on the complete chloroplast genome sequences showed that Ficus species diverged rapidly during the early to middle Miocene. This research provides basic resources for further evolutionary studies of Ficus.

Comparative analyses of chloroplast genomes from Six Rhodiola species: variable DNA markers identification and phylogenetic relationships within the genus

BackgroundAs a valuable medicinal plant, Rhodiola has a very long history of folk medicine used as an important adaptogen, tonic, and hemostatic. However, our knowledge of the chloroplast genome level of Rhodiola is limited. This drawback has limited studies on the identification, evolution, genetic diversity and other relevant studies on Rhodiola.ResultsSix Rhodiola complete chloroplast genomes were determined and compared to another Rhodiola cp genome at the genome scale. The results revealed a cp genome with a typical quadripartite and circular structure that ranged in size from 150,771 to 151,891 base pairs. High similarity of genome organization, gene number, gene order, and GC content were found among the chloroplast genomes of Rhodiola. 186 (R. wallichiana) to 200 (R. gelida) SSRs and 144 pairs of repeats were detected in the 6 Rhodiola cp genomes. Thirteen mutational hotspots for genome divergence were determined and could be used as candidate markers for phylogenetic analyses and Rhodiola species identification. The phylogenetic relationships inferred by members of Rhodiola cluster into two clades: dioecious and hermaphrodite. Our findings are helpful for understanding Rhodiola's taxonomic, phylogenetic, and evolutionary relationships.ConclusionsComparative analysis of chloroplast genomes of Rhodiola facilitates medicinal resource conservation, phylogenetic reconstruction and biogeographical research of Rhodiola.

Comparative analysis of chloroplast genomes of three medicinal Carpesium species: Genome structures and phylogenetic relationships.

Carpesium (Asteraceae) is a genus that contains many plant species with important medicinal values. However, the lack of chloroplast genome research of this genus has greatly hindered the study of its molecular evolution and phylogenetic relationship. This study used the Illumina sequencing platform to sequence three medicinal plants of the Carpesium genus: Carpesium abrotanoides, Carpesium cernuum, and Carpesium faberi, obtaining three complete chloroplast genome sequences after assembly and annotation. It was revealed that the three chloroplast genomes were typical quadripartite structures with lengths of 151,389 bp (C. abrotanoides), 151,278 bp (C. cernuum), and 151,250 bp (C. faberi), respectively. A total of 114 different genes were annotated, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Abundant SSR loci were detected in all three chloroplast genomes, with most composed of A/T. The expansion and contraction of the IR region indicate that the boundary regions of IR/SC are relatively conserved for the three species. Using C. abrotanoides as a reference, most of the non-coding regions of the chloroplast genomes were significantly different among the three species. Five different mutation hot spots (trnC-GCA-petN, psaI, petA-psbJ, ndhF, ycf1) with high nucleotide variability (Pi) can serve as potential DNA barcodes of Carpesium species. Additionally, phylogenetic evolution analysis of the three species suggests that C. cernuum has a closer genetic relationship to C. faberi than C. abrotanoides. Simultaneously, Carpesium is a monophyletic group closely related to the genus Inula. Complete chloroplast genomes of Carpesium species can help study the evolutionary and phylogenetic relationships and are expected to provide genetic marker assistance to identify Carpesium species.

Comparative Genomic and Phylogenetic Analysis of Chloroplast Genomes of Hawthorn (Crataegus spp.) in Southwest China.

The hawthorns (Crataegus spp.) are widely distributed and famous for their edible and medicinal values. There are ∼18 species and seven varieties of hawthorn in China distributed throughout the country. We now report the chloroplast genome sequences from C. scabrifolia, C. chungtienensis and C. oresbia, from the southwest of China and compare them with the previously released six species in Crataegus and four species in Rosaceae. The chloroplast genome structure of Crataegus is typical and can be divided into four parts. The genome sizes are between 159,654 and 159,898bp. The three newly sequenced chloroplast genomes encode 132 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Comparative analysis of the chloroplast genomes revealed six divergent hotspot regions, including ndhA, rps16-trnQ-UUG, ndhF-rpl32, rps16-psbK, trnR-UCU-atpA and rpl32-trnL-UAG. According to the correlation and co-occurrence analysis of repeats with indels and SNPs, the relationship between them cannot be ignored. The phylogenetic tree constructed based on the complete chloroplast genome and intergenic region sequences indicated that C. scabrifolia has a different origin from C. chungtienensis and C. oresbia. We support the placement of C. hupehensis, C. cuneata, C. scabrifolia in C. subg. Crataegus and C. kansuensis, C. oresbia, C. kansuensis in C. subg. Sanguineae. In addition, based on the morphology, geographic distribution and phylogenetic relationships of C. chungtienensis and C. oresbia, we speculate that these two species may be the same species. In conclusion, this study has enriched the chloroplast genome resources of Crataegus and provided valuable information for the phylogeny and species identification of this genus.

