Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences from Aldama (Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

Aldama (Heliantheae, Asteraceae) is a diverse genus in the sunflower family. To date, nearly 200 Asteraceae chloroplast genomes have been sequenced, but the plastomes of Aldama remain undescribed. Plastomes in Asteraceae usually show little sequence divergence, consequently, our hypothesis is that species of Aldama will be overall conserved. In this study, we newly sequenced 36 plastomes of Aldama and of five species belonging to other Heliantheae genera selected as outgroups (i.e., Dimerostemma asperatum, Helianthus tuberosus, Iostephane heterophylla, Pappobolus lanatus var. lanatus, and Tithonia diversifolia). We analyzed the structure and gene content of the assembled plastomes and performed comparative analyses within Aldama and with other closely related genera. As expected, Aldama plastomes are very conserved, with the overall gene content and orientation being similar in all studied species. The length of the plastome is also consistent and the junction between regions usually contain the same genes and have similar lengths. A large ∼20 kb and a small ∼3 kb inversion were detected in the Large Single Copy (LSC) regions of all assembled plastomes, similarly to other Asteraceae species. The nucleotide diversity is very low, with only 1,509 variable sites in 127,466 bp (i.e., 1.18% of the sites in the alignment of 36 Aldama plastomes, with one of the IRs removed, is variable). Only one gene, rbcL, shows signatures of positive selection. The plastomes of the selected outgroups feature a similar gene content and structure compared to Aldama and also present the two inversions in the LSC region. Deletions of different lengths were observed in the gene ycf2. Multiple SSRs were identified for the sequenced Aldama and outgroups. The phylogenetic analysis shows that Aldama is not monophyletic due to the position of the Mexican species A. dentata. All Brazilian species form a strongly supported clade. Our results bring new understandings into the evolution and diversity of plastomes at the species level.

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The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions

BMC Plant Biology ◽

10.1186/s12870-021-03053-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yan-Yan Guo ◽

Jia-Xing Yang ◽

Ming-Zhu Bai ◽

Guo-Qiang Zhang ◽

Zhong-Jian Liu

Keyword(s):

Gene Order ◽

Inverted Repeat ◽

Single Copy ◽

Gene Content ◽

Comparative Genomic ◽

Substitution Rates ◽

Plastome Evolution ◽

Chloroplast Genomes ◽

Ideal System ◽

Small Single Copy

Abstract Background Paphiopedilum is the largest genus of slipper orchids. Previous studies showed that the phylogenetic relationships of this genus are not well resolved, and sparse taxon sampling documented inverted repeat (IR) expansion and small single copy (SSC) contraction of the chloroplast genomes of Paphiopedilum. Results Here, we sequenced, assembled, and annotated 77 plastomes of Paphiopedilum species (size range of 152,130 – 164,092 bp). The phylogeny based on the plastome resolved the relationships of the genus except for the phylogenetic position of two unstable species. We used phylogenetic and comparative genomic approaches to elucidate the plastome evolution of Paphiopedilum. The plastomes of Paphiopedilum have a conserved genome structure and gene content except in the SSC region. The large single copy/inverted repeat (LSC/IR) boundaries are relatively stable, while the boundaries of the inverted repeat and small single copy region (IR/SSC) varied among species. Corresponding to the IR/SSC boundary shifts, the chloroplast genomes of the genus experienced IR expansion and SSC contraction. The IR region incorporated one to six genes of the SSC region. Unexpectedly, great variation in the size, gene order, and gene content of the SSC regions was found, especially in the subg. Parvisepalum. Furthermore, Paphiopedilum provides evidence for the ongoing degradation of the ndh genes in the photoautotrophic plants. The estimated substitution rates of the protein coding genes show accelerated rates of evolution in clpP, psbH, and psbZ. Genes transferred to the IR region due to the boundary shift also have higher substitution rates. Conclusions We found IR expansion and SSC contraction in the chloroplast genomes of Paphiopedilum with dense sampling, and the genus shows variation in the size, gene order, and gene content of the SSC region. This genus provides an ideal system to investigate the dynamics of plastome evolution.

