Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships

The genus Alchemilla L., known for its medicinal and ornamental value, is widely distributed in the Holarctic regions with a few species found in Asia and Africa. Delimitation of species within Alchemilla is difficult due to hybridization, autonomous apomixes, and polyploidy, necessitating efficient molecular-based characterization. Herein, we report the initial complete chloroplast (cp) genomes of Alchemilla. The cp genomes of two African (Afromilla) species Alchemilla pedata and Alchemilla argyrophylla were sequenced, and phylogenetic and comparative analyses were conducted in the family Rosaceae. The cp genomes mapped a typical circular quadripartite structure of lengths 152,438 and 152,427 base pairs (bp) in A. pedata and A. argyrophylla, respectively. Alchemilla cp genomes were composed of a pair of inverted repeat regions (IRa/IRb) of length 25,923 and 25,915 bp, separating the small single copy (SSC) region of 17,980 and 17,981 bp and a large single copy (LSC) region of 82,612 and 82,616 bp in A. pedata and A. argyrophylla, respectively. The cp genomes encoded 114 unique genes including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Additionally, 88 and 95 simple sequence repeats (SSRs) and 37 and 40 tandem repeats were identified in A. pedata and A. argyrophylla, respectively. Significantly, the loss of group II intron in atpF gene in Alchemilla species was detected. Phylogenetic analysis based on 26 whole cp genome sequences and 78 protein-coding gene sequences of 27 Rosaceae species revealed a monophyletic clustering of Alchemilla nested within subfamily Rosoideae. Based on a protein-coding region, negative selective pressure (Ka/Ks < 1) was detected with an average Ka/Ks value of 0.1322 in A. argyrophylla and 0.1418 in A. pedata. The availability of complete cp genome in the genus Alchemilla will contribute to species delineation and further phylogenetic and evolutionary studies in the family Rosaceae.

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Complete Chloroplast Genomes from Sanguisorba: Identity and Variation Among Four Species

Molecules ◽

10.3390/molecules23092137 ◽

2018 ◽

Vol 23 (9) ◽

pp. 2137 ◽

Cited By ~ 6

Author(s):

Xiang-Xiao Meng ◽

Yan-Fang Xian ◽

Li Xiang ◽

Dong Zhang ◽

Yu-Hua Shi ◽

...

Keyword(s):

Gc Content ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Future Studies ◽

Chloroplast Genomes ◽

Close Relationship ◽

Cp Genome ◽

Sanguisorba Officinalis

The genus Sanguisorba, which contains about 30 species around the world and seven species in China, is the source of the medicinal plant Sanguisorba officinalis, which is commonly used as a hemostatic agent as well as to treat burns and scalds. Here we report the complete chloroplast (cp) genome sequences of four Sanguisorba species (S. officinalis, S. filiformis, S. stipulata, and S. tenuifolia var. alba). These four Sanguisorba cp genomes exhibit typical quadripartite and circular structures, and are 154,282 to 155,479 bp in length, consisting of large single-copy regions (LSC; 84,405–85,557 bp), small single-copy regions (SSC; 18,550–18,768 bp), and a pair of inverted repeats (IRs; 25,576–25,615 bp). The average GC content was ~37.24%. The four Sanguisorba cp genomes harbored 112 different genes arranged in the same order; these identical sections include 78 protein-coding genes, 30 tRNA genes, and four rRNA genes, if duplicated genes in IR regions are counted only once. A total of 39–53 long repeats and 79–91 simple sequence repeats (SSRs) were identified in the four Sanguisorba cp genomes, which provides opportunities for future studies of the population genetics of Sanguisorba medicinal plants. A phylogenetic analysis using the maximum parsimony (MP) method strongly supports a close relationship between S. officinalis and S. tenuifolia var. alba, followed by S. stipulata, and finally S. filiformis. The availability of these cp genomes provides valuable genetic information for future studies of Sanguisorba identification and provides insights into the evolution of the genus Sanguisorba.

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Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae

Frontiers in Plant Science ◽

10.3389/fpls.2020.593984 ◽

2021 ◽

Vol 11 ◽

Author(s):

Yongtan Li ◽

Yan Dong ◽

Yichao Liu ◽

Xiaoyue Yu ◽

Minsheng Yang ◽

...

