Identification of conserved regions in the plastid genome: implications for DNA barcoding and biological function

2006 ◽  
Vol 84 (9) ◽  
pp. 1434-1443 ◽  
Author(s):  
Gernot G. Presting
Keyword(s):  
Dna Barcoding ◽  
Plastid Genome ◽  
Rational Design ◽  
Higher Plants ◽  
Dna Barcode ◽  
Single Copy ◽  
Land Plants ◽  
Computer Assisted ◽  
Plastid Genomes ◽  
Starting Point

All oligonucleotides of the sugarcane chloroplast genome that are conserved in one or more of 36 other completed plastid genomes have been identified by computer-assisted sequence comparison. These regions are of interest because they (i) are indicative of strong selection pressures to maintain specific nucleotide sequences that may yield insights into plastid biology and (ii) can be used as priming sites for amplifying intervening sequences that represent potential DNA barcodes for species identification. The majority of conserved sites are located in the inverted repeat (IR) region, but several sites in the single copy region (predominantly in tRNA and psa/psb genes) are conserved among chloroplasts of all higher plants examined here. Of particular interest are protein coding regions that have been conserved at the nucleotide level, as these may be involved in transcript regulation. This analysis also provides the basis for rational design of a DNA barcode for plastids, and several potential barcode regions have been identified. In particular, two oligonucleotides of length 33 and 25, and separated by approximately 362 nucleotides, are found in all cyanobacteria, red, brown and green algae, as well as diatoms, euglenids, apicomplexans and land plants that have been examined to date. Their widespread occurrence makes the intervening sequence a universal marker for all photosynthetic lineages. Analysis of 160 GenBank accessions illustrates that this region discriminates many algae at the species level, but lacks sufficient variation among the more recently diverged land plants to serve as a single DNA barcode for this taxon. However, this marker should be particularly useful for the DNA barcoding of algal lineages and lichens, as well as for environmental sampling. More rapidly evolving regions of the plastid genome also identified here serve as a starting point to design and test barcodes for more narrowly defined lineages, including the more recently diverged angiosperms.

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 Transcriptional profiling of gametogenesis in the green seaweed Ulva mutabilis identifies an RWP‐RK transcription factors linked to reproduction

2021 ◽  
Author(s):  
Xiaojie Liu ◽  
Jonas Blomme ◽  
Kenny Bogaert ◽  
Sofie D’hondt ◽  
Thomas Wichard ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Sexual Reproduction ◽  
Higher Plants ◽  
Crop Improvement ◽  
Functional Characterization ◽  
Land Plants ◽  
Alternative Source ◽  
Starting Point ◽  
Green Seaweed

Abstract Background The molecular mechanism underlying sexual reproduction in land plants is well understood in model plants and is a target for crop improvement. However, unlike land plants, the genetic basis involved in triggering reproduction and gamete formation remains elusive in most seaweeds, which are increasingly viewed as an alternative source of functional food and feedstock for energy applications. Results Gametogenesis of Ulva mutabilis, a model organism for green seaweeds, is studied. We analyze transcriptome dynamics at different time points during gametogenesis following induction of reproduction by fragmentation and removal of sporulation inhibitors. Analyses demonstrate that 45% of the genes in the genome are differentially expressed during gametogenesis. We identified several transcription factors that potentially play a key role in the early gametogenesis of Ulva given the function of their homologs in higher plants and microalgae. In particular, the detailed expression pattern of an evolutionary conserved transcription factor containing an RWP-RK domain suggests a key role during Ulva gametogenesis. Conclusions Transcriptomic analyses of gametogenesis in the green seaweed Ulva highlight the importance of a conserved RWP-RK transcription factor in induction of sexual reproduction. The identification of putative master regulators of gametogenesis provides a starting point for further functional characterization.

scholarly journals Comparative Plastid Genomics of Four Pilea (Urticaceae) Species: Insight into Interspecific Plastid Genome Diversity in Pilea

