Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in Pogostemon (Lamiaceae)

Pogostemon Desf., the largest genus of the tribe Pogostemoneae (Lamiaceae), consists of ca. 80 species distributed mainly from South and Southeast Asia to China. The genus contains many patchouli plants, which are of great economic importance but taxonomically difficult. Therefore, it is necessary to characterize more chloroplast (cp) genomes for infrageneric phylogeny analyses and species identification of Pogostemon, especially for patchouli plants. In this study, we newly generated four cp genomes for three patchouli plants (i.e., Pogostemon plectranthoides Desf., P. septentrionalis C. Y. Wu et Y. C. Huang, and two cultivars of P. cablin (Blanoco) Benth.). Comparison of all samples (including online available cp genomes of P. yatabeanus (Makino) Press and P. stellatus (Lour.) Kuntze) suggested that Pogostemon cp genomes are highly conserved in terms of genome size and gene content, with a typical quadripartite circle structure. Interspecific divergence of cp genomes has been maintained at a relatively low level, though seven divergence hotspot regions were identified by stepwise window analysis. The nucleotide diversity (Pi) value was correlated significantly with gap proportion (indels), but significantly negative with GC content. Our phylogenetic analyses based on 80 protein-coding genes yielded high-resolution backbone topologies for the Lamiaceae and Pogostemon. For the overall mean substitution rates, the synonymous (dS) and nonsynonymous (dN) substitution rate values of protein-coding genes varied approximately threefold, while the dN values among different functional gene groups showed a wider variation range. Overall, the cp genomes of Pogostemon will be useful for phylogenetic reconstruction, species delimitation and identification in the future.

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Characterization of the complete chloroplast genomes of five Populus species from the western Sichuan plateau, southwest China: comparative and phylogenetic analyses

PeerJ ◽

10.7717/peerj.6386 ◽

2019 ◽

Vol 7 ◽

pp. e6386 ◽

Cited By ~ 6

Author(s):

Dan Zong ◽

Anpei Zhou ◽

Yao Zhang ◽

Xinlian Zou ◽

Dan Li ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Molecular Genetic ◽

Gc Content ◽

Rrna Genes ◽

Trna Genes ◽

Nucleotide Substitutions ◽

Protein Coding ◽

Western Sichuan ◽

Protein Coding Genes ◽

Chloroplast Genomes

Species of the genus Populus, which is widely distributed in the northern hemisphere from subtropical to boreal forests, are among the most commercially exploited groups of forest trees. In this study, the complete chloroplast genomes of five Populus species (Populus cathayana, P. kangdingensis, P. pseudoglauca, P. schneideri, and P. xiangchengensis) were compared. The chloroplast genomes of the five Populus species are very similar. The total chloroplast genome sequence lengths for the five plastomes were 156,789, 156,523, 156,512, 156,513, and 156,465 bp, respectively. A total of 130 genes were identified in each genome, including 85 protein-coding genes, 37 tRNA genes and eight rRNA genes. Seven genes were duplicated in the protein-coding genes, whereas 11 genes were duplicated in the RNA genes. The GC content was 36.7% for all plastomes. We analyzed nucleotide substitutions, small inversions, simple sequence repeats and long repeats in the chloroplast genomes and found nine divergence hotspots (ccsA+ccsA-ndhD, ndhC-trnV, psbZ-trnfM, trnG-atpA, trnL-ndhJ, trnR-trnN, ycf4-cemA, ycf1, and trnR-trnN), which could be useful molecular genetic markers for future population genetic and phylogenetic studies. We also observed that two genes (rpoC2 and rbcL) were subject to positive selection. Phylogenetic analysis based on whole cp genomes showed that P. schneideri had a close relationship with P. kangdingensis and P. pseudoglauca, while P. xiangchengensis was a sister to P. cathayana.