Comparative Chloroplast Genomes of Nicotiana Species (Solanaceae): Insights Into the Genetic Variation, Phylogenetic Relationship, and Polyploid Speciation.

Nicotiana L. is a genus rich in polyploidy, which represents an ideal natural system for investigating speciation, biodiversity, and phytogeography. Despite a wealth of phylogenetic work on this genus, a robust evolutionary framework with a dated molecular phylogeny for the genus is still lacking. In this study, the 19 complete chloroplast genomes of Nicotiana species were assembled, and five published chloroplast genomes of Nicotiana were retrieved for comparative analyses. The results showed that the 24 chloroplast genomes of Nicotiana, ranging from 155,327 bp (N. paniculata) to 156,142 bp (N. heterantha) in size, exhibited typical quadripartite structure. The chloroplast genomes were rather conserved in genome structure, GC content, RNA editing sites, and gene content and order. The higher GC content observed in the IR regions could be a result of the presence of abundant rRNA and tRNA genes, which contained a relatively higher GC content. A total of seven hypervariable regions, as new molecular markers for phylogenetic analysis, were uncovered. Based on 78 protein-coding genes, we constructed a well-supported phylogenetic tree, which was largely in agreement with previous studies, except for a slight conflict in several sections. Chloroplast phylogenetic results indicated that the progenitors of diploid N. sylvestris, N. knightiana, and the common ancestor of N. sylvestris and N. glauca might have donated the maternal genomes of allopolyploid N. tabacum, N. rustica, and section Repandae, respectively. Meanwhile, the diploid section Noctiflorae lineages (N. glauca) acted as the most likely maternal progenitor of section Suaveolentes. Molecular dating results show that the polyploid events range considerably in ~0.12 million (section Nicotiana) to ~5.77 million (section Repandae) years ago. The younger polyploids (N. tabacum and N. rustica) were estimated to have arisen ~0.120 and ~0.186 Mya, respectively. The older polyploids (section Repandae and Suaveolentes) were considered to have originated from a single polyploid event at ~5.77 and ~4.49 Mya, respectively. In summary, the comparative analysis of chloroplast genomes of Nicotiana species has not only revealed a series of new insights into the genetic variation and phylogenetic relationships in Nicotiana but also provided rich genetic resources for speciation and biodiversity research in the future.

Sequencing and comparative analysis of chloroplast genomes of three medicinal plants: Gentiana manshurica, G. scabra and G. triflora.

The online version contains supplementary material available at 10.1007/s12298-022-01217-0.

Chloroplast Genomic Resources and Genetic Divergence of Endangered Species Bretschneidera sinensis (Bretschneideraceae)

Bretschneidera sinensis is an endangered woody species found in East and South China. Comprehensive intraspecies chloroplast genome studies have demonstrated novel genetic resources to assess the genetic variation and diversity of this species. Using genome skimming method, we assembled the whole chloroplast genome of 12 genotypes of B. sinensis from different geographical locations, covering most wild populations. The B. sinensis chloroplast genome size ranged from 158,959 to 159,045 base pairs (bp) and displayed a typical circular quadripartite structure. Comparative analyses of 12 B. sinensis chloroplast genome revealed 33 polymorphic simple sequence repeats (SSRs), 105 polymorphic single nucleotide polymorphisms (SNPs), and 55 indels. Phylogenetic analysis showed that the 12 genotypes were grouped into 2 branches, which is consistent with the geographical distribution (Eastern clade and Western clade). Divergence time estimates showed that the two clades were divergent from 0.6 Ma in the late Pleistocene. Ex situ conservation is essential for this species. In this study, we identified SNPs, indels, and microsatellites of B. sinensis by comparative analyses of chloroplast genomes and determined genetic variation between populations using these genomic markers. Chloroplast genomic resources are also important for further domestication, population genetic, and phylogenetic analysis, possibly in combination with molecular markers of mitochondrial and/or nuclear genomes.