Keyword(s):

Positive Selection ◽

Chloroplast Genome ◽

Gc Content ◽

Single Copy ◽

Rrna Genes ◽

Evolutionary Relationships ◽

Trna Genes ◽

Protein Coding ◽

Chloroplast Genomes ◽

Cp Genome

In this study, we assembled and annotated the chloroplast (cp) genome of the Euonymus species Euonymus fortunei, Euonymus phellomanus, and Euonymus maackii, and performed a series of analyses to investigate gene structure, GC content, sequence alignment, and nucleic acid diversity, with the objectives of identifying positive selection genes and understanding evolutionary relationships. The results indicated that the Euonymus cp genome was 156,860–157,611bp in length and exhibited a typical circular tetrad structure. Similar to the majority of angiosperm chloroplast genomes, the results yielded a large single-copy region (LSC) (85,826–86,299bp) and a small single-copy region (SSC) (18,319–18,536bp), separated by a pair of sequences (IRA and IRB; 26,341–26,700bp) with the same encoding but in opposite directions. The chloroplast genome was annotated to 130–131 genes, including 85–86 protein coding genes, 37 tRNA genes, and eight rRNA genes, with GC contents of 37.26–37.31%. The GC content was variable among regions and was highest in the inverted repeat (IR) region. The IR boundary of Euonymus happened expanding resulting that the rps19 entered into IR region and doubled completely. Such fluctuations at the border positions might be helpful in determining evolutionary relationships among Euonymus. The simple-sequence repeats (SSRs) of Euonymus species were composed primarily of single nucleotides (A)n and (T)n, and were mostly 10–12bp in length, with an obvious A/T bias. We identified several loci with suitable polymorphism with the potential use as molecular markers for inferring the phylogeny within the genus Euonymus. Signatures of positive selection were seen in rpoB protein encoding genes. Based on data from the whole chloroplast genome, common single copy genes, and the LSC, SSC, and IR regions, we constructed an evolutionary tree of Euonymus and related species, the results of which were consistent with traditional taxonomic classifications. It showed that E. fortunei sister to the Euonymus japonicus, whereby E. maackii appeared as sister to Euonymus hamiltonianus. Our study provides important genetic information to support further investigations into the phylogenetic development and adaptive evolution of Euonymus species.

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Comparison and Phylogenetic Analysis of Chloroplast Genomes of Three Medicinal and Edible Amomum Species

International Journal of Molecular Sciences ◽

10.3390/ijms20164040 ◽

2019 ◽

Vol 20 (16) ◽

pp. 4040 ◽

Cited By ~ 12

Author(s):

Yingxian Cui ◽

Xinlian Chen ◽

Liping Nie ◽

Wei Sun ◽

Haoyu Hu ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Morphological Characteristics ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Edible Plant ◽

Protein Coding ◽

Chloroplast Genomes ◽

Cp Genome ◽

Pharmacologically Active

Amomum villosum is an important medicinal and edible plant with several pharmacologically active volatile oils. However, identifying A. villosum from A. villosum var. xanthioides and A. longiligulare which exhibit similar morphological characteristics to A. villosum, is difficult. The main goal of this study, therefore, is to mine genetic resources and improve molecular methods that could be used to distinguish these species. A total of eight complete chloroplasts (cp) genomes of these Amomum species which were collected from the main producing areas in China were determined to be 163,608–164,069 bp in size. All genomes displayed a typical quadripartite structure with a pair of inverted repeat (IR) regions (29,820–29,959 bp) that separated a large single copy (LSC) region (88,680–88,857 bp) from a small single copy (SSC) region (15,288–15,369 bp). Each genome encodes 113 different genes with 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. More than 150 SSRs were identified in the entire cp genomes of these three species. The Sanger sequencing results based on 32 Amomum samples indicated that five highly divergent regions screened from cp genomes could not be used to distinguish Amomum species. Phylogenetic analysis showed that the cp genomes could not only accurately identify Amomum species, but also provide a solid foundation for the establishment of phylogenetic relationships of Amomum species. The availability of cp genome resources and the comparative analysis is beneficial for species authentication and phylogenetic analysis in Amomum.

