scholarly journals Comparative genomics plastomes of the Amaryllidaceae family species

2020 ◽  
Vol 16 (6) ◽  
Author(s):  
Horace José Jimenez ◽  
Allan Deyws Francisco da Silva ◽  
Luiza Suely Semen Martins ◽  
Reginaldo De Carvalho ◽  
Rômulo Maciel De Moraes Filho
Keyword(s):  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Gc Content ◽  
Base Pairs ◽  
Important Species ◽  
Gene Space ◽  
Chloroplast Genomes ◽  
The Family ◽  
Matk Gene ◽  
High Conservation

The genus Allium covers more than 800 species, signaling among the largest among monocotyledons. The genus contains many economically important species, including garlic, leeks, onions, chives and Chinese chives. Due to the high conservation of chloroplast genomes compared to nuclear genomes and mitochondrial genome, sequence of chloroplasts in Amaryllidaceae have been consistently used for species identification and various in silico programs and strategies have been used to identify, characterize and compare plastid genome regions. Plastome from 15 species of the Amaryllidaceae family revealed similarity in both sequences and in the organization of their gene regions. The base pairs (bp) number ranged from 145,819 (A. paradoxum) to 159,125 (A. ursinum). In respect the GC content, the species presented a variation between 36.7% (A. schoenoprasum and A. sativum) and 37.5% (A. coddii) and the gene space ranged from 84.760 (A. paradoxum) to 94.766 (A. sativum). The genes that encode proteins showed values between 78 (A. paradoxum) to 89 (A. cepa). Phylogenetic trees acquired through alignment of complete plastomas and the plastidial matK gene revealed similarity to the proposed classification for the family. For the genus Allium, there was the formation of three clades with perfect correspondence of the clusters to the three evolutionary lines of the genus.

scholarly journals Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7500 ◽  
Author(s):  
Mikhail I. Schelkunov ◽  
Maxim S. Nuraliev ◽  
Maria D. Logacheva
Keyword(s):  
Plant Species ◽  
Mutation Rate ◽  
Plastid Genome ◽  
Gene Content ◽  
High Mutation Rate ◽  
Base Pairs ◽  
Plastid Genomes ◽  
The Family

Although most plant species are photosynthetic, several hundred species have lost the ability to photosynthesize and instead obtain nutrients via various types of heterotrophic feeding. Their plastid genomes markedly differ from the plastid genomes of photosynthetic plants. In this work, we describe the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, which belongs to the family Balanophoraceae and feeds by parasitizing other plants. The genome is highly reduced (18,622 base pairs vs. approximately 150 kbp in autotrophic plants) and possesses an extraordinarily high AT content, 86.8%, which is inferior only to AT contents of plastid genomes of Balanophora, a genus from the same family. The gene content of this genome is quite typical of heterotrophic plants, with all of the genes related to photosynthesis having been lost. The remaining genes are notably distorted by a high mutation rate and the aforementioned AT content. The high AT content has led to sequence convergence between some of the remaining genes and their homologs from AT-rich plastid genomes of protists. Overall, the plastid genome of R. phalloides is one of the most unusual plastid genomes known.

scholarly journals Whole Chloroplast Genomes reveals the uniqueness of Bolivian native cacao (Theobroma cacao) from the northern part of Bolivia

2021 ◽  
Author(s):  
Marcia Gumiel ◽  
Oscar M Rollano-Penaloza ◽  
Carmelo Peralta-Rivero ◽  
Leslie Tejeda ◽  
Valeria D. Palma Encinas ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Theobroma Cacao ◽  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Next Generation ◽  
Center Of Origin ◽  
Chloroplast Genomes ◽  
Geographical Locations ◽  
Generation Sequencing

We report the complete chloroplast sequences of two varieties of Theobroma cacao collected in the Bolivian Amazonia using Next-Generation Sequencing. Comparisons made between these two chloroplast genomes and the Belizean reference plastid genome identified 19 and 22 nucleotide variants. The phylogenetic analysis reported three main T. cacao clades belonging to the Forastero, Criollo and Trinitario groups. The Bolivian Native Cacao varieties were located inside the Trinitario group forming their unique branch. The Bolivian Native Cacao branch reveals a possible new subpopulation different from the well-characterized T. cacao subpopulations. The phylogenetic trees showed that the relationships among the T. cacao varieties were consistent with their geographical locations placing the Cacao Center of Origin in Western Amazon. The data presented here will contribute to the usage of ultrabarcoding to distinguish different T. cacao varieties and to identify native cacaos from introduced cacaos. Thus helping in the conservation of local native varieties of T. cacao.

