Phylogenetic study on Scenedesmacae with the description of a new genus Coccoidesmus gen.nov.(Chlorophyceae,Chlorophyta)and chloroplast genome analyses

Members of the family Scenedesmaceae are some of the most common algal taxa in inland ecosystems,and they are widely distributed in freshwaters,aerial,and sub-aerial habitats.With the continuous updating of methods,the classic morphological taxonomy of this family needs to be revised.In recent years,many genera of Scenedesmaceae have been established via the use of molecular methods.The phylogenetic relationships within Scenedesmaceae were analyzed using different molecular markers and morphological data,and the new freshwater genus Coccoidesmus Wang,Hou et Liu gen.nov.was described.Two new species in this genus were also described.Phylogenetic analysis based on tufA genes revealed that the new genus formed an independent clade closely related to Comasiella.However,these two genera are characterized by significant morphological differences in colony arrangement and cell shape.The chloroplast genome of the type species was assembled and annotated,and analyses of genome structure and sequences were conducted.More genome data could help clarify the phylogenetic relationships within this family.

Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of 19 Species in Rosaceae Family

Rosaceae represents a vast and complex group of species,with its classification being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the Rosaceae.The cp genomes,vary-ing in size from 153,366 to 159,895 bp,followed the typical quadripartite organization consisting of a large single-copy(LSC)region(84,545 to 87,883 bp),a small single-copy(SSC)region(18,174 to 19,259 bp),and a pair of inverted repeat(IR)regions(25,310 to 26,396 bp).These genomes contained 132–138 annotated genes,including 87 to 93 protein-coding genes(PCGs),37 tRNA genes,and 8 rRNA genes using MISA software,52 to 121 simple sequence repeat(SSR)loci were identified.D.arbuscular contained the least of SSRs and did not have hexanotides,A.lineata contained the richest SSRs.Long terminal repeats(LTRs)were primarily composed of palindromic and forward repeat sequences,meanwhile,The richest LTRs were found in Argentina lineata.Except for Argentina lineata,Fragariastrum eriocarpum,and Prunus trichostoma,which varied in gene type and position on both sides of the boundary,the remaining species were found to be mostly conserved according to IR boundary analysis.The examination of the Ka/Ks ratio revealed that only the infA gene had a value greater than 1,indicating that this gene was primarily subjected to positive selection during evolution.Additionally,9 hotspots of variation were identified in the LSC and SSC regions.Phylogenetic analysis confirmed the scientific validity of the genus Prunus L.sensu lato(s.l.)within the Rosaceae family.The separation of the three genera Argentina Hill,Fragariastrum Heist.ex Fabr.and Dasiphora Raf.from Potentilla L.may be a more scientific classification.These results offer fresh perspectives on the taxonomy of the Rosaceae.

Structural Characterization of Chloroplast Genome in Alpinia japonica(Thunb.)Miq.,a Medicinal Plant of the Genus Alpinia

The analysis of chloroplast gene characteristics in Alpinia japonica(Thunb.)Miq.is of great significance for developing relevant genetic resources.The high-throughput sequencing and bioinformatic research were performed to analyze the chloroplast genome characteristics of A.japonica.The total chloroplast genome length of A.japonica was 161,906 bp,with a typical circular tetrameric structure.And 133 genes were annotated,comprising 87 protein-coding,38 tRNA,and 8 rRNA genes.Furthermore,22 genes contained two copies,and 18 genes owned introns.Repeat sequence analysis showed that it contains 321 simple sequence repeats(SSRs)and 37 long segment repeats.Compared with the chloroplast genomes of eight representative plants in the genus Alpinia,the gene structure,type,and quantity were relatively conservative.Rps12 was the highest variation site in the entire chloroplast gene.A phylogenetic tree showed that the genus Alpinia was the most closely related to the genus Amomum.Meanwhile,A.japonica is the most closely related to Alpinia chinensis belonging to the genus Alpinia.Overall,the chloroplast genome of a new species was reported in the genus Alpinia,and a basis was provided for the utilization of Alpinia plants as a medical resource.