Complete chloroplast genome of Gentianopsis barbata and comparative analysis with related species from Gentianaceae.

Gentianopsis barbata is an essential medicinal plant in China with high ornamental and medicinal values. Unfortunately, the study of the chloroplast genome of this plant still has a gap. This study sequenced and characterized the complete chloroplast genome of G. barbata. The complete chloroplast genome of G. barbata is a typical circular structure of 151 123bp. It consists of a large single-copy region (82 690bp) and a small single-copy region (17 887bp) separated by a pair of inverted repeats (25 273bp), which covers 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. The long repeat sequence analysis showed that the P-type (palindromic) sequences were the major long repeat sequences. Thirty-seven simple sequence repeats were identified, most of which were single nucleotides. The Bayesian inference tree, maximum likelihood tree, and neighbor-joining tree suggested that G. barbata is grouped with Gentianopsis grandis and Gentianopsis paludosa. The divergence time analysis showed that G. barbata diverged at 1.243 Mya. Comparative analysis of chloroplast genomes can reveal interspecific diversity, and regions with high variation can be used to develop molecular markers applicable to various research areas. Our results provide a new insight into plastome evolution and a valuable resource for further studies on G. barbata.

Fifteen complete chloroplast genomes of Trapa species (Trapaceae): insight into genome structure, comparative analysis and phylogenetic relationships.

BackgroundTrapa L. is a floating-leaved aquatic plant with important economic and ecological values. However, the species identification and phylogenetic relationship within Trapa are still controversial, which necessitates the need for plastid genome information of Trapa. In this study, complete chloroplast genomes of 13 Trapa species/taxa were sequenced and annotated. Combined with released sequences, comparative analyses of chloroplast genomes were performed on the 15 Trapa species/taxa for the first time.ResultsThe Trapa chloroplast genomes exhibited typical quadripartite structures with lengths from 155,453 to 155,559 bp. The gene orders and contents within Trapa were conservative, but several changes were found in the microstructure. The intron loss of rpl2, also detected in Lythraceae, was found in all Trapa species/taxa, suggesting close genetic relationship between Lythraceae and Trapaceae. Notably, two small-seed species (T. incisa and T. maximowiczii) showed the smallest genome size with 155,453 and 155,477 bp, respectively. Each cp genome contained the same 130 genes consisting of 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Trapa species/taxa showed 37 (T. incisa and T. maximowiczii) to 41 (T. sibirica) long repeats, including forward, palindromic, reversed and complementary repeats. There were 110 (T. quadrispinosa) to 123 (T. incisa and T. maximowiczii) SSR (simple sequence repeat) loci in Trapa chloroplast genomes. Comparative analyses revealed that two hotspot regions (atpA—atpF and rps2—rpoC2) in Trapa chloroplast genomes could be served as potential molecular markers. Three phylogenetic analyses (ML, MP and BI) consistently showed that there were two clusters within Trapa, including large- and small-seed species/taxa, respectively; for the large-seed Trapa, they clustered according to their geographical origin and tubercle morphology on the surface of seeds.ConclusionIn summary, we have acquired the sequences of 13 Trapa chloroplast genomes, and performed the comparative analyses within Trapa for the first time. The results have helped us better identify the Trapa species/taxa and deepen the understanding of genetic basis and phylogenetic relationship of Trapa, which will facilitate the effective management and utilization of the important genetic resources in the future.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-022-03608-7.

Comparative analysis of chloroplast genomes reveals phylogenetic relationships and intraspecific variation in the medicinal plant Isodon rubescens.

