Genome Analysis of the Ancient Tracheophyte Selaginella tamariscina Reveals Evolutionary Features Relevant to the Acquisition of Desiccation Tolerance

Molecular Plant, Journal Year: 2018, Volume and Issue: 11(7), P. 983 - 994

Published: May 17, 2018

Resurrection plants, which are the "gifts" of natural evolution, ideal models for studying genetic basis plant desiccation tolerance. Here, we report a high-quality genome assembly 301 Mb diploid spike moss Selaginella tamariscina, primitive vascular resurrection plant. We predicated 27 761 protein-coding genes from assembled S. tamariscina genome, 11.38% (2363) showed significant expression changes in response to desiccation. Approximately 60.58% was annotated as repetitive DNA, is an almost 2-fold increase that desiccation-sensitive moellendorffii. Genomic and transcriptomic analyses highlight unique evolution complex regulations including species-specific expansion oleosin pentatricopeptide repeat gene families, pathways reactive oxygen species generation scavenging, enhanced abscisic acid (ABA) biosynthesis potentially distinct regulation ABA signaling response. Comparative analysis chloroplast genomes several revealed structural rearrangement complete loss NAD(P)H dehydrogenase (NDH) suggesting link between absence NDH Taken together, our comparative genomic reveal common tolerance strategies providing insights into mechanism plants.

Language: Английский

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Complete Chloroplast Genomes of Papaver rhoeas and Papaver orientale: Molecular Structures, Comparative Analysis, and Phylogenetic Analysis

Molecules, Journal Year: 2018, Volume and Issue: 23(2), P. 437 - 437

Published: Feb. 16, 2018

Papaver rhoeas L. and P. orientale L., which belong to the family Papaveraceae, are used as ornamental medicinal plants. The chloroplast genome has been for molecular markers, evolutionary biology, barcoding identification. In this study, complete sequences of reported. Results show that genomes have typical quadripartite structures, comprised circular 152,905 152,799-bp-long molecules, respectively. A total 130 genes were identified in each genome, including 85 protein-coding genes, 37 tRNA 8 rRNA genes. Sequence divergence analysis four species from Papaveraceae indicated most divergent regions found non-coding spacers with minimal differences among three species. These include ycf1 gene intergenic regions, such rpoB-trnC, trnD-trnT, petA-psbJ, psbE-petL, ccsA-ndhD. hypervariable can be specific DNA barcodes. This finding suggested could a powerful tool resolve phylogenetic positions relationships Papaveraceae. results offer valuable information future research identification will benefit further investigations these

Language: Английский

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

International Journal of Molecular Sciences, Journal Year: 2019, Volume and Issue: 20(16), P. 4040 - 4040

Published: Aug. 19, 2019

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

Language: Английский

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Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia

BMC Genomics, Journal Year: 2021, Volume and Issue: 22(1)

Published: Feb. 26, 2021

Abstract Background Chloroplast genome resources can provide useful information for the evolution of plant species. Tea ( Camellia sinensis ) is among most economically valuable member . Here, we determined chloroplast first natural triploid Chinary type tea (‘Wuyi narcissus’ cultivar var. , CWN and conducted comparison with diploid CSS two types Assamica teas assamica : Chinese tea, CSA Indian CIA ). Further, evolutionary mechanism relationships species based on were discussed. Results Comparative analysis showed dynamics repeats insertion-deletions (indels), distribution repeats, indels substitutions significantly correlated. had significant differences in structural characteristic codon usage genome. Analysis sequence characterized amplified region (SCAR) using sequences intergenic spacers (trnE/trnT) none 292 different cultivars similar to but other four did. Estimations divergence time that diverged from common ancestor about 6.2 Mya (CI: 4.4–8.1 Mya). each 0.8 0.4–1.5 Moreover, phylogenetic clustering was not exactly consistent current taxonomy Conclusions The repeat-induced indel-induced mutations important contributed diversification which mutually exclusive. might have undergone selection pressures. transfer occurred during polyploid In addition, our results supported three domestication origins tea. And, classification some need be further

Language: Английский

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Complete Chloroplast Genome Sequences of Kaempferia Galanga and Kaempferia Elegans: Molecular Structures and Comparative Analysis