cpSSR: a New Tool to Analyze Chloroplast Genome of Citrus Somatic Hybrids

Chloroplast simple sequence repeat (cpSSR) markers in Citrus were developed and successfully used to analyze chloroplast genome inheritance of Citrus somatic hybrids. Twenty-two previously reported cpSSR primer pairs from pine (Pinus thunbergii Parl.), rice (Otyza sativa L.) and tobacco (Nicotiana tabacum L.) were tested in Citrus, nine of which could amplify intensive PCR products by agarose gel electrophoresis. Chloroplast genome inheritance of Citrus somatic hybrids from nine fusions was then analyzed, and five of the nine pre-screened primer pairs showed polymorphisms by polyacrylamide gel electrophoresis. The results revealed the random inheritance nature of chloroplast genome in all analyzed Citrus somatic hybrids, which was in agreement with previous reports based on RFLP or CAPS analyses. It was also shown that cpSSR is a more efficient tool in chloroplast genome analyses of somatic hybrids in higher plants, compared with the conventional RFLP or CAPS analyses.

Research Progress of Sugarcane Chloroplast Genome

Along with the development of modern molecular biology technologies, complete chloroplast genomes have been sequenced in various plant species to date, and the structure, function and expression of these genes have been deter-mined. The chloroplast genome structure in most higher plants is stable, since the gene number, arrangement and composition are conservative. The determination of sugarcane chloroplast genome sequence laid a good foundation for sugarcane chloroplast related research. This article gives a review on the research progress of sugarcane chloroplast genome through the chloroplast genome map, gene structure, function, chloroplast RNA editing, and phylogenetic analysis in Saccharum and relat-ed genera. This study held great potential to clarify more directions in researches, including sugarcane chloroplast genetic transformation, complete chloroplast nu-cleotide sequence determination in Saccharum and closely related genera, cpSSRs development and application.

Molecular phylogeny and inflorescence evolution of Prunus(Rosaceae)based on RAD-seq and genome skimming analyses

Prunus is an economically important genus widely distributed in the temperate Northern Hemisphere.Previous studies on the genus using a variety of loci yielded conflicting phylogenetic hypotheses.Here,we generated nuclear reduced representation sequencing data and plastid genomes for 36 Prunus individuals and two outgroups.Both nuclear and plastome data recovered a well-resolved phylogeny.The species were divided into three main clades corresponding to their inflorescence types,-the racemose group,the solitary-flower group and the corymbose group-with the latter two sister to one another.Prunus was inferred to have diversified initially in the Late Cretaceous around 67.32 million years ago.The diversification of the three major clades began between the Paleocene and Miocene,suggesting that paleoclimatic events were an important driving force for Prunus diversification.Ancestral state reconstructions revealed that the most recent common ancestor of Prunus had racemose inflorescences,and the solitary-flower and corymb inflorescence types were derived by reduction of flower number and suppression of the rachis,respectively.We also tested the hybrid origin hypothesis of the racemose group proposed in previous studies.Prunus has undergone extensive hybridization events,although it is difficult to identify conclusively specific instances of hybridization when using SNP data,especially deep in the phylogeny.Our study provides well-resolved nuclear and plastid phylogenies of Prunus,reveals substantial cytonuclear discord at shallow scales,and sheds new light on inflorescence evolution in this economically important lineage.