Isodon rubescens (Hemsley) H. Hara (Lamiaceae) is a traditional Chinese medicine plant that has been used to treat various human diseases and conditions such as inflammation, respiratory and gastrointestinal bacterial infections, and malignant tumors. However, the contents of the main active components of I. rubescens from different origins differ significantly, which greatly affected its quality. Therefore, a molecular method to identify and classify I. rubescens is needed. Here, we report the DNA sequence of the chloroplast genome of I. rubescens collected from Lushan, Henan province. The genome is 152,642 bp in length and has a conserved structure that includes a pair of IR regions (25,726 bp), a LSC region (83,527 bp) and a SSC region (17,663 bp). The chloroplast genome contains 113 unique genes, four rRNA genes, 30 tRNA genes, and 79 protein-coding genes, 23 of which contain introns. The protein-coding genes account for a total of 24,412 codons, and most of them are A/T biased usage. We identified 32 simple sequence repeats (SSRs) and 48 long repeats. Furthermore, we developed valuable chloroplast molecular resources by comparing chloroplast genomes from three Isodon species, and both mVISTA and DnaSP analyses showed that rps16-trnQ, trnS-trnG, and ndhC-trnM are candidate regions that will allow the identification of intraspecific differences within I. rubescens. Also 14 candidate fragments can be used to identify interspecific differences between species in Isodon. A phylogenetic analysis of the complete chloroplast genomes of 24 species in subfamily Nepetoideae was performed using the maximum likelihood method, and shows that I. rubescens clustered closer to I. serra than I. lophanthoides. Interestingly, our analysis showed that I. rubescens (MW018469.1) from Xianyang, Shaanxi Province (IR-X), is closer to I. serra than to the other two I. rubescens accessions. These results strongly indicate that intraspecific diversity is present in I. rubescens. Therefore, our results provide further insight into the phylogenetic relationships and interspecific diversity of species in the genus Isodon.

Comparative analyses of chloroplast genomes in 'Red Fuji' apples: low rate of chloroplast genome mutations.

BackgroundFuji is a vital apple cultivar, and has been propagated clonally for nearly a century. The chloroplast genome variation of Fuji apples in China has not been investigated.MethodsThis study used next-generation high-throughput sequencing and bioinformatics to compare and analyze the chloroplast genome of 24 Red Fuji varieties from nine regions in China.ResultsThe results showed that the 24 chloroplast genomes were highly conserved in genome size, structure, and organization. The length of the genomes ranged from 160,063 to 160,070 bp, and the GC content was 36.6%. Each of the 24 chloroplast genomes encoded 131 genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The results of repeat sequence detection were consistent; the most common sequence was forward repeats (53.1%), and the least common sequence was complementary repeats (4.1%). The chloroplast genome sequence of Red Fuji was highly conserved. Two indels were detected, but the PI value was 0, and there were no SNP loci. The chloroplast genome variation rate of Red Fuji was low.

Comparative Analysis of Chloroplast Genomes of Seven Chaetoceros Species Revealed Variation Hotspots and Speciation Time.

Chaetoceros is a species-rich diatom genus with broad distribution and plays an important role in global carbon cycle and aquatic ecosystems. However, genomic information of Chaetoceros species is limited, hindering advanced researches on Chaetoceros biodiversity and their differential impact on ecology. In this study, we constructed full-length chloroplast genomes (cpDNAs) for seven Chaetoceros species, including C. costatus, C. curvisetus, C. laevisporus, C. muelleri, C. pseudo-curvisetus, C. socialis, and C. tenuissimus. All of these cpDNAs displayed a typical quadripartite structure with conserved genome arrangement and specific divergence. The sizes of these cpDNAs were similar, ranging from 116,421 to 119,034 bp in size, and these cpDNAs also displayed similar GC content, ranging from 30.26 to 32.10%. Despite extensive synteny conservation, discrete regions showed high variations. Divergence time estimation revealed that the common ancestor of Chaetoceros species, which formed a monophyletic clade at approximately 58 million years ago (Mya), split from Acanthoceras zachariasii at about 70 Mya. The availability of cpDNAs of multiple Chaetoceros species provided valuable reference sequences for studying evolutionary relationship among Chaetoceros species, as well as between Chaetoceros species and other diatom species.