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Comparative Analyses of Chloroplast Genomes of Cucurbitaceae Species: Lights into Selective Pressures and Phylogenetic Relationships

Molecules ◽

10.3390/molecules23092165 ◽

2018 ◽

Vol 23 (9) ◽

pp. 2165 ◽

Cited By ~ 3

Author(s):

Xiao Zhang ◽

Tao Zhou ◽

Jia Yang ◽

Jingjing Sun ◽

Miaomiao Ju ◽

...

Keyword(s):

Chloroplast Genome ◽

Sequence Divergence ◽

Economic Plant ◽

Genome Sequences ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Phylogenetic Studies ◽

Chloroplast Genomes ◽

Representative Species ◽

Translation Initiation Codon

Cucurbitaceae is the fourth most important economic plant family with creeping herbaceous species mainly distributed in tropical and subtropical regions. Here, we described and compared the complete chloroplast genome sequences of ten representative species from Cucurbitaceae. The lengths of the ten complete chloroplast genomes ranged from 155,293 bp (C. sativus) to 158,844 bp (M. charantia), and they shared the most common genomic features. 618 repeats of three categories and 813 microsatellites were found. Sequence divergence analysis showed that the coding and IR regions were highly conserved. Three protein-coding genes (accD, clpP, and matK) were under selection and their coding proteins often have functions in chloroplast protein synthesis, gene transcription, energy transformation, and plant development. An unconventional translation initiation codon of psbL gene was found and provided evidence for RNA editing. Applying BI and ML methods, phylogenetic analysis strongly supported the position of Gomphogyne, Hemsleya, and Gynostemma as the relatively original lineage in Cucurbitaceae. This study suggested that the complete chloroplast genome sequences were useful for phylogenetic studies. It would also determine potential molecular markers and candidate DNA barcodes for coming studies and enrich the valuable complete chloroplast genome resources of Cucurbitaceae.

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Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots

BMC Evolutionary Biology ◽

10.1186/1471-2148-8-36 ◽

2008 ◽

Vol 8 (1) ◽

pp. 36 ◽

Cited By ~ 175

Author(s):

Rui-Jiang Wang ◽

Chiao-Lei Cheng ◽

Ching-Chun Chang ◽

Chun-Lin Wu ◽

Tian-Mu Su ◽

...

Keyword(s):

Inverted Repeat ◽

Single Copy ◽

Large Single Copy ◽

Chloroplast Genomes

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RFPlasmid: Predicting plasmid sequences from short read assembly data using machine learning

10.1101/2020.07.31.230631 ◽

2020 ◽

Cited By ~ 1

Author(s):

Linda van der Graaf van Bloois ◽

Jaap A. Wagenaar ◽

Aldert L. Zomer

Keyword(s):

Bacterial Species ◽

Draft Genome ◽

Single Copy ◽

Chromosomal Marker ◽

Web Interface ◽

Large Single Copy ◽

Genome Sequences ◽

Multiple Features ◽

E Coli ◽

Marker Proteins

AbstractAntimicrobial resistance (AMR) genes in bacteria are often carried on plasmids and these plasmids can transfer AMR genes between bacteria. For molecular epidemiology purposes and risk assessment, it is important to know if the genes are located on highly transferable plasmids or in the more stable chromosomes. However, draft whole genome sequences are fragmented, making it difficult to discriminate plasmid and chromosomal contigs. Current methods that predict plasmid sequences from draft genome sequences rely on single features, like k-mer composition, circularity of the DNA molecule, copy number or sequence identity to plasmid replication genes, all of which have their drawbacks, especially when faced with large single copy plasmids, which often carry resistance genes. With our newly developed prediction tool RFPlasmid, we use a combination of multiple features, including k-mer composition and databases with plasmid and chromosomal marker proteins, to predict if the likely source of a contig is plasmid or chromosomal. The tool RFPlasmid supports models for 17 different bacterial species, including Campylobacter, E. coli, and Salmonella, and has a species agnostic model for metagenomic assemblies or unsupported organisms. RFPlasmid is available both as standalone tool and via web interface.