A Comparative Analysis of the Chloroplast Genomes of Four Salvia Medicinal Plants

Herbgenomics is an emerging field of traditional Chinese medicine(TCM)research and development.By combining TCM research with genomics,herbgenomics can help to establish the scientific validity of TCM and bring it into wider usage within the field of medicine.Salvia Linn.(S.Linn.)is a large genus of Labiatae that includes important medicinal plants.In this herbgenomics study,the complete chloroplast(cp)genomes of two Salvia spp.—namely,S.przewalskii and S.bulleyana,which are used as a surrogate for S.miltiorrhiza—were sequenced and compared with those of two other reported Salvia spp.—namely,S.miltiorrhiza and S.japonica.The genome organization,gene number,type,and repeat sequences were compared.The annotation results showed that both Salvia plants contain 114 unique genes,including 80 protein-coding,30 transfer RNA(tRNA),and four ribosomal RNA(rRNA)genes.Repeat sequence analysis revealed 21 forward and 22 palindromic sequences in both Salvia cp genomes,and 17 and 21 tandem repeats in S.przewalskii and S.bulleyana,respectively.A synteny comparison of the Salvia spp.cp genomes showed a high degree of sequence similarity in the coding regions and a relatively high divergence of the intergenic spacers.Pairwise alignment and single-nucleotide polymorphism(SNP)analyses found some candidate fragments to identify Salvia spp.,such as the intergenic region of the trnV–ndhC,trnQ–rps16,atpI–atpH,psbA–ycf3,ycf1,rpoC2,ndhF,matK,rpoB,rpoA,and accD genes.All of the results—including the repeat sequences and SNP sites,the inverted repeat(IR)region border,and the phylogenetic analysis—showed that S.przewalskii and S.bulleyana are extremely similar from a genetic standpoint.The cp genome sequences of the two Salvia spp.reported here will pave the way for breeding,species identification,phylogenetic evolution,and cp genetic engineering studies of Salvia medicinal plants.

De novo assembly of chloroplast genomes of Corchorus capsularis and C.olitorius yields species-specific InDel markers

Jute(Corchorus spp.)is a member of the Malvaceae family,which comprises more than 100 species.The systematic positions of jute species have remained unsettled.Chloroplasts are maternally inherited and their genomes are widely used for plant phylogenetic studies.In the present study,the chloroplast genomes of Corchorus capsularis and C.olitorius were assembled,with sizes of respectively 161,088 and 161,766 bp.Both genomes contained 112 unique genes(78 protein-coding,four rRNA,and 30 tRNA genes).Four regionswith high variation between the two species were located in single-copy rather than inverted-repeat regions.A total of 66 simple sequence repeats(SSRs)were identified in the C.capsularis chloroplast genome and 56 in that of C.olitorius.Comparison of the two chloroplast genome sequences permitted the evaluation of nucleotide variation including 2417 single-nucleotide polymorphisms sites and 294 insertion or deletion sites,of which one marker(cpInDel 205)could discriminate the two jute species.Comparison of the C.capsularis and C.olitorius chloroplast genomeswith those of other species in theMalvaceae revealed breakpoints in the accD locus,which is involved in fatty acid synthesis,in C.capsularis and C.olitorius.This finding suggests that genes from the chloroplast genomemight have been transferred to the nuclear genome in some Corchorus species.This hypothesis was supported by synteny analysis of the accD region among the nuclear,chloroplast,and mitochondrial genomes.To our knowledge,this is the first report of the assembled chloroplast genome sequences of C.capsularis and C.olitorius.C.capsularis and C.olitorius are closely related to Gossypium species and there are abundant microstructure variations between these two genera.These results will expand our understanding of the systematics of species in the Malvaceae.

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 7&and of long repeats ranged from 31 to 35.Eight highly divergent regions(ndhF,psbC-psbZ,psbK-psbl,rpoB-tmCjGCA,tmK_UUU-tmQ_UUG,tmS_GCU-tmG_UCC,tmT_UGU-tmL_UAA and ycfl)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.