2020 ◽  
Author(s):  
Jingling Li ◽  
Jianmin Tang ◽  
Siyuan Zeng ◽  
Fang Han ◽  
Jing Yuan ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Plastid Genome ◽  
Dna Barcode ◽  
Sequence Divergence ◽  
Rrna Genes ◽  
Bootstrap Support ◽  
Trna Genes ◽  
Hypervariable Regions ◽  
Plastid Genomes ◽  
Insight Into

Abstract Background: Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca 'Greizy', Pilea peperomioides and Pilea serpyllacea 'Globosa') and performed comprehensive comparative analysis.Results: The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae.Conclusion: Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.

scholarly journals Transcriptional dynamics of gametogenesis in the green seaweed Ulva mutabilis identifies an RWP-RK transcription factor linked to reproduction

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaojie Liu ◽  
Jonas Blomme ◽  
Kenny A. Bogaert ◽  
Sofie D’hondt ◽  
Thomas Wichard ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Sexual Reproduction ◽  
Higher Plants ◽  
Crop Improvement ◽  
Functional Characterization ◽  
Model Organism ◽  
Land Plants ◽  
Alternative Source ◽  
Starting Point ◽  
Green Seaweed

Abstract Background The molecular mechanism underlying sexual reproduction in land plants is well understood in model plants and is a target for crop improvement. However, unlike land plants, the genetic basis involved in triggering reproduction and gamete formation remains elusive in most seaweeds, which are increasingly viewed as an alternative source of functional food and feedstock for energy applications. Results Gametogenesis of Ulva mutabilis, a model organism for green seaweeds, was studied. We analyzed transcriptome dynamics at different time points during gametogenesis following induction of reproduction by fragmentation and removal of sporulation inhibitors. Analyses demonstrated that 45% of the genes in the genome were differentially expressed during gametogenesis. We identified several transcription factors that potentially play a key role in the early gametogenesis of Ulva given the function of their homologs in higher plants and microalgae. In particular, the detailed expression pattern of an evolutionarily conserved transcription factor containing an RWP-RK domain suggested a key role during Ulva gametogenesis. Conclusions Transcriptomic analyses of gametogenesis in the green seaweed Ulva highlight the importance of a conserved RWP-RK transcription factor in the induction of sexual reproduction. The identification of putative master regulators of gametogenesis provides a starting point for further functional characterization.

scholarly journals Comparative Survey of Morphological Variations and Plastid Genome Sequencing Reveals Phylogenetic Divergence between Four Endemic Ilex Species

Forests ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 964
Author(s):  
Tao Su ◽  
Mengru Zhang ◽  
Zhenyu Shan ◽  
Xiaodong Li ◽  
Biyao Zhou ◽  
...  
Keyword(s):  
Plastid Genome ◽  
Strong Association ◽  
Nuclear Genome ◽  
Image Cytometry ◽  
Single Copy ◽  
Reproductive Organs ◽  
Rrna Genes ◽  
Phenotypic Traits ◽  
Trna Genes ◽  
Plastid Genomes

Holly (Ilex L.), from the monogeneric Aquifoliaceae, is a woody dioecious genus cultivated as pharmaceutical and culinary plants, ornamentals, and industrial materials. With distinctive leaf morphology and growth habitats, but uniform reproductive organs (flowers and fruits), the evolutionary relationships of Ilex remain an enigma. To date, few contrast analyses have been conducted on morphology and molecular patterns in Ilex. Here, the different phenotypic traits of four endemic Ilex species (I. latifolia, I. suaveolens, I. viridis, and I. micrococca) on Mount Huangshan, China, were surveyed through an anatomic assay and DNA image cytometry, showing the unspecified link between the examined morphology and the estimated nuclear genome size. Concurrently, the newly-assembled plastid genomes in four Ilex have lengths ranging from 157,601 bp to 157,857 bp, containing a large single-copy (LSC, 87,020–87,255 bp), a small single-copy (SSC, 18,394–18,434 bp), and a pair of inverted repeats (IRs, 26,065–26,102 bp) regions. The plastid genome annotation suggested the presence of numerable protein-encoding genes (89–95), transfer RNA (tRNA) genes (37–40), and ribosomal RNA (rRNA) genes (8). A comprehensive comparison of plastomes within eight Ilex implicated the conserved features in coding regions, but variability in the junctions of IRs/SSC and the divergent hotspot regions potentially used as the DNA marker. The Ilex topology of phylogenies revealed the incongruence with the traditional taxonomy, whereas it informed a strong association between clades and geographic distribution. Our work herein provided novel insight into the variations in the morphology and phylogeography in Aquifoliaceae. These data contribute to the understanding of genetic diversity and conservation in the medicinal Ilex of Mount Huangshan.

