scholarly journals Cuscuta Species Identification Based on the Morphology of Reproductive Organs and Complete Chloroplast Genome Sequences

2019 ◽  
Vol 20 (11) ◽  
pp. 2726 ◽  
Author(s):  
Inkyu Park ◽  
Jun-Ho Song ◽  
Sungyu Yang ◽  
Wook Jin Kim ◽  
Goya Choi ◽  
...  
Keyword(s):  
Herbal Medicine ◽  
Chloroplast Genome ◽  
Morphological Characteristics ◽  
Reproductive Organs ◽  
Crop Damage ◽  
Sequence Information ◽  
Evolutionary Analysis ◽  
Accurate Identification ◽  
Chloroplast Genomes ◽  
Cuscuta Species

The genus Cuscuta (Convolvulaceae) comprises well-known parasitic plants. Cuscuta species are scientifically valuable, as their life style causes extensive crop damage. Furthermore, dried seeds of C. chinensis are used as a Korean traditional herbal medicine. Despite the importance of Cuscuta species, it is difficult to distinguish these plants by the naked eye. Moreover, plastid sequence information available for Cuscuta species is limited. In this study, we distinguished between C. chinensis and C. japonica using morphological characterisation of reproductive organs and molecular characterisation of chloroplast genomes. The differences in morphological characteristics of reproductive organs such as style, stigma, infrastaminal scale, seed shape and testa ornamentation were useful for distinguishing between C. japonica and C. chinensis. Analysis of chloroplast genomes revealed drastic differences in chloroplast genome length and gene order between the two species. Although both species showed numerous gene losses and genomic rearrangements, chloroplast genomes showed highly similar structure within subgenera. Phylogenetic analysis of Cuscuta chloroplast genomes revealed paraphyletic groups within subgenera Monogynella and Grammica, which is consistent with the APG IV system of classification. Our results provide useful information for the taxonomic, phylogenetic and evolutionary analysis of Cuscuta and accurate identification of herbal medicine.

scholarly journals Gene Loss and Evolution of the Plastome

2019 ◽  
Author(s):  
Tapan Kumar Mohanta ◽  
Awdhesh Kumar Mishra ◽  
Adil Khan ◽  
Abeer Hashem ◽  
Elsayed Fathi Abd_Allah ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Dna Sequences ◽  
Nuclear Genome ◽  
Evolutionary Process ◽  
Life Forms ◽  
Evolutionary Analysis ◽  
Origin And Evolution ◽  
The Earth ◽  
Chloroplast Genomes ◽  
Duplication Events

AbstractChloroplasts are unique organelles within the plant cells and are responsible for sustaining life forms on the earth due to their ability to conduct photosynthesis. Multiple functional genes within the chloroplast are responsible for a variety of metabolic processes that occur in the chloroplast. Considering its fundamental role in sustaining life on the earth, it is important to identify the level of diversity present in the chloroplast genome, what genes and genomic content have been lost, what genes have been transferred to the nuclear genome, duplication events, and the overall origin and evolution of the chloroplast genome. Our analysis of 2511 chloroplast genomes indicated that the genome size and number of coding DNA sequences (CDS) in the chloroplasts genome of algae are higher relative to other lineages. Approximately 10.31% of the examined species have lost the inverted repeats (IR) in the chloroplast genome that span across all the lineages. Genome-wide analyses revealed the loss of the Rbcl gene in parasitic and heterotrophic plants occurred approximately 56 Ma ago. PsaM, Psb30, ChlB, ChlL, ChlN, and Rpl21 were found to be characteristic signature genes of the chloroplast genome of algae, bryophytes, pteridophytes, and gymnosperms; however, none of these genes were found in the angiosperm or magnoliid lineage which appeared to have lost them approximately 203–156 Ma ago. A variety of chloroplast-encoded genes were lost across different species lineages throughout the evolutionary process. The Rpl20 gene, however, was found to be the most stable and intact gene in the chloroplast genome and was not lost in any of the analyzed species, suggesting that it is a signature gene of the plastome. Our evolutionary analysis indicated that chloroplast genomes evolved from multiple common ancestors ~1293 Ma ago and have undergone vivid recombination events across different taxonomic lineages.