Comparative chloroplast genome analysis of medicinally important Veratrum (Melanthiaceae) in China: Insights into genomic characterization and phylogenetic relationships

Members of Veratrum are perennial herbs widely used in traditional Chinese medicine to induce vomiting, resolve blood stasis and relieve pain. However, the intrageneric classification and phylogenetic relationships within Veratrum have long been controversial due to the complexity of morphological variations and lack of high-resolution molecular markers. In this study, we reevaluated the infrageneric relationships with the genus Veratrum using complete chloroplast genome sequence data. Herein, the complete cp genomes of ten species of Veratrum were newly sequenced and characterized. The complete cp genomes of ten species of Veratrum had the typical quadripartite structure, ranging from 151,597 bp to 153,711 bp in size and comprising a total of 135 genes. The structure of Veratrum cp genomes (i.e., gene order, content, and genome components) was highly similar across species. The number of simple sequence repeats (SSRs) ranged from 63 to 78, and of long repeats ranged from 31 to 35. Eight highly divergent regions (ndhF, psbC-psbZ, psbK-psbI, rpoB-trnC_GCA, trnK_UUU-trnQ_UUG, trnS_GCU-trnG_UCC, trnT_UGU-trnL_UAA and ycf1) were identified and are potentially useful for the DNA barcoding of Veratrum. Phylogenetic analysis among 29 taxa based on cp genomes, total genes, protein-coding genes and intergenic regions strongly supported the monophyly of Veratrum. The circumscription and relationships of the infrageneric taxa of Veratrum were well-presented with great resolution. These results will facilitate the identification, taxonomy, and utilization of Veratrum plants as well as the evolutionary studies of Melanthiaceae.

The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China

BackgroundStauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triterpenoid saponins with anticancer and anti-inflammatory activities. However, the wild resources of this species and its relatives were threatened by over-exploitation before the genetic diversity and evolutionary analysis were uncovered. Thus, the complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily.ResultsA series of analyses including genome structure, GC content, repeat structure, SSR component, nucleotide diversity and codon usage were performed by comparing chloroplast genomes of Stauntonia chinensis and its relatives. Although the chloroplast genomes of eight Lardizabaloideae plants were evolutionary conserved, the comparative analysis also showed several variation hotspots, which were considered as highly variable regions. Additionally, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Lardizabaloideae species underwent purifying selection, whereas 25 chloroplast protein coding genes were identified with positive selection in this subfamily species by using branch-site model. Bayesian and ML phylogeny on CCG (complete chloroplast genome) and CDs (coding DNA sequences) produced a well-resolved phylogeny of Lardizabaloideae plastid lineages.ConclusionsThis study enhanced the understanding of the evolution of Lardizabaloideae and its relatives. All the obtained genetic resources will facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of subfamily Lardizabaloideae.

Comparative analysis of chloroplast genomes of kenaf cytoplasmic male sterile line and its maintainer line

Kenaf is a great source of bast fiber and possesses significantly industrial interests. Cytoplasmic male sterility (CMS) is the basis of heterosis utilization in kenaf. Chloroplast, an important organelle for photosynthesis, could be associated with CMS. To understand the phylogenetic position and molecular basis of kenaf CMS from the perspective of chloroplast, the chloroplast (cp) genomes of the CMS line P3A and its maintainer line P3B were characterized and their comparative analysis was also performed. In this study, the chloroplast genomes of P3B and P3A were sequenced with 163,597 bp and 163,360 bp in length, respectively. A total of 131 genes including 85 protein coding genes (PCGs), 38 transfer RNA (tRNA) genes, and 8 ribosome RNA (rRNA) genes were annotated in P3B, while 132 genes containing 83 PCGs, 41 tRNA genes, and 8 rRNA genes were found in P3A. The phylogenetic tree revealed that kenaf was closely related to Hibiscus syriacus and Abelmoschus esculentus. Further analysis of single nucleotide polymorphism (SNP) and insertion and deletion (InDel) showed that compared with P3B, a total of 22 SNPs and 53 InDels were detected in gene coding region, gene intron, and intergenic regions of P3A. Remarkably, a total of 9 SNPs including 6 synonymous SNPs and 3 nonsynonymous SNPs were found in psbK, atpA, rpoC2, atpB, rpl20, clpP, rpoA, and ycf1. The present study provided basic information for further study of kenaf CMS mechsnism.