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Insights into phylogenetic relationships and genome evolution of subfamily Commelinoideae (Commelinaceae Mirb.) inferred from complete chloroplast genomes

BMC Genomics ◽

10.1186/s12864-021-07541-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Joonhyung Jung ◽

Changkyun Kim ◽

Joo-Hwan Kim

Keyword(s):

Nucleotide Diversity ◽

Structural Variations ◽

Protein Coding ◽

Protein Coding Genes ◽

Chloroplast Protein ◽

Genome Data ◽

Plastid Genomes ◽

Chloroplast Genomes ◽

Current Classification

Abstract Background Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Currently, many researchers have been using complete chloroplast genome data for inferring the evolution of land plants. In this study, we completed 15 new plastid genome sequences of subfamily Commelinoideae using the Mi-seq platform. We utilized genome data to reveal the structural variations and reconstruct the problematic positions of genera for the first time. Results All examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15), and the former two might be a synapomorphy within Commelinales. Only four species in tribe Commelineae presented IR expansion, which affected duplication of the rpl22 gene. We identified inversions that range from approximately 3 to 15 kb in four taxa (Amischotolype, Belosynapsis, Murdannia, and Streptolirion). The phylogenetic analysis using 77 chloroplast protein-coding genes with maximum parsimony, maximum likelihood, and Bayesian inference suggests that Palisota is most closely related to tribe Commelineae, supported by high support values. This result differs significantly from the current classification of Commelinaceae. Also, we resolved the unclear position of Streptoliriinae and the monophyly of Dichorisandrinae. Among the ten CDS (ndhH, rpoC2, ndhA, rps3, ndhG, ndhD, ccsA, ndhF, matK, and ycf1), which have high nucleotide diversity values (Pi > 0.045) and over 500 bp length, four CDS (ndhH, rpoC2, matK, and ycf1) show that they are congruent with the topology derived from 77 chloroplast protein-coding genes. Conclusions In this study, we provide detailed information on the 15 complete plastid genomes of Commelinoideae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used to infer the family evolutionary history. Also, further research is needed to revise the position of Palisota in the current classification of Commelinaceae.

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Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes

Genes ◽

10.3390/genes11010115 ◽

2020 ◽

Vol 11 (1) ◽

pp. 115

Author(s):

Yuxin Hu ◽

Weiyue Xing ◽

Zhengyu Hu ◽

Guoxiang Liu

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Genome ◽

Phylogenetic Relationship ◽

Phylogenetic Analyses ◽

Mitochondrial Protein ◽

Substitution Rates ◽

Protein Coding ◽

Protein Coding Genes ◽

Chloroplast Genomes ◽

Volvocine Algae

We sequenced the mitochondrial genome of six colonial volvocine algae, namely: Pandorina morum, Pandorina colemaniae, Volvulina compacta, Colemanosphaera angeleri, Colemanosphaera charkowiensi, and Yamagishiella unicocca. Previous studies have typically reconstructed the phylogenetic relationship between colonial volvocine algae based on chloroplast or nuclear genes. Here, we explore the validity of phylogenetic analysis based on mitochondrial protein-coding genes. We found phylogenetic incongruence of the genera Yamagishiella and Colemanosphaera. In Yamagishiella, the stochastic error and linkage group formed by the mitochondrial protein-coding genes prevent phylogenetic analyses from reflecting the true relationship. In Colemanosphaera, a different reconstruction approach revealed a different phylogenetic relationship. This incongruence may be because of the influence of biological factors, such as incomplete lineage sorting or horizontal gene transfer. We also analyzed the substitution rates in the mitochondrial and chloroplast genomes between colonial volvocine algae. Our results showed that all volvocine species showed significantly higher substitution rates for the mitochondrial genome compared with the chloroplast genome. The nonsynonymous substitution (dN)/synonymous substitution (dS) ratio is similar in the genomes of both organelles in most volvocine species, suggesting that the two counterparts are under a similar selection pressure. We also identified a few chloroplast protein-coding genes that showed high dN/dS ratios in some species, resulting in a significant dN/dS ratio difference between the mitochondrial and chloroplast genomes.

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Comparative Chloroplast Genomes of Four Lycoris Species (Amaryllidaceae) Provides New Insight into Interspecific Relationship and Phylogeny

Biology ◽

10.3390/biology10080715 ◽

2021 ◽

Vol 10 (8) ◽

pp. 715

Author(s):

Fengjiao Zhang ◽

Ning Wang ◽

Guanghao Cheng ◽

Xiaochun Shu ◽

Tao Wang ◽

...