scholarly journals The Complete Plastid Genome of Artocarpus camansi: A High Degree of Conservation of the Plastome Structure in the Family Moraceae

Forests ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1179
Author(s):  
Ueric José Borges de Souza ◽  
Luciana Cristina Vitorino ◽  
Layara Alexandre Bessa ◽  
Fabiano Guimarães Silva
Keyword(s):  
Plastid Genome ◽  
Structural Characteristics ◽  
Gc Content ◽  
Single Copy ◽  
Chloroplast Genes ◽  
Artocarpus Heterophyllus ◽  
Plastid Genomes ◽  
The Family ◽  
High Degree ◽  
Degree Of Similarity

Understanding the plastid genome is extremely important for the interpretation of the genetic mechanisms associated with essential physiological and metabolic functions, the identification of possible marker regions for phylogenetic or phylogeographic analyses, and the elucidation of the modes through which natural selection operates in different regions of this genome. In the present study, we assembled the plastid genome of Artocarpus camansi, compared its repetitive structures with Artocarpus heterophyllus, and searched for evidence of synteny within the family Moraceae. We also constructed a phylogeny based on 56 chloroplast genes to assess the relationships among three families of the order Rosales, that is, the Moraceae, Rhamnaceae, and Cannabaceae. The plastid genome of A. camansi has 160,096 bp, and presents the typical circular quadripartite structure of the Angiosperms, comprising a large single copy (LSC) of 88,745 bp and a small single copy (SSC) of 19,883 bp, separated by a pair of inverted repeat (IR) regions each with a length of 25,734 bp. The total GC content was 36.0%, which is very similar to Artocarpus heterophyllus (36.1%) and other moraceous species. A total of 23,068 codons and 80 SSRs were identified in the A. camansi plastid genome, with the majority of the SSRs being mononucleotide (70.0%). A total of 50 repeat structures were observed in the A. camansi plastid genome, in contrast with 61 repeats in A. heterophyllus. A purifying selection signal was found in 70 of the 79 protein-coding genes, indicating that they have all been highly conserved throughout the evolutionary history of the genus. The comparative analysis of the structural characteristics of the chloroplast among different moraceous species found a high degree of similarity in the sequences, which indicates a highly conserved evolutionary model in these plastid genomes. The phylogenetic analysis also recovered a high degree of similarity between the chloroplast genes of A. camansi and A. heterophyllus, and reconfirmed the hypothesis of the intense conservation of the plastome in the family Moraceae.

scholarly journals Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastid genomes

2018 ◽  
Vol 123 (5) ◽  
pp. 857-865 ◽  
Author(s):  
Jacqueline Heckenhauer ◽  
Ovidiu Paun ◽  
Mark W Chase ◽  
Peter S Ashton ◽  
A S Kamariah ◽  
...  
Keyword(s):  
Related Species ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Gc Content ◽  
Genome Sequences ◽  
Closely Related Species ◽  
Plastid Genomes ◽  
Snp Data ◽  
Phylogenomic Analyses

Abstract Background and Aims Phylogenetic relationships within tribe Shoreeae, containing the main elements of tropical forests in Southeast Asia, present a long-standing problem in the systematics of Dipterocarpaceae. Sequencing whole plastomes using next-generation sequencing- (NGS) based genome skimming is increasingly employed for investigating phylogenetic relationships of plants. Here, the usefulness of complete plastid genome sequences in resolving phylogenetic relationships within Shoreeae is evaluated. Methods A pipeline to obtain alignments of whole plastid genome sequences across individuals with different amounts of available data is presented. In total, 48 individuals, representing 37 species and four genera of the ecologically and economically important tribe Shoreeae sensu Ashton, were investigated. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and Bayesian inference. Key Results Here, the first fully sequenced plastid genomes for the tribe Shoreeae are presented. Their size, GC content and gene order are comparable with those of other members of Malvales. Phylogenomic analyses demonstrate that whole plastid genomes are useful for inferring phylogenetic relationships among genera and groups of Shorea (Shoreeae) but fail to provide well-supported phylogenetic relationships among some of the most closely related species. Discordance in placement of Parashorea was observed between phylogenetic trees obtained from plastome analyses and those obtained from nuclear single nucleotide polymorphism (SNP) data sets identified in restriction-site associated sequencing (RADseq). Conclusions Phylogenomic analyses of the entire plastid genomes are useful for inferring phylogenetic relationships at lower taxonomic levels, but are not sufficient for detailed phylogenetic reconstructions of closely related species groups in Shoreeae. Discordance in placement of Parashorea was further investigated for evidence of ancient hybridization.