Molecules, Journal Year: 2019, Volume and Issue: 24(3), P. 474 - 474

Published: Jan. 29, 2019

Kaempferia galanga and elegans, which belong to the genus family Zingiberaceae, are used as valuable herbal medicine ornamental plants, respectively. The chloroplast genomes have been for molecular markers, species identification phylogenetic studies. In this study, complete genome sequences of K. elegans reported. Results show that is 163,811 bp long, having a quadripartite structure with large single copy (LSC) 88,405 small (SSC) 15,812 separated by inverted repeats (IRs) 29,797 bp. Similarly, 163,555 in IRs 29,773 length separates 88,020 LSC 15,989 SSC. A total 111 genes 113 comprised 79 protein-coding 4 ribosomal RNA (rRNA) genes, well 28 30 transfer (tRNA) gene order, GC content orientation two exhibited high similarity. location distribution simple sequence (SSRs) long repeat were determined. Eight highly variable regions between identified 643 mutation events, including 536 single-nucleotide polymorphisms (SNPs) 107 insertion/deletions (indels), accurately located. Sequence divergences whole calculated among related Zingiberaceae species. analysis based on SNPs eleven strongly supported formed cluster within Zingiberaceae. This study unique characteristics entire contribute our understanding DNA evolution It provides information Kaempferia.

Language: Английский

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Comparative and Phylogenetic Analyses of Ginger (Zingiber officinale) in the Family Zingiberaceae Based on the Complete Chloroplast Genome

Plants, Journal Year: 2019, Volume and Issue: 8(8), P. 283 - 283

Published: Aug. 12, 2019

Zingiberofficinale, commonly known as ginger, is an important plant of the family Zingiberaceae and widely used herbal medicine condiment. The lack chloroplast genomic information hinders molecular research phylogenetic analysis on ginger. We introduced complete genome Z. officinale identified its position in Zingiberaceae. 162,621 bp with a four-part circular structure 36.1% GC content. All 113 unique genes were annotated. A total 78 simple sequence repeats (SSRs) 42 long repeat sequences, which are potential areas for species authentication, found. Comparative revealed some highly variable regions, including rps16-trnQ-UUG, atpH-atpI, trnT-UGU-trnL-UAA, ycf1, psaC-ndhE. Moreover, small single-copy (SSC) region was most all four shared indicating that it may be undergoing rapid nucleotide substitution Phylogenetic based available chloroplasts Zingiberales National Center Biotechnology Information indicated Zingiber sister branch to Kaempferia species. availability provided invaluable data species-level authentication can thus benefit further investigations

Language: Английский

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Insights Into Chloroplast Genome Evolution Across Opuntioideae (Cactaceae) Reveals Robust Yet Sometimes Conflicting Phylogenetic Topologies

Frontiers in Plant Science, Journal Year: 2020, Volume and Issue: 11

Published: June 19, 2020

Chloroplast genomes are frequently treated as highly conserved among plants. However, many lineages of vascular plants have experienced structural rearrangements, including inversions and modifications to the size content genes. Cacti one these lineages, containing smallest plastome known for an obligately photosynthetic angiosperm, loss copy inverted repeat ndh gene suite, but only a few cacti from subfamily Cactoideae been characterized. Here, we investigated variation sequences across second-major lineage Cactaceae, Opuntioideae, address 1) how variable is arrangement chloroplast genome subfamily, 2) phylogenetically informative resolving major relationships clades Opuntioideae. Our de novo assembly Opuntia quimilo recovered organelle 150,347 bp in length with both copies presence all suite. An expansion large single unit reduction small was observed, translocations inversion genes well putative pseudogenization some loci. Comparative analyses within Opuntioideae suggested that structure vary taxa this independent losses suite disparate further demonstrating dynamic nature plastomes Cactaceae. dataset robust three tribes high support Opuntioideae: Cylindropuntieae, Tephrocacteae Opuntieae. conflicting topologies were when exploring different assemblies markers. A plastome-wide survey phylogenetic markers revealed previously unused regions future use Sanger-based studies, presenting valuable primers designed continued evolutionary studies These results bring new insights into evolution cacti, suggesting should be carried out ecological drivers, physiological constraints morphological traits may related common rearrangements reported family.