scholarly journals Gene Loss and Evolution of the Plastome

2020 ◽  
Author(s):  
Tapan Kumar Mohanta ◽  
Adil Khan ◽  
Abdul Latif Khan ◽  
Abeer Hashem ◽  
Elsayed Fathi Abd_Allah ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Nuclear Genome ◽  
Evolutionary Process ◽  
Life Forms ◽  
Inverted Repeats ◽  
Rbcl Gene ◽  
Evolutionary Analysis ◽  
Origin And Evolution ◽  
Chloroplast Genomes ◽  
Duplication Events

Abstract Chloroplasts are unique organelles within plant cells and are ultimately responsible for sustaining life forms on the earth due to their ability to conduct photosynthesis. Multiple functional genes within the chloroplast are responsible for a variety of metabolic processes that occur in the chloroplast. Considering its fundamental role in sustaining life on earth, it is important to identify the level of diversity present in the chloroplast genome, what genes and genomic content have been lost, what genes have been transferred to the nuclear genome, duplication events, and the overall origin and evolution of the chloroplast genome. Our analysis of 2511 chloroplast genomes indicated that the genome size and number of CDS in the chloroplasts of algae are higher relative to other lineages. Approximately 10.31% of the examined species have lost the inverted repeats (IR) that span across the lineages that comprise algae, bryophytes, pteridophytes, gymnosperm, angiosperms, magnoliids, and protists. Genome-wide analyses revealed that the loss of the Rbcl gene in parasitic and heterotrophic plant species occurred approximately 56 Ma ago. PsaM, Psb30, ChlB, ChlL, ChlN, and Rpl21 were found to be characteristic signature genes of chloroplast genome of algae, bryophytes, pteridophytes, and gymnosperms; while none of these genes were found in the angiosperm or magnoliid lineage which appeared to have lost them approximately 203-156 Ma ago. A variety of chloroplast encoding genes were lost across different species lineages throughout the evolutionary process. The Rpl20 gene, however, was found to be the most stable and intact gene in the chloroplast genome and was not lost in any of the analysed species; suggesting that it is a signature gene of the plastome. Our evolutionary analysis indicated that chloroplast genomes evolved from multiple common ancestors ~1293 Ma ago and have undergone vivid recombination events across different taxonomic lineages. Additionally, our findings support the hypothesis that these recombination events are the most probable cause behind the dynamic loss of chloroplast genes and inverted repeats in different species.

scholarly journals Gene Loss and Evolution of the Plastome

2019 ◽  
Author(s):  
Tapan Kumar Mohanta ◽  
Adil Khan ◽  
Abdul Latif Khan ◽  
Abeer Hashem ◽  
Elsayed Fathi Abd_Allah ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Nuclear Genome ◽  
Evolutionary Process ◽  
Life Forms ◽  
Inverted Repeats ◽  
Rbcl Gene ◽  
Evolutionary Analysis ◽  
Origin And Evolution ◽  
Chloroplast Genomes ◽  
Duplication Events

Abstract Chloroplasts are unique organelles within plant cells and are ultimately responsible for sustaining life forms on the earth due to their ability to conduct photosynthesis. Multiple functional genes within the chloroplast are responsible for a variety of metabolic processes that occur in the chloroplast. Considering its fundamental role in sustaining life on earth, it is important to identify the level of diversity present in the chloroplast genome, what genes and genomic content have been lost, what genes have been transferred to the nuclear genome, duplication events, and the overall origin and evolution of the chloroplast genome. Our analysis of 2511 chloroplast genomes indicated that the genome size and number of CDS in the chloroplasts of algae are higher relative to other lineages. Approximately 10.31% of the examined species have lost the inverted repeats (IR) that span across the lineages that comprise algae, bryophytes, pteridophytes, gymnosperm, angiosperms, magnoliids, and protists. Genome-wide analyses revealed that the loss of the RBCL gene in parasitic and heterotrophic plant species occurred approximately 56 Ma ago. PsaM, Psb30, ChlB, ChlL, ChlN, and RPL21 were found to be characteristic signature genes of chloroplast genome of algae, bryophytes, pteridophytes, and gymnosperms; while none of these genes were found in the angiosperm or magnoliid lineage which appeared to have lost them approximately 203-156 Ma ago. A variety of chloroplast encoding genes were lost across different species lineages throughout the evolutionary process. The Rpl20 gene, however, was found to be the most stable and intact gene in the chloroplast genome and was not lost in any of the analysed species; suggesting that it is a signature gene of the plastome. Our evolutionary analysis indicated that chloroplast genomes evolved from multiple common ancestors ~1293 Ma ago and have undergone vivid recombination events across different taxonomic lineages. Additionally, our findings support the hypothesis that these recombination events are the most probable cause behind the dynamic loss of chloroplast genes and inverted repeats in different species.