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Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

PeerJ ◽

10.7717/peerj.8450 ◽

2020 ◽

Vol 8 ◽

pp. e8450 ◽

Cited By ~ 2

Author(s):

Sunan Huang ◽

Xuejun Ge ◽

Asunción Cano ◽

Betty Gaby Millán Salazar ◽

Yunfei Deng

Keyword(s):

Adaptive Evolution ◽

Phylogenetic Relationships ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Evolutionary Analysis ◽

Protein Coding ◽

Variable Regions ◽

Protein Coding Genes ◽

Chloroplast Genomes

The genus Dicliptera (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of Dilciptera (D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata) in this study. These cp genomes have circular structures of 150,689–150,811 bp and exhibit quadripartite organizations made up of a large single copy region (LSC, 82,796–82,919 bp), a small single copy region (SSC, 17,084–17,092 bp), and a pair of inverted repeat regions (IRs, 25,401–25,408 bp). Guanine-Cytosine (GC) content makes up 37.9%–38.0% of the total content. The complete cp genomes contain 114 unique genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analyses of nucleotide variability (Pi) reveal the five most variable regions (trnY-GUA-trnE-UUC, trnG-GCC, psbZ-trnG-GCC, petN-psbM, and rps4-trnL-UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of Dicliptera. A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five Dicliptera species. Phylogenetic analysis identified a close relationship between D. ruiziana and D. montana, followed by D. acuminata, D. peruviana, and D. mucronata. Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, ycf15, to be under positive selection, which may contribute to future studies of its adaptive evolution. The completed genomes are useful for future research on species identification, phylogenetic relationships, and the adaptive evolution of the Dicliptera species.

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Phylogeny of the Styracaceae Revisited Based on Whole Plastome Sequences, Including Novel Plastome Data from Parastyrax

Systematic Botany ◽

10.1600/036364421x16128061189576 ◽

2021 ◽

Vol 46 (1) ◽

pp. 162-174

Author(s):

Ming-Hui Yan ◽

Chun-Yang Li ◽

Peter W. Fritsch ◽

Jie Cai ◽

Heng-Chang Wang

Keyword(s):

Phylogenetic Relationships ◽

Phylogenetic Signal ◽

Strong Support ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

The Family ◽

Small Single Copy

Abstract—The phylogenetic relationships among 11 out of the 12 genera of the angiosperm family Styracaceae have been largely resolved with DNA sequence data based on all protein-coding genes of the plastome. The only genus that has not been phylogenomically investigated in the family with molecular data is the monotypic genus Parastyrax, which is extremely rare in the wild and difficult to collect. To complete the sampling of the genera comprising the Styracaceae, examine the plastome composition of Parastyrax, and further explore the phylogenetic relationships of the entire family, we sequenced the whole plastome of P. lacei and incorporated it into the Styracaceae dataset for phylogenetic analysis. Similar to most others in the family, the plastome is 158189 bp in length and contains a large single-copy region of 88085 bp and a small single-copy region of 18540 bp separated by two inverted-repeat regions of 25781 bp each. A total of 113 genes was predicted, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic relationships among all 12 genera of the family were constructed with 79 protein-coding genes. Consistent with a previous study, Styrax, Huodendron, and a clade of Alniphyllum + Bruinsmia were successively sister to the remainder of the family. Parastyrax was strongly supported as sister to an internal clade comprising seven other genera of the family, whereas Halesia and Pterostyrax were both recovered as polyphyletic, as in prior studies. However, when we employed either the whole plastome or the large- or small-single copy regions as datasets, Pterostyrax was resolved as monophyletic with 100% support, consistent with expectations based on morphology and indicating that non-coding regions of the Styracaceae plastome contain informative phylogenetic signal. Conversely Halesia was still resolved as polyphyletic but with novel strong support.

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Complete Chloroplast Genome of Argania spinosa: Structural Organization and Phylogenetic Relationships in Sapotaceae

Plants ◽

10.3390/plants9101354 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1354

Author(s):

Slimane Khayi ◽

Fatima Gaboun ◽

Stacy Pirro ◽

Tatiana Tatusova ◽

Abdelhamid El Mousadik ◽

...

Keyword(s):

Chloroplast Genome ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Important Species ◽

Complete Chloroplast Genome ◽

Argania Spinosa ◽

Protein Coding Genes ◽

Cp Genome

Argania spinosa (Sapotaceae), an important endemic Moroccan oil tree, is a primary source of argan oil, which has numerous dietary and medicinal proprieties. The plant species occupies the mid-western part of Morocco and provides great environmental and socioeconomic benefits. The complete chloroplast (cp) genome of A. spinosa was sequenced, assembled, and analyzed in comparison with those of two Sapotaceae members. The A. spinosa cp genome is 158,848 bp long, with an average GC content of 36.8%. The cp genome exhibits a typical quadripartite and circular structure consisting of a pair of inverted regions (IR) of 25,945 bp in length separating small single-copy (SSC) and large single-copy (LSC) regions of 18,591 and 88,367 bp, respectively. The annotation of A. spinosa cp genome predicted 130 genes, including 85 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. A total of 44 long repeats and 88 simple sequence repeats (SSR) divided into mononucleotides (76), dinucleotides (7), trinucleotides (3), tetranucleotides (1), and hexanucleotides (1) were identified in the A. spinosa cp genome. Phylogenetic analyses using the maximum likelihood (ML) method were performed based on 69 protein-coding genes from 11 species of Ericales. The results confirmed the close position of A. spinosa to the Sideroxylon genus, supporting the revisiting of its taxonomic status. The complete chloroplast genome sequence will be valuable for further studies on the conservation and breeding of this medicinally and culinary important species and also contribute to clarifying the phylogenetic position of the species within Sapotaceae.