Keyword(s):

Large Scale ◽

Phylogenetic Analyses ◽

Gc Content ◽

Natural Hybridization ◽

Comparative Genomic ◽

Protein Coding ◽

Chloroplast Genomes ◽

A Genome ◽

Cp Genome ◽

Conserved Gene

The genus Lycoris (Amaryllidaceae) consists of about 20 species, which is endemic to East Asia. Although the Lycoris species is of great horticultural and medical importance, challenges in accurate species identification persist due to frequent natural hybridization and large-scale intraspecific variation. In this study, we sequenced chloroplast genomes of four Lycoris species and retrieved seven published chloroplast (cp) genome sequences in this genus for comparative genomic and phylogenetic analyses. The cp genomes of these four newly sequenced species were found to be 158,405–158,498 bp with the same GC content of 37.8%. The structure of the genomes exhibited the typical quadripartite structure with conserved gene order and content. A total of 113 genes (20 duplicated) were identified, including 79 protein-coding genes (PCGs), 30 tRNAs, and 4 rRNAs. Phylogenetic analysis showed that the 11 species were clustered into three main groups, and L. sprengeri locate at the base of Lycoriss. The L. radiata was suggested to be the female donor of the L. incarnata, L. shaanxiensis, and L. squamigera. The L. straminea and L. houdyshelii may be derived from L. anhuiensis, L. chinensis, or L. longituba. These results could not only offer a genome-scale platform for identification and utilization of Lycoris but also provide a phylogenomic framework for future studies in this genus.

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Comparative Analysis of Complete Chloroplast Genome Sequences in Edgeworthia (Thymelaeaceae) and New Insights Into Phylogenetic Relationships

Frontiers in Genetics ◽

10.3389/fgene.2021.643552 ◽

2021 ◽

Vol 12 ◽

Author(s):

Shaojuan Qian ◽

Yonghong Zhang ◽

Shiou Yih Lee

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Analyses ◽

Gc Content ◽

Bootstrap Support ◽

Additional Species ◽

Protein Coding ◽

Chloroplast Genomes ◽

Strong Bootstrap Support ◽

Phylogenetic Evolution ◽

Simple Repeats

The complete chloroplast genomes of three species of Edgeworthia namely, Edgeworthia albiflora, Edgeworthia chrysantha, and Edgeworthia gardneri (Thymelaeaceae), are reported and characterized. The chloroplast genomes displayed a typical quadripartite structure with conserved genome arrangement and specific divergence. The genomes ranged in length from 172,708 to 173,621 bp and displayed similar GC content of 36.5–36.7%. A total of 138–139 genes were predicted, including 92–93 protein-coding, 38 tRNAs and eight rRNAs genes. Variation in the number of short simple repeats and inverted region boundaries of the three cp genomes were observed. A mutational hotspot was detected along the nucleotide sequence from the ndhF to the trnL-UAG genes. The chloroplast genome-based and internal transcribed spacer (ITS)-based phylogenetic analyses using maximum-likelihood (ML) and Bayesian inference (BI) revealed that E. albiflora diverged before E. chrysantha and E. gardneri and placed the Edgeworthia clade at the base of the Eurasian Daphne group with strong bootstrap support. With an effective taxonomic treatment of the species of Edgeworthia, further molecular analyses of their intra- and interspecific genetic variation are inclined to support the treatment of E. albiflora and E. gardneri as two natural groups. The genetic information obtained from this study will provide valuable genomic resources for the identification of additional species and for deducing the phylogenetic evolution of Edgeworthia.

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Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)

BMC Plant Biology ◽

10.1186/s12870-021-03315-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Dong-Mei Li ◽

Jie Li ◽

Dai-Rong Wang ◽

Ye-Chun Xu ◽

Gen-Fa Zhu

Keyword(s):