scholarly journals Characterization of the complete chloroplast genome sequence of Dalbergia species and its phylogenetic implications

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Yun Song ◽  
Yongjiang Zhang ◽  
Jin Xu ◽  
Weimin Li ◽  
MingFu Li
Keyword(s):  
Chloroplast Genome ◽  
Size Structure ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Intergenic Spacer ◽  
Dna Barcodes ◽  
Ecological Value ◽  
Accurate Identification ◽  
Chloroplast Genomes ◽  
Phylogenetic Implications

AbstractThe pantropical plant genus Dalbergia comprises approximately 250 species, most of which have a high economic and ecological value. However, these species are among the most threatened due to illegal logging and the timber trade. To enforce protective legislation and ensure effective conservation of Dalbergia species, the identity of wood being traded must be accurately validated. For the rapid and accurate identification of Dalbergia species and assessment of phylogenetic relationships, it would be highly desirable to develop more effective DNA barcodes for these species. In this study, we sequenced and compared the chloroplast genomes of nine species of Dalbergia. We found that these chloroplast genomes were conserved with respect to genome size, structure, and gene content and showed low sequence divergence. We identified eight mutation hotspots, namely, six intergenic spacer regions (trnL-trnT, atpA-trnG, rps16-accD, petG-psaJ, ndhF-trnL, and ndhG-ndhI) and two coding regions (ycf1a and ycf1b), as candidate DNA barcodes for Dalbergia. Phylogenetic analyses based on whole chloroplast genome data provided the best resolution of Dalbergia, and phylogenetic analysis of the Fabaceae showed that Dalbergia was sister to Arachis. Based on comparison of chloroplast genomes, we identified a set of highly variable markers that can be developed as specific DNA barcodes.

scholarly journals Comparative Analysis of the Chloroplast Genome for Four Pennisetum Species: Molecular Structure and Phylogenetic Relationships

2021 ◽  
Vol 12 ◽  
Author(s):  
Jin Xu ◽  
Chen Liu ◽  
Yun Song ◽  
Mingfu Li
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Future Research ◽  
Trna Genes ◽  
Evolutionary Analysis ◽  
Chloroplast Genomes

The genus Pennisetum (Poaceae) is both a forage crop and staple food crop in the tropics. In this study, we obtained chloroplast genome sequences of four species of Pennisetum (P. alopecuroides, P. clandestinum, P. glaucum, and P. polystachion) using Illumina sequencing. These chloroplast genomes have circular structures of 136,346–138,119 bp, including a large single-copy region (LSC, 79,380–81,186 bp), a small single-copy region (SSC, 12,212–12,409 bp), and a pair of inverted repeat regions (IRs, 22,284–22,372 bp). The overall GC content of these chloroplast genomes was 38.6–38.7%. The complete chloroplast genomes contained 110 different genes, including 76 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analysis of nucleotide variability identified nine intergenic spacer regions (psbA-matK, matK-rps16, trnN-trnT, trnY-trnD-psbM, petN-trnC, rbcL-psaI, petA-psbJ, psbE-petL, and rpl32-trnL), which may be used as potential DNA barcodes in future species identification and evolutionary analysis of Pennisetum. The phylogenetic analysis revealed a close relationship between P. polystachion and P. glaucum, followed by P. clandestinum and P. alopecuroides. The completed genomes of this study will help facilitate future research on the phylogenetic relationships and evolution of Pennisetum species.

scholarly journals Comparative Analysis of Actaea Chloroplast Genomes and Molecular Marker Development for the Identification of Authentic Cimicifugae Rhizoma

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 157 ◽  
Author(s):  
Inkyu Park ◽  
Jun-Ho Song ◽  
Sungyu Yang ◽  
Byeong Cheol Moon
Keyword(s):  
Herbal Medicine ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Comparative Sequence Analysis ◽  
Indel Marker ◽  
Sequence Information ◽  
Genome Sequences ◽  
Chloroplast Genomes ◽  
Cp Genome ◽  
Rna Genes