Transcriptome and Comparative Chloroplast Genome Analysis of Vincetoxicum versicolor: Insights Into Molecular Evolution and Phylogenetic Implication.

Vincetoxicum versicolor (Bunge) Decne is the original plant species of the Chinese herbal medicine Cynanchi Atrati Radix et Rhizoma. The lack of information on the transcriptome and chloroplast genome of V. versicolor hinders its evolutionary and taxonomic studies. Here, the V. versicolor transcriptome and chloroplast genome were assembled and functionally annotated. In addition, the comparative chloroplast genome analysis was conducted between the genera Vincetoxicum and Cynanchum. A total of 49,801 transcripts were generated, and 20,943 unigenes were obtained from V. versicolor. One thousand thirty-two unigenes from V. versicolor were classified into 73 functional transcription factor families. The transcription factors bHLH and AP2/ERF were the most significantly abundant, indicating that they should be analyzed carefully in the V. versicolor ecological adaptation studies. The chloroplast genomes of Vincetoxicum and Cynanchum exhibited a typical quadripartite structure with highly conserved gene order and gene content. They shared an analogous codon bias pattern in which the codons of protein-coding genes had a preference for A/U endings. The natural selection pressure predominantly influenced the chloroplast genes. A total of 35 RNA editing sites were detected in the V. versicolor chloroplast genome by RNA sequencing (RNA-Seq) data, and one of them restored the start codon in the chloroplast ndhD of V. versicolor. Phylogenetic trees constructed with protein-coding genes supported the view that Vincetoxicum and Cynanchum were two distinct genera.

Comparative Analyses of Chloroplast Genomes From 14 Zanthoxylum Species: Identification of Variable DNA Markers and Phylogenetic Relationships Within the Genus.

Zanthoxylum L. is an economic crop with a long history of cultivation and domestication and has important economic, ecological, and medicinal value. To solve the classification problems caused by the similar morphological characteristics of Zanthoxylum and establish a credible phylogenetic relationship, we sequenced and annotated six Zanthoxylum chloroplast (cp) genomes (Z. piasezkii, Z. armatum, Z. motuoense, Z. oxyphyllum, Z. multijugum, and Z. calcicola) and combined them with previously published genomes for the Zanthoxylum species. We used bioinformatics methods to analyze the genomic characteristics, contraction, and expansion of inverted repeat (IR) regions; differences in simple sequence repeats (SSRs) and long repeat sequences; species pairwise Ka/Ks ratios; divergence hotspots; and phylogenetic relationships of the 14 Zanthoxylum species. The results revealed that cp genomes of Zanthoxylum range in size from 158,071 to 158,963 bp and contain 87 protein-coding, 37 tRNA, and 8 rRNA genes. Seven mutational hotspots were identified as candidate DNA barcode sequences to distinguish Zanthoxylum species. The phylogenetic analysis strongly supported the genus Fagara as a subgenus of Zanthoxylum and proposed the possibility of a new subgenus in Zanthoxylum. The availability of these genomes will provide valuable information for identifying species, molecular breeding, and evolutionary analysis of Zanthoxylum.

Comparative analysis of chloroplast genomes indicated different origin for Indian tea (Camellia assamica cv TV1) as compared to Chinese tea

Based upon the morphological characteristics, tea is classified botanically into 2 main types i.e. Assam and China, which are morphologically very distinct. Further, they are so easily pollinated among themselves, that a third category, Cambod type is also described. Although the general consensus of origin of tea is India, Burma and China adjoining area, yet specific origin of China and Assam type tea are not yet clear. Thus, we made an attempt to understand the origin of Indian tea through the comparative analysis of different chloroplast (cp) genomes under the Camellia genus by performing evolutionary study and comparing simple sequence repeats (SSRs) and codon usage distribution patterns among them. The Cp genome based phylogenetic analysis indicated that Indian Tea, TV1 formed a different group from that of China tea, indicating that TV1 might have undergone different domestications and hence owe different origins. The simple sequence repeats (SSRs) analysis and codon usage distribution patterns also supported the clustering order in the cp genome based phylogenetic tree.