Molecular Markers ◽

Evolutionary Dynamics ◽

Phylogenetic Analyses ◽

Evolutionary Relationship ◽

Single Copy ◽

Rrna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

Chloroplast Genomes ◽

Usage Patterns

Abstract Background Zingiberoideae is a large and diverse subfamily of the family Zingiberaceae. Four genera in subfamily Zingiberoideae each possess 50 or more species, including Globba (100), Hedychium (> 80), Kaempferia (50) and Zingiber (150). Despite the agricultural, medicinal and horticultural importance of these species, genomic resources and suitable molecular markers for them are currently sparse. Results Here, we have sequenced, assembled and analyzed ten complete chloroplast genomes from nine species of subfamily Zingiberoideae: Globba lancangensis, Globba marantina, Globba multiflora, Globba schomburgkii, Globba schomburgkii var. angustata, Hedychium coccineum, Hedychium neocarneum, Kaempferia rotunda ‘Red Leaf’, Kaempferia rotunda ‘Silver Diamonds’ and Zingiber recurvatum. These ten chloroplast genomes (size range 162,630–163,968 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 87,172–88,632 bp), a small single copy (SSC, 15,393–15,917 bp) and a pair of inverted repeats (IRs, 29,673–29,833 bp). The genomes contain 111–113 different genes, including 79 protein coding genes, 28–30 tRNAs and 4 rRNA genes. The dynamics of the genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats exhibit similarities, with slight differences observed among the ten genomes. Further comparative analysis of seventeen related Zingiberoideae species, 12 divergent hotspots are identified. Positive selection is observed in 14 protein coding genes, including accD, ccsA, ndhA, ndhB, psbJ, rbcL, rpl20, rpoC1, rpoC2, rps12, rps18, ycf1, ycf2 and ycf4. Phylogenetic analyses, based on the complete chloroplast-derived single-nucleotide polymorphism data, strongly support that Globba, Hedychium, and Curcuma I + “the Kaempferia clade” consisting of Curcuma II, Kaempferia and Zingiber, form a nested evolutionary relationship in subfamily Zingiberoideae. Conclusions Our study provides detailed information on ten complete Zingiberoideae chloroplast genomes, representing a valuable resource for future studies that seek to understand the molecular evolutionary dynamics in family Zingiberaceae. The identified divergent hotspots can be used for development of molecular markers for phylogenetic inference and species identification among closely related species within four genera of Globba, Hedychium, Kaempferia and Zingiber in subfamily Zingiberoideae.

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Legionella becoming a mutualist: adaptive processes shaping the genome of symbiont in the louse Polyplax serrata

10.1101/155820 ◽

2017 ◽

Author(s):

Jana Říhová ◽

Eva Nováková ◽

Filip Husník ◽

Václav Hypša

Keyword(s):

Convergent Evolution ◽

Phylogenetic Analyses ◽

Gc Content ◽

The Other ◽

Intracellular Bacteria ◽

Metabolic Function ◽

Protein Coding ◽

Protein Coding Genes ◽

Adaptive Processes ◽

Insect Symbionts

AbstractLegionellaceae are intracellular bacteria known as important pathogens of man. In the environment, they are mainly found in biofilms associated with amoebas. In contrast to another gammaproteobacterial family Enterobacteriaceae which established a broad spectrum of symbioses with many insect taxa, the only instance of legionella-like symbiont has been reported from lice of the genus Polyplax. Here, we sequenced the complete genome of this symbiont and compared its main characteristics to other Legionella species and insect symbionts. Based on rigorous multigene phylogenetic analyses, we confirm this bacterium as a member of the genus Legionella and propose the name Candidatus Legionella polyplacis, sp.n. We show that the genome of Ca. Legionella polyplacis underwent massive degeneration, including considerable size reduction (529.746 bp, 484 protein coding genes) and a severe decrease in GC content (23%). We identify several possible constraints underlying the evolution of this bacterium. On one hand, Ca. Legionella polyplacis and the louse symbionts Riesia and Puchtella experienced convergent evolution, perhaps due to adaptation to similar hosts. On the other hand, some metabolic differences are likely to reflect different phylogenetic positions of the symbionts and hence availability of particular metabolic function in the ancestor. This is exemplified by different arrangements of thiamine metabolism in Ca. Legionella polyplacis and Riesia. Finally, horizontal gene transfer is shown to play a significant role in the adaptive and diversification process. Particularly, we show that Ca. L. polyplacis horizontally acquired a complete biotin operon (bioADCHFB) that likely assisted this bacterium when becoming an obligate mutualist.

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Comparative Chloroplast Genomics of Litsea Lam. (Lauraceae) and Its Phylogenetic Implications

Forests ◽

10.3390/f12060744 ◽

2021 ◽

Vol 12 (6) ◽

pp. 744

Author(s):

Yunyan Zhang ◽

Yongjing Tian ◽

David Y. P. Tng ◽

Jingbo Zhou ◽

Yuntian Zhang ◽

...