scholarly journals Land plants and DNA barcodes: short-term and long-term goals

2005 ◽  
Vol 360 (1462) ◽  
pp. 1889-1895 ◽  
Author(s):  
Mark W Chase ◽  
Nicolas Salamin ◽  
Mike Wilkinson ◽  
James M Dunwell ◽  
Rao Prasad Kesanakurthi ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Plastid Dna ◽  
Land Plant ◽  
Land Plants ◽  
Nuclear Ribosomal Dna ◽  
Short Term ◽  
Species Limits ◽  
Variable Regions

Land plants have had the reputation of being problematic for DNA barcoding for two general reasons: (i) the standard DNA regions used in algae, animals and fungi have exceedingly low levels of variability and (ii) the typically used land plant plastid phylogenetic markers (e.g. rbcL , trnL-F , etc.) appear to have too little variation. However, no one has assessed how well current phylogenetic resources might work in the context of identification (versus phylogeny reconstruction). In this paper, we make such an assessment, particularly with two of the markers commonly sequenced in land plant phylogenetic studies, plastid rbcL and internal transcribed spacers of the large subunits of nuclear ribosomal DNA (ITS), and find that both of these DNA regions perform well even though the data currently available in GenBank/EBI were not produced to be used as barcodes and BLAST searches are not an ideal tool for this purpose. These results bode well for the use of even more variable regions of plastid DNA (such as, for example, psbA-trnH ) as barcodes, once they have been widely sequenced. In the short term, efforts to bring land plant barcoding up to the standards being used now in other organisms should make swift progress. There are two categories of DNA barcode users, scientists in fields other than taxonomy and taxonomists. For the former, the use of mitochondrial and plastid DNA, the two most easily assessed genomes, is at least in the short term a useful tool that permits them to get on with their studies, which depend on knowing roughly which species or species groups they are dealing with, but these same DNA regions have important drawbacks for use in taxonomic studies (i.e. studies designed to elucidate species limits). For these purposes, DNA markers from uniparentally (usually maternally) inherited genomes can only provide half of the story required to improve taxonomic standards being used in DNA barcoding. In the long term, we will need to develop more sophisticated barcoding tools, which would be multiple, low-copy nuclear markers with sufficient genetic variability and PCR-reliability; these would permit the detection of hybrids and permit researchers to identify the ‘genetic gaps’ that are useful in assessing species limits.

scholarly journals Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jingling Li ◽  
Jianmin Tang ◽  
Siyuan Zeng ◽  
Fang Han ◽  
Jing Yuan ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Plastid Genome ◽  
Dna Barcode ◽  
Sequence Divergence ◽  
Rrna Genes ◽  
Bootstrap Support ◽  
Trna Genes ◽  
Hypervariable Regions ◽  
Plastid Genomes ◽  
Insight Into

Abstract Background Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca ‘Greizy’, Pilea peperomioides and Pilea serpyllacea ‘Globosa’) and performed comprehensive comparative analysis. Results The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae. Conclusion Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.

scholarly journals Comparative analysis of the complete plastid genomes of Mangifera species and gene transfer between plastid and mitochondrial genomes

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10774
Author(s):  
Yingfeng Niu ◽  
Chengwen Gao ◽  
Jin Liu
Keyword(s):  
Plastid Genome ◽  
Genome Structure ◽  
Dna Barcode ◽  
Intergenic Spacer ◽  
Mitochondrial Genomes ◽  
Dna Barcodes ◽  
Total Size ◽  
Genome Data ◽  
Plastid Genomes ◽  
High Support