Actaea (Ranunculaceae; syn. Cimicifuga) is a controversial and complex genus. Dried rhizomes of Actaea species are used as Korean traditional herbal medicine. Although Actaea species are valuable, given their taxonomic classification and medicinal properties, sequence information of Actaea species is limited. In this study, we determined the complete chloroplast (cp) genome sequences of three Actaea species, including A. simplex, A. dahurica, and A. biternata. The cp genomes of these species varied in length from 159,523 to 159,789 bp and contained 112 unique functional genes, including 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Gene order, orientation, and content were well conserved in the three cp genomes. Comparative sequence analysis revealed the presence of hotspots, including ndhC-trnV-UAC, in Actaea cp genomes. High-resolution phylogenetic relationships were established among Actaea species based on cp genome sequences. Actaea species were clustered into each Actaea section, consistent with the Angiosperm Phylogeny Group (APG) IV system of classification. We also developed a novel indel marker, based on copy number variation of tandem repeats, to facilitate the authentication of the herbal medicine Cimicifugae Rhizoma. The availability Actaea cp genomes will provide abundant information for the taxonomic and phylogenetic analyses of Actaea species, and the Actaea (ACT) indel marker will be useful for the authentication of the herbal medicine.

scholarly journals Comparative Analyses of Chloroplast Genomes From 14 Zanthoxylum Species: Identification of Variable DNA Markers and Phylogenetic Relationships Within the Genus

2021 ◽  
Vol 11 ◽  
Author(s):  
Kaihui Zhao ◽  
Lianqiang Li ◽  
Hong Quan ◽  
Junbo Yang ◽  
Zhirong Zhang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Dna Barcode ◽  
Morphological Characteristics ◽  
Rrna Genes ◽  
Evolutionary Analysis ◽  
Classification Problems ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Medicinal Value ◽  
Mutational Hotspots

Zanthoxylum L. is an economic crop with a long history of cultivation and domestication and has important economic, ecological, and medicinal value. To solve the classification problems caused by the similar morphological characteristics of Zanthoxylum and establish a credible phylogenetic relationship, we sequenced and annotated six Zanthoxylum chloroplast (cp) genomes (Z. piasezkii, Z. armatum, Z. motuoense, Z. oxyphyllum, Z. multijugum, and Z. calcicola) and combined them with previously published genomes for the Zanthoxylum species. We used bioinformatics methods to analyze the genomic characteristics, contraction, and expansion of inverted repeat (IR) regions; differences in simple sequence repeats (SSRs) and long repeat sequences; species pairwise Ka/Ks ratios; divergence hotspots; and phylogenetic relationships of the 14 Zanthoxylum species. The results revealed that cp genomes of Zanthoxylum range in size from 158,071 to 158,963 bp and contain 87 protein-coding, 37 tRNA, and 8 rRNA genes. Seven mutational hotspots were identified as candidate DNA barcode sequences to distinguish Zanthoxylum species. The phylogenetic analysis strongly supported the genus Fagara as a subgenus of Zanthoxylum and proposed the possibility of a new subgenus in Zanthoxylum. The availability of these genomes will provide valuable information for identifying species, molecular breeding, and evolutionary analysis of Zanthoxylum.

scholarly journals The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Feng Wen ◽  
Xiaozhu Wu ◽  
Tongjian Li ◽  
Mingliang Jia ◽  
Xinsheng Liu ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Dna Sequences ◽  
Dna Barcode ◽  
Species Discrimination ◽  
Evolutionary Analysis ◽  
Variable Regions ◽  
Triterpenoid Saponins ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genomes

Abstract Background Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triterpenoid saponins with anticancer and anti-inflammatory activities. However, the wild resources of this species and its relatives were threatened by over-exploitation before the genetic diversity and evolutionary analysis were uncovered. Thus, the complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily. Results A series of analyses including genome structure, GC content, repeat structure, SSR component, nucleotide diversity and codon usage were performed by comparing chloroplast genomes of Stauntonia chinensis and its relatives. Although the chloroplast genomes of eight Lardizabaloideae plants were evolutionary conserved, the comparative analysis also showed several variation hotspots, which were considered as highly variable regions. Additionally, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Lardizabaloideae species underwent purifying selection, whereas 25 chloroplast protein coding genes were identified with positive selection in this subfamily species by using branch-site model. Bayesian and ML phylogeny on CCG (complete chloroplast genome) and CDs (coding DNA sequences) produced a well-resolved phylogeny of Lardizabaloideae plastid lineages. Conclusions This study enhanced the understanding of the evolution of Lardizabaloideae and its relatives. All the obtained genetic resources will facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of subfamily Lardizabaloideae.