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Analyses ◽

Eastern China ◽

Chloroplast Microsatellites ◽

Endangered Tree ◽

Protein Coding ◽

Intergenic Spacers ◽

Chloroplast Genomes ◽

Phylogenetic Implications ◽

Chloroplast Genome Sequence

Litsea Lam. is an ecological and economic important genus of the “core Lauraceae” group in the Lauraceae. The few studies to date on the comparative chloroplast genomics and phylogenomics of Litsea have been conducted as part of other studies on the Lauraceae. Here, we sequenced the whole chloroplast genome sequence of Litsea auriculata, an endangered tree endemic to eastern China, and compared this with previously published chloroplast genome sequences of 11 other Litsea species. The chloroplast genomes of the 12 Litsea species ranged from 152,132 (L. szemaois) to 154,011 bp (L. garrettii) and exhibited a typical quadripartite structure with conserved genome arrangement and content, with length variations in the inverted repeat regions (IRs). No codon usage preferences were detected within the 30 codons used in the chloroplast genomes, indicating a conserved evolution model for the genus. Ten intergenic spacers (psbE–petL, trnH–psbA, petA–psbJ, ndhF–rpl32, ycf4–cemA, rpl32–trnL, ndhG–ndhI, psbC–trnS, trnE–trnT, and psbM–trnD) and five protein coding genes (ndhD, matK, ccsA, ycf1, and ndhF) were identified as divergence hotspot regions and DNA barcodes of Litsea species. In total, 876 chloroplast microsatellites were located within the 12 chloroplast genomes. Phylogenetic analyses conducted using the 51 additional complete chloroplast genomes of “core Lauraceae” species demonstrated that the 12 Litsea species grouped into four sub-clades within the Laurus-Neolitsea clade, and that Litsea is polyphyletic and closely related to the genera Lindera and Laurus. Our phylogeny strongly supported the monophyly of the following three clades (Laurus–Neolitsea, Cinnamomum–Ocotea, and Machilus–Persea) among the above investigated “core Lauraceae” species. Overall, our study highlighted the taxonomic utility of chloroplast genomes in Litsea, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of L. auriculata and other Litsea species.

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Chloroplast genome variation and phylogenetic relationships of Atractylodes species

BMC Genomics ◽

10.1186/s12864-021-07394-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yiheng Wang ◽

Sheng Wang ◽

Yanlei Liu ◽

Qingjun Yuan ◽

Jiahui Sun ◽

...

Keyword(s):

Chloroplast Genome ◽

High Throughput Sequencing ◽

Phylogenetic Analyses ◽

Herbal Medicines ◽

Structural Genomic ◽

Protein Coding ◽

Chloroplast Genomes ◽

Original Plant ◽

Morphological Differences ◽

Rna Genes

Abstract Background Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing. Results The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42–47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Conclusions Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.

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Mitogenome of Alaudala cheleensis (Passeriformes: Alaudidae) and comparative analyses of Sylvioidea mitogenomes

Zootaxa ◽

10.11646/zootaxa.4952.2.7 ◽

2021 ◽

Vol 4952 (2) ◽

pp. 331-353

Author(s):

CHAO YANG ◽

LE ZHAO ◽

QINGXIONG WANG ◽

HAO YUAN ◽

XUEJUAN LI ◽

...

Keyword(s):

Secondary Structure ◽

Gene Order ◽

Phylogenetic Relationships ◽

Gene Rearrangement ◽

Phylogenetic Analyses ◽

Protein Coding ◽

Comparative Analyses ◽

Protein Coding Genes ◽

Basal Position

To gain a better understanding of mitogenome features and phylogenetic relationships in Sylvioidea, a superfamily of Passerida, suborder Passeri, Passeriformes, the whole mitogenome of Alaudala cheleensis Swinhoe (Alaudidae) was sequenced, a comparative mitogenomic analysis of 18 Sylvioidea species was carried out, and finally, a phylogeny was reconstructed based on the mitochondrial dataset. Gene order of the A. cheleensis mitogenome was similar to that of other Sylvioidea species, including the gene rearrangement of cytb-trnT-CR1-trnP-nad6-trnE-remnant CR2-trnF-rrnS. There was slightly higher A+T content than that of G+C in the mitogenome, with an obvious C skew. The ATG codon initiated all protein-coding genes, while six terminating codons were used. The secondary structure of rrnS contained three domains and 47 helices, whereas rrnL included six domains and 60 helices. All tRNAs could be folded into a classic clover-leaf secondary structure except for trnS (AGY). The CR1 could be divided into three domains, including several conserved boxes (C-string, F, E, D, C and B-box, Bird similarity box, CSB1). Comparative analyses within Sylvioidea mitogenomes showed that most mitochondrial features were consistent with that of the A. cheleensis mitogenome. The basal position of the Alaudidae within the Sylvioidea in our phylogenetic analyses is consistent with other recent studies.

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