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The complete mitochondrial genomes of four Baikal molluscs from the endemic family Baicaliidae (Caenogastropoda: Truncatelloida)

Journal of Molluscan Studies ◽

10.1093/mollus/eyaa004 ◽

2020 ◽

Vol 86 (3) ◽

pp. 201-209

Author(s):

T E Peretolchina ◽

T Ya Sitnikova ◽

D Yu Sherbakov

Keyword(s):

Lake Baikal ◽

Ribosomal Rna ◽

Rrna Genes ◽

Trna Genes ◽

Coding Region ◽

Base Pairs ◽

Protein Coding ◽

Phylogenetic Studies ◽

Canonical Base ◽

Complete Mitochondrial Genomes

Abstract Here, we present the complete mitochondrial (mt) genomes of four members of the Baicaliidae Fisher, 1885, a truncatelloidean family that is endemic to Lake Baikal (East Siberia). The mt genomes are those of Korotnewia korotnevi (15,171 bp), Godlewskia godlewskii (15,224 bp), Baicalia turriformis (15,127) and Maackia herderiana (15,154 bp). All these mt genomes contain 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. We detected non-canonical base pairs in some of the tRNA genes and variable numbers of non-coding spacers; some tRNAs do not have a TψC loop. We found gene order to be highly conserved in these Lake Baikal species and similar to the majority of caenogastropod mt genomes available on GenBank. A position of the putative control region is delimited to the non-coding region between trnF and the cox3 gene. It contains the ‘GAA(A)nT’ motif at the 3′ end and is similar to the replication origin found in most Caenogastropoda studied to date. We also compared the evolutionary rates of different genes to evaluate their use in different kinds of population or phylogenetic studies of this group of gastropods.

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Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations

International Journal of Molecular Sciences ◽

10.3390/ijms21134685 ◽

2020 ◽

Vol 21 (13) ◽

pp. 4685

Author(s):

Zhenhai Li ◽

Min Li ◽

Shannan Xu ◽

Li Liu ◽

Zuozhi Chen ◽

...

Keyword(s):

Divergence Time ◽

Rrna Genes ◽

12S Rrna ◽

Trna Genes ◽

Coding Region ◽

Protein Coding ◽

Protein Coding Genes ◽

Gc Skew ◽

The Family ◽

Conserved Genes

Carangidae are ecologically and economically important marine fish. The complete mitogenomes of three Carangidae species (Alectis indicus, Decapterus tabl, and Alepes djedaba) were sequenced, characterized, and compared with 29 other species of the family Carangidae in this study. The length of the three mitogenomes ranged from 16,530 to 16,610 bp, and the structures included 2 rRNA genes (12S rRNA and 16S rRNA), 1 control region (a non-coding region), 13 protein-coding genes, and 22 tRNA genes. Among the 22 tRNA genes, only tRNA-Ser (GCT) was not folded into a typical cloverleaf secondary structure and had no recognizable DHU stem. The full-length sequences and protein-coding genes (PCGs) of the mitogenomes of the three species all had obvious AT biases. The majority of the AT-skew and GC-skew values of the PCGs among the three species were negative, demonstrating bases T and C were more plentiful than A and G. Analyses of Ka/Ks and overall p-genetic distance demonstrated that ATP8 showed the highest evolutionary rate and COXI/COXII were the most conserved genes in the three species. The phylogenetic tree based on PCGs sequences of mitogenomes using maximum likelihood and Bayesian inference analyses showed that three clades were divided corresponding to the subfamilies Caranginae, Naucratinae, and Trachinotinae. The monophyly of each superfamily was generally well supported. The divergence time analyses showed that Carangidae evolved during three geological periods, the Cretaceous, Paleogene, and Neogene. A. indicus began to differentiate from other species about 27.20 million years ago (Mya) in the early Miocene, while D. tabl (21.25 Mya) and A. djedaba (14.67 Mya) differentiated in the middle Oligocene.