Structural characterization and comparative analysis of the chloroplast genome of Ginkgo biloba and other gymnosperms

Ginkgo biloba is a famous living“fossil”and has played an important role in the evolution of the Plant Kingdom.Here,the complete chloroplast genome of G.biloba was sequenced and analysed.The chloroplast genome was 156,990 bp long and predicted to encode 134 genes including 85 protein-coding genes,41 tRNA genes and 8 rRNA genes.The chloroplast genome has a typical quadripartite structure with a pair of inverted repeat regions(IRa and IRb,17,732 bp),a large(LSC,99,259 bp)and small single(SSC,22,267 bp)copy region.After an extensive comparison to previously published gymnosperm plastomes,the gene content and organisation of G.biloba showed high divergence,although part was relatively conserved.The two typical IR regions in the G.biloba chloroplast genome were relatively shorter because it the ycf2 gene.In addition,it was obvious that the IR regions and gene loss were responsible for changes in chloroplast genome size and structure stability,which influenced plastome evolution in different gymnosperms.Phylogenetic analysis revealed that G.biloba is sister to cycads rather than to gnetophytes,cupressophytes,and Pinaceae.Overall,the study showed that the genomic characteristics of G.biloba would be of great help in the further research on the taxonomy,species identification and evolutionary history of gymnosperms,especially for their position in plant systematics and evolution.

Characterization and comparison of chloroplast genomes from two sympatric Hippophae species(Elaeagnaceae)

The genus Hippophae includes deciduous shrubs or small trees,which provide many ecological,economic,and social benefi ts.We assembled and annotated the chloroplast genomes of sympatric Hippophae gyantsensis(Rousi)Lian and Hippophae rhamnoides Linn subsp.yunnanensis Rousi and comparatively analyzed their sequences.The fulllength chloroplast genomes of H.gyantsensis and H.rhamnoides subsp.yunnanensis were 155,260 and 156,415 bp,respectively;both featured a quadripartite structure with two copies of a large inverted repeat(IR)separated by small(SSC)and large(LSC)single-copy regions.Each Hippophae chloroplast genome contained 131 genes,comprising 85 protein-coding,8 ribosomal RNA,and 38 transfer RNA genes.Of 1302 nucleotide substitutions found between these twogenomes,824(63.29%)occurred in the intergenic region or intron sequences,and 478(36.71%)were located in the coding sequences.The SSC region had the highest mutation rate,followed by the LSC region and IR regions.Among the protein-coding genes,three had a ratio of nonsynonymous to synonymous substitutions(Ka/Ks)>1 yet none were signifi-cant,and 66 had Ka/Ks<1,of which 46 were signifi cant.We found 20 and 16 optimal codons,most of which ended with A or U,for chloroplast protein-coding genes of H.gyantsensis and H.rhamnoides subsp.yunnanensis,respectively.Phylogenetic analysis of fi ve available whole chloroplast genome sequences in the family Elaeagnaceae—using one Ziziphus jujube sequence as the outgroup—revealed that all fi ve plant species formed a monophyletic clade with two subclades:one subclade consisted of three Hippophae species,while the other was formed by two Elaeagnus species,supported by 100%bootstrap values.Together,these results suggest the chloroplast genomes among Hippophae species are conserved,both in structure and gene composition,due to general purifying selection;like many other plants,a signifi cant AT preference was discerned for most proteincoding genes in the Hippophae chloroplast genome.This study provides a valuable reference tool for future research on the general characteristics and evolution of chloroplast genomes in the genus Hippophae.

Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines

Whole-genome shogun sequence(WGS)data generated by next-generation sequencing(NGS)platforms are a valuable resource for crop improvement.We produced 5–6×WGS coverage of 44 Brassica oleracea breeding lines representing seven subspecies/morphotypes:cabbage,broccoli,cauliflower,kailan,kale,Brussels sprout,and kohlrabi to systematically evaluate the nuclear and chloroplast(Cp)diversity in the 44 B.oleracea breeding lines.We then exploited the impact of low-coverage NGS by evaluating nuclear genome diversity and assembly,annotation of complete chloroplast(Cp)genomes and 45 S nuclear ribosomal DNA(45S nrDNA)sequences,and copy number variation for major repeats.Nuclear genome diversity analysis has revealed a total of 496463 SNPs and 37493 indels in the nuclear genome across the 44 accessions.Interestingly,some SNPs showed subspecies enrichment at certain chromosomal regions.The assembly of complete Cp genomes contained 153361–153372 bp with 37 variants including SNPs and indels.The 45S nrDNA transcription unit was 5802 bp long with a total of 31 SNPs from the 44 lines.The phylogenetic tree inferred from the nuclear and Cp genomes coincided and clustered broccoli,cauliflower,and kailan in one group and cabbage,Brussels sprout,kale,and kohlrabi in another group.The morphotypes diverged during the last 0.17 million years.The Cp genome diversity reflected the unique cytoplasm of each subspecies,and revealed that the cytoplasm of many breeding lines was replaced and intermingled via inter-subspecies crosses during the breeding process instead.The polymorphic Cp markers provide a classification system for the cytoplasm types in B.oleracea.Furthermore,copy numbers of major transposable elements(TEs)showed high diversity among the 44 accessions,indicating that many TEs have become active recently.Overall,we demonstrated a comprehensive utilization of low-coverage NGS data and might shed light on the genetic diversity and evolution of diverse B.oleracea morphotypes.

The Complete Chloroplast Genome of <i>Poa pratensis</i>(Poaceae), a High-Quality Forage

Poa pratensis L. (Poaceae) is a hardy, persistent, attractive forage and turf grass adapted to a wide range of soils and climate. In this study, we release and detail the complete chloroplast genome sequences of P. pratensis. The whole chloroplast genome was 135,649 bp in length and comprised 131 genes, including 85 protein-coding genes, 38 tRNA genes, 8 rRNA genes. The P. pratensis chloroplast genome had a GC content of 38.3%. The result of phylogenetic analysis showed that P. pratensis was closely related to P. pratensis cv. Qinghai and P. poophagorum. This study would provide useful genetic information for the protection of P. pratensis and other related species.

Comparative chloroplast genomes of Ulva prolifera and U.linza(Ulvophyceae)provide genetic resources for the development of interspecific markers

The green seaweeds Ulva linza and U.prolifera are closely related species.They usually co-occur widely and have important ecological significance as primary producers thriving in the intertidal zone.In the Yellow Sea,a genetically unique floating ecotype of U.prolifera even bloomed to cause serious green tides.However,there is still a lack of appropriate molecular markers to distinguish these two species,partially due to limited evaluations on the intraspecific variations in U.prolifera among dif ferent ecotypes.Since organelle genomes could provide rich genetic resources for phylogenetic analysis and development of genetic markers,in this study,the chloroplast genome from one attached population of U.prolifera was completely sequenced,and comparative genomic analyses were performed with other existing chloroplast genomes from U.linza and the floating ecotype of U.prolifera.The results showed that in spite of the high level of collinearity among three genomes,there were plenty of genetic variations especially within the non-coding regions,including introns and gene spacer regions.A strategy was proposed that only those signals of variation,which were identical between two ecotypes of U.prolifera but divergent between U.linza and U.prolifera,were selected to develop the interspecific markers for U.linza and U.prolifera.Two candidate markers,psa B and pet B,were shown to be able to distinguish these two closely related species and were applicable to more attached populations of U.prolifera from a wide range of geographical sources.In addition to the interspecific marker,this study would also provide resources for the development of intraspecific markers for U.prolifera.These markers might contribute to the surveys for Ulva species composition and green tide monitoring especially in the Yellow Sea region.