Mango is an important commercial fruit crop belonging to the genus Mangifera. In this study, we reported and compared four newly sequenced plastid genomes of the genus Mangifera, which showed high similarities in overall size (157,780–157,853 bp), genome structure, gene order, and gene content. Three mutation hotspots (trnG-psbZ, psbD-trnT, and ycf4-cemA) were identified as candidate DNA barcodes for Mangifera. These three DNA barcode candidate sequences have high species identification ability. We also identified 12 large fragments that were transferred from the plastid genome to the mitochondrial genome, and found that the similarity was more than 99%. The total size of the transferred fragment was 35,652 bp, accounting for 22.6% of the plastid genome. Fifteen intact chloroplast genes, four tRNAs and numerous partial genes and intergenic spacer regions were identified. There are many of these genes transferred from mitochondria to the chloroplast in other species genomes. Phylogenetic analysis based on whole plastid genome data provided a high support value, and the interspecies relationships within Mangifera were resolved well.

scholarly journals The first complete chloroplast genome sequences in Resedaceae: Genome structure and comparative analysis

2021 ◽  
Vol 104 (4) ◽  
pp. 003685042110599
Author(s):  
Dhafer Alzahrani ◽  
Enas Albokhari ◽  
Abidina Abba ◽  
Samaila Yaradua
Keyword(s):  
Plastid Genome ◽  
High Throughput Sequencing ◽  
Genome Structure ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Plastid Genomes ◽  
Small Single Copy

Caylusea hexagyna and Ochradenus baccatus are two species in the Resedaceae family. In this study, we analysed the complete plastid genomes of these two species using high-throughput sequencing technology and compared their genomic data. The length of the plastid genome of C. hexagyna was 154,390 bp while that of O. baccatus was 153,380 bp. The lengths of the inverted repeats (IR) regions were 26,526 bp and 26,558 bp, those of the large single copy (LSC) regions were 83,870 bp and 83,023 bp; and those of the small single copy (SSC) regions were 17,468 bp and 17,241 bp in C. hexagyna and O. baccatus, respectively. Both genomes consisted of 113 genes: 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Repeat analysis showed that the plastid genome included all types of repeats, with more frequent occurrences of palindromic sequences. Comparative studies of SSR markers showed that there were 256 markers in C. hexagyna and 255 in O. baccatus; the majority of the SSRs in these plastid genomes were mononucleotide repeats (A/T). All the clusters in the phylogenetic tree had high support. This study reported the first complete plastid genomes of the genera Caylusea and Ochradenus and the first for the Resedaceae family.

scholarly journals Gametogenesis in the green seaweed Ulva mutabilis coincides with massive transcriptional restructuring

2021 ◽  
Author(s):  
Xiaojie Liu ◽  
Jonas Blomme ◽  
Kenny Bogaert ◽  
Sofie Dhondt ◽  
Thomas Wichard ◽  
...  
Keyword(s):  
Higher Plants ◽  
Crop Improvement ◽  
Functional Characterization ◽  
Model Organism ◽  
Land Plants ◽  
Alternative Source ◽  
Master Regulators ◽  
Energy Applications ◽  
Starting Point ◽  
Green Seaweed

The molecular mechanism underlying sexual reproduction in land plants is well understood in model plants and is a target for crop improvement. However, unlike land plants, the genetic basis involved in triggering reproduction and gamete formation remains elusive in most seaweeds, which are increasingly viewed as an alternative source of functional food and feedstock for energy applications. Here, gametogenesis of Ulva mutabilis, a model organism for green seaweeds, is studied. We analyze transcriptome dynamics at different time points during gametogenesis following induction of reproduction by fragmentation and removal of sporulation inhibitors. Analyses demonstrate that 45% of the genes in the genome are differentially expressed during gametogenesis. We identified several transcription factors that potentially play a key role in the early gametogenesis of Ulva given the function of their homologs in higher plants and microalgae. In particular, the detailed expression pattern of an evolutionary conserved transcription factor containing an RWP-RK domain suggests a key role during Ulva gametogenesis. The identification of putative master regulators of gametogenesis provides a starting point for further functional characterization.

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