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Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses

PeerJ ◽

10.7717/peerj.6032 ◽

2018 ◽

Vol 6 ◽

pp. e6032 ◽

Cited By ~ 12

Author(s):

Zhenyu Zhao ◽

Xin Wang ◽

Yi Yu ◽

Subo Yuan ◽

Dan Jiang ◽

...

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Analyses ◽

Single Copy ◽

Genome Sequences ◽

Complete Chloroplast Genome ◽

Genomic Resources ◽

Chloroplast Genomes ◽

The Family ◽

Small Single Copy

Dioscorea L., the largest genus of the family Dioscoreaceae with over 600 species, is not only an important food but also a medicinal plant. The identification and classification of Dioscorea L. is a rather difficult task. In this study, we sequenced five Dioscorea chloroplast genomes, and analyzed with four other chloroplast genomes of Dioscorea species from GenBank. The Dioscorea chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted repeats separated by a large single-copy region, and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined, and the rapidly evolving chloroplast genome regions (trnK-trnQ, trnS-trnG, trnC-petN, trnE-trnT, petG-trnW-trnP, ndhF, trnL-rpl32, and ycf1) were detected. Phylogenetic relationships of Dioscorea inferred from chloroplast genomes obtained high support even in shortest internodes. Thus, chloroplast genome sequences provide potential molecular markers and genomic resources for phylogeny and species identification.

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Complete Chloroplast Genome Sequences of Kaempferia Galanga and Kaempferia Elegans: Molecular Structures and Comparative Analysis

Molecules ◽

10.3390/molecules24030474 ◽

2019 ◽

Vol 24 (3) ◽

pp. 474 ◽

Cited By ~ 13

Author(s):

Dong-Mei Li ◽

Chao-Yi Zhao ◽

Xiao-Fei Liu

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

Species Identification ◽

Single Copy ◽

Rrna Genes ◽

Genome Sequences ◽

Variable Regions ◽

Complete Chloroplast Genome ◽

Kaempferia Galanga ◽

Chloroplast Genomes

Kaempferia galanga and Kaempferia elegans, which belong to the genus Kaempferia family Zingiberaceae, are used as valuable herbal medicine and ornamental plants, respectively. The chloroplast genomes have been used for molecular markers, species identification and phylogenetic studies. In this study, the complete chloroplast genome sequences of K. galanga and K. elegans are reported. Results show that the complete chloroplast genome of K. galanga is 163,811 bp long, having a quadripartite structure with large single copy (LSC) of 88,405 bp and a small single copy (SSC) of 15,812 bp separated by inverted repeats (IRs) of 29,797 bp. Similarly, the complete chloroplast genome of K. elegans is 163,555 bp long, having a quadripartite structure in which IRs of 29,773 bp length separates 88,020 bp of LSC and 15,989 bp of SSC. A total of 111 genes in K. galanga and 113 genes in K. elegans comprised 79 protein-coding genes and 4 ribosomal RNA (rRNA) genes, as well as 28 and 30 transfer RNA (tRNA) genes in K. galanga and K. elegans, respectively. The gene order, GC content and orientation of the two Kaempferia chloroplast genomes exhibited high similarity. The location and distribution of simple sequence repeats (SSRs) and long repeat sequences were determined. Eight highly variable regions between the two Kaempferia species were identified and 643 mutation events, including 536 single-nucleotide polymorphisms (SNPs) and 107 insertion/deletions (indels), were accurately located. Sequence divergences of the whole chloroplast genomes were calculated among related Zingiberaceae species. The phylogenetic analysis based on SNPs among eleven species strongly supported that K. galanga and K. elegans formed a cluster within Zingiberaceae. This study identified the unique characteristics of the entire K. galanga and K. elegans chloroplast genomes that contribute to our understanding of the chloroplast DNA evolution within Zingiberaceae species. It provides valuable information for phylogenetic analysis and species identification within genus Kaempferia.