Language: Английский

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Species Identification of Dracaena Using the Complete Chloroplast Genome as a Super-Barcode

Frontiers in Pharmacology, Journal Year: 2019, Volume and Issue: 10

Published: Nov. 29, 2019

The taxonomy and nomenclature of Dracaena plants are much disputed, particularly for several species in Asia. However, neither morphological features nor common DNA regions ideal identification spp. Meanwhile, although multiple sources the rare traditional medicine dragon's blood, Pharmacopoeia People's Republic China has defined cochinchinensis as only source plant. inaccurate will inevitably affect clinical efficacy blood. It is therefore important to find a better method distinguish these species. Here, we report complete chloroplast (CP) genomes six spp., D. cochinchinensis, cambodiana, angustifolia, terniflora, hokouensis, elliptica, obtained through high-throughput Illumina sequencing. These CP exhibited typical circular tetramerous structure, their sizes ranged from 155,055 (D. elliptica) 155,449 bp cochinchinensis). GC content each genome was 37.5%. Furthermore, contained 130 genes, including 84 protein-coding 38 tRNA 8 rRNA genes. There were no potential coding or non-coding species, but maximum likelihood tree other related revealed that whole can be used super-barcode identify This study provides not invaluable data safe medical application also an reference foundation phylogeny Liliaceae plants.

Language: Английский

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Sequencing and Comparative Analysis of the Chloroplast Genome of Angelica polymorpha and the Development of a Novel Indel Marker for Species Identification

Molecules, Journal Year: 2019, Volume and Issue: 24(6), P. 1038 - 1038

Published: March 15, 2019

The genus Angelica (Apiaceae) comprises valuable herbal medicines. In this study, we determined the complete chloroplast (CP) genome sequence of A. polymorpha and compared it with that Ligusticum officinale (GenBank accession no. NC039760). CP genomes L. were 148,430 147,127 bp in length, respectively, 37.6% GC content. Both harbored 113 unique functional genes, including 79 protein-coding, four rRNA, 30 tRNA genes. Comparative analysis two revealed conserved structure, gene content, order. However, highly variable regions, sufficient to distinguish between officinale, identified hypothetical open reading frame1 (ycf1) ycf2 genic regions. Nucleotide diversity (Pi) indicated ycf4⁻chloroplast envelope membrane protein (cemA) intergenic region was species. Phylogenetic well clustered at family Apiaceae. ycf4-cemA carried a 418 deletion officinale. This used for development novel indel marker, LYCE, which successfully discriminated accessions. Our results provide important taxonomic phylogenetic information on medicines facilitate their authentication using marker.

Language: Английский

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Gene loss, genome rearrangement, and accelerated substitution rates in plastid genome of Hypericum ascyron (Hypericaceae)

BMC Plant Biology, Journal Year: 2022, Volume and Issue: 22(1)

Published: March 23, 2022

Comparative genomic analysis exhibits dynamic evolution of plastid genome (plastome) in the clusioid clade Malpighiales, which comprise five families, including multiple inversions and gene losses. Little is known about plastome Hypericaceae, a large family clade. Only one species, Cratoxylum cochinchinense, has been published.We generated complete sequence for Hypericum ascyron, providing first from tribe Hypericeae (Hypericaceae). The H. ascyron changes intron content, structure, divergence compared to C. cochinchinense Cratoxyleae Transcriptome data determined evolutionary fate missing genes infA, rps7, rps16, rpl23, rpl32 ascyron. Putative functional transfers were detected nucleus, whereas rps16 rpl23 substituted by nuclear-encoded homologs. was integrated into SODcp gene. Our findings suggested that transferred had undergone subfunctionalization duplication rather than alternative splicing. rearrangements involved seven inversions, at least three inverted repeat (IR) boundary shifts, relocations duplications. Accelerated substitution rates observed with genes. higher accD clpP correlated structural change, insertion amino acids losses two introns, respectively. In addition, we found evidence positive selection clpP, matK, rps3 branches related particular, matK repeatedly under within Hypericaceae. Selective pressure associated loss trnK-UUU relocation IR region.The provides valuable information improving understanding among Malpighiales. Evidence intracellular transfer nucleus nuclear transcriptome, insight

Language: Английский

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