scholarly journals Gene Loss and Evolution of the Plastome

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1133
Author(s):  
Tapan Kumar Mohanta ◽  
Awdhesh Kumar Mishra ◽  
Adil Khan ◽  
Abeer Hashem ◽  
Elsayed Fathi Abd_Allah ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Dna Sequences ◽  
Nuclear Genome ◽  
Evolutionary Process ◽  
Life Forms ◽  
Rbcl Gene ◽  
Evolutionary Analysis ◽  
Origin And Evolution ◽  
The Earth ◽  
Chloroplast Genomes

Chloroplasts are unique organelles within the plant cells and are responsible for sustaining life forms on the earth due to their ability to conduct photosynthesis. Multiple functional genes within the chloroplast are responsible for a variety of metabolic processes that occur in the chloroplast. Considering its fundamental role in sustaining life on the earth, it is important to identify the level of diversity present in the chloroplast genome, what genes and genomic content have been lost, what genes have been transferred to the nuclear genome, duplication events, and the overall origin and evolution of the chloroplast genome. Our analysis of 2511 chloroplast genomes indicated that the genome size and number of coding DNA sequences (CDS) in the chloroplasts genome of algae are higher relative to other lineages. Approximately 10.31% of the examined species have lost the inverted repeats (IR) in the chloroplast genome that span across all the lineages. Genome-wide analyses revealed the loss of the Rbcl gene in parasitic and heterotrophic plants occurred approximately 56 Ma ago. PsaM, Psb30, ChlB, ChlL, ChlN, and Rpl21 were found to be characteristic signature genes of the chloroplast genome of algae, bryophytes, pteridophytes, and gymnosperms; however, none of these genes were found in the angiosperm or magnoliid lineage which appeared to have lost them approximately 203–156 Ma ago. A variety of chloroplast-encoded genes were lost across different species lineages throughout the evolutionary process. The Rpl20 gene, however, was found to be the most stable and intact gene in the chloroplast genome and was not lost in any of the analyzed species, suggesting that it is a signature gene of the plastome. Our evolutionary analysis indicated that chloroplast genomes evolved from multiple common ancestors ~1293 Ma ago and have undergone vivid recombination events across different taxonomic lineages.

scholarly journals Chloroplast Genome Variation and Evolutionary Analysis of Olea europaea L.

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 879
Author(s):  
Erli Niu ◽  
Chengying Jiang ◽  
Wei Wang ◽  
Yu Zhang ◽  
Shenlong Zhu
Keyword(s):  
Chloroplast Genome ◽  
Olea Europaea ◽  
Group Identification ◽  
Evolutionary Analysis ◽  
Next Generation Sequencing Technology ◽  
Coding Regions ◽  
Olea Europaea L ◽  
Chloroplast Genomes ◽  
African Group ◽  
Olea Europaéa

Olive (Olea europaea L.) is a very important woody tree and favored by consumers because of the fruit’s high-quality olive oil. Chloroplast genome analysis will provide insights into the chloroplast variation and genetic evolution of olives. The complete chloroplast genomes of three accessions (O. europaea subsp. cuspidata isolate Yunnan, O. europaea subsp. europaea var. sylvestris, and O. europaea subsp. europaea var. frantoio) were obtained by next-generation sequencing technology. A total of 133 coding regions were identified in the three chloroplast genomes without rearrangement. O. europaea subsp. europaea var. sylvestris and O. europaea subsp. europaea var. frantoio had the same sequences (155,886 bp), while O. europaea subsp. cuspidata isolate Yunnan (155,531 bp) presented a large gap between rps16 and trnQ-UUG genes with six small gaps and fewer microsatellites. The whole chloroplast genomes of 11 O. europaea were divided into two main groups by a phylogenetic tree and O. europaea subsp. cuspidata formed a separate group (Cuspidata group) with the other subspecies (Mediterranean/North African group). Identification of consistency and diversity among O. europaea subspecies will benefit the exploration of domestication events and facilitate molecular-assisted breeding for O. europaea.

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