scholarly journals Chloroplast Genome of Phyllanthus Emblica and Leptopus Cordifolius: Comparative Analysis and Phylogenetic within Family Phyllanthaceae

2021 ◽  
Author(s):  
Umar Rehman ◽  
Nighat Sultana ◽  
Abdullah . ◽  
Abbas Jamal ◽  
Maryam Muzaffar ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Related Species ◽  
Gc Content ◽  
Single Copy ◽  
Phyllanthus Emblica ◽  
Protein Coding ◽  
Coding Sequences ◽  
Tropical Regions ◽  
Chloroplast Genomes ◽  
The Family

Family Phyllanthaceae is one of the largest segregates of the eudicot order Malpighiales and its species are herb, shrub, and tree, which are mostly distributed in tropical regions. Certain taxonomic discrepancies exist at genus and family level. Here, we report chloroplast genomes of three Phyllanthaceae species—Phyllanthus emblica, Flueggea virosa, and Leptopus cordifolius— and compare them with six others previously reported Phyllanthaceae chloroplast genomes. The species of Phyllanthaceae displayed quadripartite structure, comprising inverted repeat regions (IRa and IRb) that separate large single copy (LSC) and small single copy (SSC) regions. The length of complete chloroplast genome ranged from 154,707 bp to 161,093 bp; LSC from 83,627 bp to 89,932 bp; IRs from 23,921 bp to 27,128 bp; and SSC from 17,424 bp to 19,441 bp. Chloroplast genomes contained 111 to 112 unique genes, including 77 to 78 protein-coding, 30 transfer RNA (tRNA), and 4 ribosomal RNA (rRNA) that showed similarities in arrangement. The number of protein-coding genes varied due to deletion/pseudogenization of rps16 genes in Baccaurea ramiflora and Leptopus cordifolius. High variability was seen in number of oligonucleotide repeats while analysis of guanine-cytosine (GC) content, codon usage, amino acid frequency, simple sequence repeats analysis, synonymous and non-synonymous substitutions, and transition and transversion substitutions showed similarities in all Phyllanthaceae species. We detected a higher number of transition substitutions in the coding sequences than non-coding sequences. Moreover, the high number of transition substitutions was determined among the distantly related species in comparison to closely related species. Phylogenetic analysis shows the polyphyletic nature of the genus Phyllanthus which requires further verification. We also determined suitable polymorphic coding genes, including rpl22, ycf1, matK, ndhF, and rps15 which may be helpful for the reconstruction of the high-resolution phylogenetic tree of the family Phyllanthaceae using a large number of species in the future. Overall, the current study provides insight into chloroplast genome evolution in Phyllanthaceae.

scholarly journals Complete Chloroplast Genomes and Comparative Analysis of Sequences Evolution among Seven Aristolochia (Aristolochiaceae) Medicinal Species

2019 ◽  
Vol 20 (5) ◽  
pp. 1045 ◽  
Author(s):  
Xiaoqin Li ◽  
Yunjuan Zuo ◽  
Xinxin Zhu ◽  
Shuai Liao ◽  
Jinshuang Ma
Keyword(s):  
Genomic Structure ◽  
Gc Content ◽  
Medicinal Species ◽  
Nucleotide Substitutions ◽  
Protein Coding ◽  
Aristolochic Acids ◽  
Chloroplast Genomes ◽  
The Family ◽  
Cp Genome ◽  
Genome Arrangement

Aristolochiaceae, comprising about 600 species, is a unique plant family containing aristolochic acids (AAs). In this study, we sequenced seven species of Aristolochia, and retrieved eleven chloroplast (cp) genomes published for comparative genomics analysis and phylogenetic constructions. The results show that the cp genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The cp genomes range from 159,308 bp to 160,520 bp in length and have a similar GC content of 38.5%–38.9%. A total number of 113 genes were identified, including 79 protein-coding genes, 30 tRNAs and four rRNAs. Although genomic structure and size were highly conserved, the IR-SC boundary regions were variable between these seven cp genomes. The trnH-GUG genes, are one of major differences between the plastomes of the two subgenera Siphisia and Aristolochia. We analyzed the features of nucleotide substitutions, distribution of repeat sequences and simple sequences repeats (SSRs), positive selections in the cp genomes, and identified 16 hotspot regions for genomes divergence that could be utilized as potential markers for phylogeny reconstruction. Phylogenetic relationships of the family Aristolochiaceae inferred from the 18 cp genome sequences were consistent and robust, using maximum parsimony (MP), maximum likelihood (ML), and Bayesian analysis (BI) methods.