Comparative Analysis of the Complete Chloroplast Genome Sequences of Four Origin Plants of Lonicerae Flos(Lonicera;Caprifoliaceae)

Lonicerae Flos(LF)derived from the dried flower buds or opening flowers of four Lonicera plants(Lonicera macranthoides,L.hypoglauca,L.confusa,and L.fulvotnetosa),is a popular traditional Chinese medicine.Because the four origin plants are very similar in morphology,it is difficult to control the quality of LF in actual production.Over the past decade,many reports have pointed out the differences among them,including the botanical characteristics and active ingredients.However,there is still a lack of rapid methods that can be applied to the identification of the four origins.In this study,comparative analysis of the four chloroplast genomes was performed,and they showed low diversity(Pi=0.00267),three variation hotspots regions(rbcL-accD,rps12-ndhF and rps12-trnN-trnG)were identified as potentially molecular marker of highly informative.Meanwhile,the most obvious difference in SSR comparative analysis is reverse and complement repeats were only identified in L.confusa and L.hypoglauca,respectively.Lastly,the phylogenetic tree showed that L.confusa is more closely related to L.fulvotnetosa,while L.macranthoides is closer to L.hypoglauca.This study systematically revealed the differences among the four chloroplast genomes,and it provides valuable genetic information for identifying the origin of LF.

Analysis of the chloroplast genomes of four Pinus species in Northeast China:Insights into hybrid speciation and identification of DNA molecular markers

Species of the Pinus genus provide a classical model for studying hybrid speciation.Although studies on two narrowly distributed species(P inus funebris and P.takahasii)concluded that they originated from two widespread species(P.sylvestris and P.densiflora)via hybrid speciation,the conclusion was based on a low number of informative restriction sites.In this study,we analyzed the sequences of four Pinus chloroplast(cp)genomes(P.sylvestris,P.densiflora,P.funebris and P.takahasii)to clarify whether hybrid speciation was involved.The complete cp-genomes of Pinus species ranged in size from 119,865 to 119,890 bp,similar to other Pinus species.Phylogenetic results based on the whole cp-genomes showed P.sylvestris clustered with P.funebris and P.takahasii,which suggested that P.sylvestris was the paternal parent in hybridization events.In an analysis of simple sequence repeats(SSRs),we detected a total of 69 SSRs repeats among the four Pinus cp-genomes;most were A or T bases.In addition,we identified divergent hotspot regions among the four Pinus cp-genomes(trnE-clpP,cemA-ycf4,petD-rpoA,psbD-trnT,and trnN-chlL),in P.sylvestris(psbD-trnT,trnN-chlL,psbB and rps8)and in P.densiflora(trnE-clpP,petD-rpoA,ycf3 intron,psbD-trnT,and trnN-chlL).The genome information found in this study provides new insights into hybrid speciation in P inus and contributes to a better understanding of the phylogenetic relationships within the Pinus genus.

A Reevaluation of the Status of Lilium nepalense Based on Complete Chloroplast Genome Sequences

Lilium nepalense D. Don is an ornamental plant and exhibits high morphological variation across its distribution range in China. There is incongruence between different data sets for the status of it in Lilium. In this study, we reported a complete chloroplast genome of L. nepalense sampled in Hengduan Mountains, China. The whole chloroplast genome possessed a total length of 152,206 bp with typical circular structure, and contained a large single copy (LSC) of 81,854 bp and a small single copy (SSC) of 17,563 bp, which were separated by a pair of inverted repeats (IRa/IRb) of 26,399 bp. The average GC content among the whole chloroplast genome sequence was 37%, and the GC content in LSC, SSC, IRs regions were 34.8%, 30.6%, and 42.5%, respectively. There were 135 genes detected from the whole chloroplast genome sequence, including 89 protein-coding genes, 38 tRNAs, and 8 rRNAs. Phylogenetic results using maximum likelihood and Bayesian methods showed congruent results that L. nepalense together with the other two L. nepalense samples collected from different habitats formed a single branch, indicating a close relationship of L. nepalense with L. taliense belonging to the section Sinomartagon. This newly characterized chloroplast genome will provide essential data for the further population genetics research of L. nepalense.