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The complete mitochondrial genome of Orancistrocerus aterrimus aterrimus and comparative analysis in the family Vespidae (Hymenoptera, Vespidae, Eumeninae)

ZooKeys ◽

10.3897/zookeys.790.25356 ◽

2018 ◽

Vol 790 ◽

pp. 127-144 ◽

Cited By ~ 2

Author(s):

Qiao-Hua Zhang ◽

Pan Huang ◽

Bin Chen ◽

Ting-Jing Li

Keyword(s):

Mitochondrial Genome ◽

Stop Codon ◽

Translation Termination ◽

Complete Mitochondrial Genome ◽

Rrna Genes ◽

Trna Genes ◽

Coding Region ◽

Protein Coding ◽

Tandem Repeat Sequences ◽

The Family

To date, only one mitochondrial genome (mitogenome) in the Eumeninae has been reported in the world and this is the first report in China. The mitogenome ofO.a.aterrimusis 17 972 bp long, and contains 38 genes, including 13 protein coding genes (PCGs), 23 tRNA genes, two rRNA genes, a long non-coding region (NCR), and a control region (CR). The mitogenome has 79.43% A + T content, its 13 PCGs use ATN as the initiation codon except forcox1using TTG, and nine genes used complete translation termination TAA and four genes have incomplete stop codon T (cox2,cox3,nad4, andcytb). Twenty-two of 23 tRNAs can form the typical cloverleaf secondary structure except fortrnS1. The CR is 1 078 bp long with 84.69% A+T content, comprising 28 bp tandem repeat sequences and 13 bp T-strech. There are two gene rearrangements which are an extratrnM2located betweentrnQandnad2and thetrnL2in the upstream ofnad1. Within all rearrangements of these mitogenomes reported in the family Vespidae, the translocation betweentrnS1andtrnEgenes only appears in Vespinae, and the translocation oftrnYin Polistinae and Vespinae. The absent codons of 13 PCGs in Polistinae are more than those both in Vespinae and Eumeninae in the family Vespidae. The study reports the complete mitogenome ofO.a.aterrimus, compares the characteristics and construct phylogenetic relationships of the mitogenomes in the family Vespidae.

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Complete Chloroplast Genome of Rhipsalis baccifera, the only Cactus with Natural Distribution in the Old World: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies

Plants ◽

10.3390/plants9080979 ◽

2020 ◽

Vol 9 (8) ◽

pp. 979

Author(s):

Millicent Akinyi Oulo ◽

Jia-Xin Yang ◽

Xiang Dong ◽

Vincent Okelo Wanga ◽

Elijah Mbandi Mkala ◽

...

Keyword(s):

Genome Rearrangement ◽

Single Copy ◽

Base Pairs ◽

Protein Coding ◽

Old World ◽

Chloroplast Genomes ◽

Outgroup Species ◽

History Of ◽

Cp Genome ◽

Future Work

Rhipsalis baccifera is the only cactus that naturally occurs in both the New World and the Old World, and has thus drawn the attention of most researchers. The complete chloroplast (cp) genome of R. baccifera is reported here for the first time. The cp genome of R. baccifera has 122, 333 base pairs (bp), with a large single-copy (LSC) region (81,459 bp), SSC (23,531 bp) and two inverted repeat (IR) regions each 8530 bp. The genome contains 110 genes, with 73 protein-coding genes, 31 tRNAs, 4 rRNAs and 2 pseudogenes. Twelve genes have introns, with loss of introns being observed in, rpoc1clpP and rps12 genes. 49 repeat sequences and 62 simple sequence repeats (SSRs) were found in the genome. Comparative analysis with eight species of the ACPT (Anacampserotaceae, Cactaceae, Portulacaceae, and Talinaceae) clade of the suborder Portulacineae species, showed that R. baccifera genome has higher number of rearrangements, with a 19 gene inversion in its LSC region representing the most significant structural change in terms of its size. Inversion of the SSC region seems common in subfamily Cactoideae, and another 6 kb gene inversion between rbcL- trnM was observed in R. baccifera and Carnegiea gigantea. The IRs of R. baccifera are contracted. The phylogenetic analysis among 36 complete chloroplast genomes of Caryophyllales species and two outgroup species supported monophyly of the families of the ACPT clade. R. baccifera occupied a basal position of the family Cactaceae clade in the tree. A high number of rearrangements in this cp genome suggests a larger number mutation events in the history of evolution of R. baccifera. These results provide important tools for future work on R. baccifera and in the evolutionary studies of the suborder Portulacineae.

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