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

2020 ◽  
Vol 11 ◽  
Author(s):  
Peninah Cheptoo Rono ◽  
Xiang Dong ◽  
Jia-Xin Yang ◽  
Fredrick Munyao Mutie ◽  
Millicent A. Oulo ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Coding Region ◽  
Base Pairs ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
The Family ◽  
Cp Genome

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.

scholarly journals Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known

2018 ◽  
Author(s):  
Mikhail I. Schelkunov ◽  
Maxim S. Nuraliev ◽  
Maria D. Logacheva
Keyword(s):  
Plant Species ◽  
Mutation Rate ◽  
Plastid Genome ◽  
Gene Content ◽  
High Mutation Rate ◽  
Base Pairs ◽  
Plastid Genomes ◽  
The Family

AbstractAlthough most plant species are photosynthetic, several hundred species have lost the ability to photosynthesize and instead obtain nutrients via various types of heterotrophic feeding. Their genomes, especially plastid genomes, markedly differ from the genomes of photosynthetic plants. In this work, we describe the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, which belongs to the family Balanophoraceae and feeds by parasitizing on other plants. The genome is highly reduced (18 622 base pairs versus approximately 150 kilobase pairs in autotrophic plants) and possesses an outstanding AT content, 86.8%, the highest of all sequenced plant plastid genomes. The gene content of this genome is quite typical of heterotrophic plants, with all of the genes related to photosynthesis having been lost. The remaining genes are notably distorted by a high mutation rate and the aforementioned AT content. The high AT content has led to sequence convergence between some of the remaining genes and their homologues from AT-rich plastid genomes of protists. Overall, the plastid genome of R. phalloides is one of the most unusual plastid genomes known.

scholarly journals The plastid genome in Cladophorales green algae is encoded by hairpin plasmids

2017 ◽  
Author(s):  
Andrea Del Cortona ◽  
Frederik Leliaert ◽  
Kenny A. Bogaert ◽  
Monique Turmel ◽  
Christian Boedeker ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Green Algae ◽  
Plastid Genome ◽  
High Throughput Sequencing ◽  
Gc Content ◽  
Genome Architecture ◽  
Dna Molecules ◽  
Chloroplast Genes ◽  
Dna And Rna ◽  
Chloroplast Genomes

AbstractVirtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100-200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin plasmids. Short and long read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genes of Boodlea composita are encoded on 1-7 kb DNA contigs with an exceptionally high GC-content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression. We propose that these contigs correspond to linear single-stranded DNA molecules that fold onto themselves to form hairpin plasmids. The Boodlea chloroplast genes are highly divergent from their corresponding orthologs. The origin of this highly deviant chloroplast genome likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes and highlights unexpected variation in the plastid genome architecture.

scholarly journals Complete chloroplast genomes of Rubus species (Rosaceae) and comparative analysis within the genus

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Jiaojun Yu ◽  
Jun Fu ◽  
Yuanping Fang ◽  
Jun Xiang ◽  
Hongjin Dong
Keyword(s):  
Comparative Analysis ◽  
Ornamental Plants ◽  
Gc Content ◽  
Central China ◽  
Dabie Mountains ◽  
Nucleotide Variability ◽  
Chloroplast Genomes ◽  
The Family ◽  
Cp Genome ◽  
Rna Genes

Abstract Background Rubus is the largest genus of the family Rosaceae and is valued as medicinal, edible, and ornamental plants. Here, we sequenced and assembled eight chloroplast (cp) genomes of Rubus from the Dabie Mountains in Central China. Fifty-one Rubus species were comparatively analyzed for the cp genomes including the eight newly discovered genomes and forty-three previously reported in GenBank database (NCBI). Results The eight newly obtained cp genomes had the same quadripartite structure as the other cp genomes in Rubus. The length of the eight plastomes ranged from 155,546 bp to 156,321 bp with similar GC content (37.0 to 37.3%). The results indicated 133–134 genes were annotated for the Rubus plastomes, which contained 88 or 89 protein coding genes (PCGs), 37 transfer RNA genes (tRNAs), and eight ribosomal RNA genes (rRNAs). Among them, 16 (or 18) of the genes were duplicated in the IR region. Structural comparative analysis results showed that the gene content and order were relatively preserved. Nucleotide variability analysis identified nine hotspot regions for genomic divergence and multiple simple sequences repeats (SSRs), which may be used as markers for genetic diversity and phylogenetic analysis. Phylogenetic relationships were highly supported within the family Rosaceae, as evidenced by sub-clade taxa cp genome sequences. Conclusion Thus, the whole plastome may be used as a super-marker in phylogenetic studies of this genus.

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