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Stable and widespread structural heteroplasmy in chloroplast genomes revealed by a new long-read quantification method

10.1101/692798 ◽

2019 ◽

Author(s):

Weiwen Wang ◽

Robert Lanfear

Keyword(s):

Chloroplast Genome ◽

Single Copy ◽

Land Plant ◽

Inverted Repeats ◽

Equal Frequency ◽

Large Single Copy ◽

Chloroplast Genomes ◽

Long Read ◽

Small Single Copy ◽

Large Single Copy Region

AbstractThe chloroplast genome usually has a quadripartite structure consisting of a large single copy region and a small single copy region separated by two long inverted repeats. It has been known for some time that a single cell may contain at least two structural haplotypes of this structure, which differ in the relative orientation of the single copy regions. However, the methods required to detect and measure the abundance of the structural haplotypes are labour-intensive, and this phenomenon remains understudied. Here we develop a new method, Cp-hap, to detect all possible structural haplotypes of chloroplast genomes of quadripartite structure using long-read sequencing data. We use this method to conduct a systematic analysis and quantification of chloroplast structural haplotypes in 61 land plant species across 19 orders of Angiosperms, Gymnosperms and Pteridophytes. Our results show that there are two chloroplast structural haplotypes which occur with equal frequency in most land plant individuals. Nevertheless, species whose chloroplast genomes lack inverted repeats or have short inverted repeats have just a single structural haplotype. We also show that the relative abundance of the two structural haplotypes remains constant across multiple samples from a single individual plant, suggesting that the process which maintains equal frequency of the two haplotypes operates rapidly, consistent with the hypothesis that flip-flop recombination mediates chloroplast structural heteroplasmy. Our results suggest that previous claims of differences in chloroplast genome structure between species may need to be revisited.Significance StatementChloroplast genome consists of a large single copy region, a small single copy region, and two inverted repeats. Some decades ago, a discovery showed that there are two types chloroplast genome in some plants, which differ the way that the four regions are put together. However, this phenomenon has been shown in just a small number of species, and many open questions remain. Here, we develop a fast method to measure the chloroplast genome structures, based on long-reads. We show that almost all plants we analysed contain two possible genome structures, while a few plants contain only one structure. Our findings hint at the causes of the phenomenon, and provide a convenient new method with which to make rapid progress.

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The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography

PeerJ ◽

10.7717/peerj.6320 ◽

2019 ◽

Vol 7 ◽

pp. e6320 ◽

Cited By ~ 5

Author(s):

Zhen Yang ◽

Guixi Wang ◽

Qinghua Ma ◽

Wenxu Ma ◽

Lisong Liang ◽

...

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Relationships ◽

Single Copy ◽

Molecular Dating ◽

Phylogenetic Position ◽

Comparative Genomic ◽

Genome Sequences ◽

Genome Variation ◽

Genome Data ◽

Chloroplast Genomes

Background Previous phylogenetic conclusions on the family Betulaceae were based on either morphological characters or traditional single loci, which may indicate some limitations. The chloroplast genome contains rich polymorphism information, which is very suitable for phylogenetic studies. Thus, we sequenced the chloroplast genome sequences of three Betulaceae species and performed multiple analyses to investigate the genome variation, resolve the phylogenetic relationships, and clarify the divergence history. Methods Chloroplast genomes were sequenced using the high-throughput sequencing. A comparative genomic analysis was conducted to examine the global genome variation and screen the hotspots. Three chloroplast partitions were used to reconstruct the phylogenetic relationships using Maximum Likelihood and Bayesian Inference approaches. Then, molecular dating and biogeographic inferences were conducted based on the whole chloroplast genome data. Results Betulaceae chloroplast genomes consisted of a small single-copy region and a large single copy region, and two copies of inverted repeat regions. Nine hotspots can be used as potential DNA barcodes for species delimitation. Phylogenies strongly supported the division of Betulaceae into two subfamilies: Coryloideae and Betuloideae. The phylogenetic position of Ostryopsis davidiana was controversial among different datasets. The divergence time between subfamily Coryloideae and Betuloideae was about 70.49 Mya, and all six extant genera were inferred to have diverged fully by the middle Oligocene. Betulaceae ancestors were probably originated from the ancient Laurasia. Discussions This research elucidates the potential of chloroplast genome sequences in the application of developing molecular markers, studying evolutionary relationships and historical dynamic of Betulaceae.It also reveals the advantages of using chloroplast genome data to illuminate those phylogenies that have not been well solved yet by traditional approaches in other plants.