Comparative Analyses and Phylogenetic Relationships between Cryptomeria fortunei and Related Species Based on Complete Chloroplast Genomes

Cryptomeria fortunei(Chinese cedar)is a highly adaptable woody species and one of the main forest plantation trees in subtropical high-altitude areas in China.However,there are few studies on its chloroplast(cp)genome.In this study,the complete cp genome of C.fortunei was sequenced and evaluated via comparative analyses with those of related species(formerly the Taxodiaceae)in Cupressaceae.The C.fortunei cp genome was 131,580 bp in length,and the GC content of the whole genome was 35.38%.It lost one relevant large inverted repeat and contained 114 unique genes,including 82 protein-coding genes,28 tRNAs and 4 rRNAs.The relative synonymous codon usage(RSCU)of codons ending with A/U was more than twice that of codons ending with G/C.Thirty long repeat structures(LRSs)and 213 simple sequence repeat(SSR)loci were detected in the C.fortunei cp genome.Comparative analyses of 10 cp genomes revealed that substantial rearrangements occurred in the gene organization.Additionally,6 cp hotspot regions(trnS-GGA,ycf1,trnP-GGG,trnC-GCA,psbZ and accD)were identified,and 4 genes(petL,psbM,rpl22 and psaM)had likely underwent positive selection.Phylogenetic analysis showed that Cupressaceae,Taxaceae and Cephalotaxaceae clustered to form a clade and that C.fortunei was most closely related to C.japonica(Japanese cedar),C.japonica cv.Wogon Hort and Taxodium distichum(baldcypress).These results provide references for future studies of population genetics,phylogenetic status and molecular markers among Cupressaceae species and for the cultivation of improved varieties.

The Chloroplast Genome of Cerasus Campanulata Diverges from Other Prunoideae Genomes

Cerasus Campanulata is one of several species belonging to the Prunoideae focke,a subfamily of the flowering plant Rosaceae.We investigated the details of its chloroplast genome which may reveal its genus independent of morphological determination.Here,we determined the complete chloroplast(cp)genome sequence of C.campanulata and performed sequence analysis to reveal the presence of 18 forward repeats,20 palindrome repeats,2 complement repeats,4 reverse repeats and 93 simple sequence repeats(SSRs).We additionally performed a comparative study of C.campanulata and seven other Prunoideae focke species.Then,maximum parsimony(MP)and maximum likelihood(ML)phylogenetic analyses were carried out in the little part of Rosaceae,respectively.The results strongly support a position of C.campanulata as a member of the Cerasus in the Rosaceae family.Moreover,the complete cp genome can be used for plant phylogenetic and evolutionary studies that will provide insight into the degree of gene conservation.

Genetic diversity of food-medicinal Lycium spp.in China:Insights from chloroplast genome

Objective:Goji(fruits of Lycium spp.)is commonly consumed as food and medicine.The increasing market demand for goji has led to its wide cultivation and broad breeding,which might cause loss of genetic diversity.This study aims to uncover the genetic diversity of the cultivated and wild Lycium.Methods:The chloroplast genome(CPG)of 34 accessions of Chinese food-medicinal Lycium spp.,including the popular cultivars and their wild relatives,was re-sequenced and assembled,based on which the genetic diversity was evaluated.Results:Sequence structural comparison shows that CPG is comparatively conserved within species.Phylogenetic analysis indicates that CPG is sufficient for the discrimination of Lycium species;combined with nuclear ribosomal internal transcribed spacer(Nr ITS)sequences,materials with mixed genetic backgrounds can be identified.Nucleotide diversity analysis reveals that the modern cultivars are probably with a common maternal parent,while the wild accessions are with higher level of genetic diversity.Conclusion:For the first time this study reveals the intraspecies genetic diversity of Lycium spp.using CPG,highlighting the urgent conservation demand of wild genetic resources of Lycium.Our study also demonstrates that CPG provides crucial evidence for identification of Lycium species with mixed genetic backgrounds and highlights the importance of the wild relatives in genetic diversity conservation.This CPG-based technology will contribute to the sustainable development of medicinal plants broadly.