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Species Identification of Oaks (Quercus L., Fagaceae) from Gene to Genome

International Journal of Molecular Sciences ◽

10.3390/ijms20235940 ◽

2019 ◽

Vol 20 (23) ◽

pp. 5940

Author(s):

Xinbo Pang ◽

Hongshan Liu ◽

Suran Wu ◽

Yangchen Yuan ◽

Haijun Li ◽

...

Keyword(s):

Chloroplast Genome ◽

Species Identification ◽

Genome Sequence ◽

Dna Barcode ◽

Single Copy ◽

Genome Sequences ◽

Complete Chloroplast Genome ◽

Chloroplast Genomes ◽

Quercus Species ◽

Chloroplast Genome Sequence

Species identification of oaks (Quercus) is always a challenge because many species exhibit variable phenotypes that overlap with other species. Oaks are notorious for interspecific hybridization and introgression, and complex speciation patterns involving incomplete lineage sorting. Therefore, accurately identifying Quercus species barcodes has been unsuccessful. In this study, we used chloroplast genome sequence data to identify molecular markers for oak species identification. Using next generation sequencing methods, we sequenced 14 chloroplast genomes of Quercus species in this study and added 10 additional chloroplast genome sequences from GenBank to develop a DNA barcode for oaks. Chloroplast genome sequence divergence was low. We identified four mutation hotspots as candidate Quercus DNA barcodes; two intergenic regions (matK-trnK-rps16 and trnR-atpA) were located in the large single copy region, and two coding regions (ndhF and ycf1b) were located in the small single copy region. The standard plant DNA barcode (rbcL and matK) had lower variability than that of the newly identified markers. Our data provide complete chloroplast genome sequences that improve the phylogenetic resolution and species level discrimination of Quercus. This study demonstrates that the complete chloroplast genome can substantially increase species discriminatory power and resolve phylogenetic relationships in plants.

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Chloroplast Genomes and Comparative Analyses among Thirteen Taxa within Myrsinaceae s.str. Clade (Myrsinoideae, Primulaceae)

International Journal of Molecular Sciences ◽

10.3390/ijms20184534 ◽

2019 ◽

Vol 20 (18) ◽

pp. 4534 ◽

Cited By ~ 1

Author(s):

Xiaokai Yan ◽

Tongjian Liu ◽

Xun Yuan ◽

Yuan Xu ◽

Haifei Yan ◽

...

Keyword(s):

Nucleotide Diversity ◽

Gene Evolution ◽

Phylogenetic Reconstruction ◽

Single Copy ◽

Synonymous Substitution ◽

Chloroplast Genomes ◽

Ssr Loci ◽

Synonymous Substitution Rates ◽

Large Single Copy Region ◽

Simple Sequence

The Myrsinaceae s.str. clade is a tropical woody representative in Myrsinoideae of Primulaceae and has ca. 1300 species. The generic limits and alignments of this clade are unclear due to the limited number of genetic markers and/or taxon samplings in previous studies. Here, the chloroplast (cp) genomes of 13 taxa within the Myrsinaceae s.str. clade are sequenced and characterized. These cp genomes are typical quadripartite circle molecules and are highly conserved in size and gene content. Three pseudogenes are identified, of which ycf15 is totally absent from five taxa. Noncoding and large single copy region (LSC) exhibit higher levels of nucleotide diversity (Pi) than other regions. A total of ten hotspot fragments and 796 chloroplast simple sequence repeats (SSR) loci are found across all cp genomes. The results of phylogenetic analysis support the notion that the monophyletic Myrsinaceae s.str. clade has two subclades. Non-synonymous substitution rates (dN) are higher in housekeeping (HK) genes than photosynthetic (PS) genes, but both groups have a nearly identical synonymous substitution rate (dS). The results indicate that the PS genes are under stronger functional constraints compared with the HK genes. Overall, the study provides hypervariable molecular markers for phylogenetic reconstruction and contributes to a better understanding of plastid gene evolution in Myrsinaceae s.str. clade.

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