Development of microsatellite loci in Mediterranean sarsaparilla (<i>Smilax aspera</i>; Smilacaceae) using transcriptome data

Qi, Zhe-Chen; Shen, Chao; Han, Yuwei; Shen, Wei; Mu, Yang; Liu, Jinliang; Liang, Zongsuo; Pan, Li; Fu, Chengxin

doi:10.3732/apps.1700005

Cited by 8 publications

(7 citation statements)

References 12 publications

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“…We developed 126 and 452 intergeneric and intrageneric polySSR markers between Oresitrophe and Mukdenia and within Oresitrophe . Twelve pairs of candidate gSSR primers were selected to test their transferability following Qi et al [ 94 ], primer transferability was detected using 2% agarose gels, and amplification was considered successful when one clear distinct band was visible in the expected size range. In total, 100% of the developed microsatellite markers we selected could be successfully amplified in two populations of M. rossii and four populations of O. rupifraga .…”

Section: Discussionmentioning

confidence: 99%

Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data

et al. 2018

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BackgroundEpilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae) have an epilithic habitat (rocky slopes) and a parapatric distribution in East Asia, which makes them an ideal model for a more comprehensive understanding of the demographic and divergence history and the influence of climate changes in East Asia. However, the genetic background and resources for these two genera are scarce.ResultsThe complete chloroplast (cp) genomes of two Oresitrophe rupifraga and one Mukdenia rossii individuals were reconstructed and comparative analyses were conducted to examine the evolutionary pattern of chloroplast genomes in Saxifragaceae. The cp genomes ranged from 156,738 bp to 156,960 bp in length and had a typical quadripartite structure with a conserved genome arrangement. Comparative analysis revealed the intron of rpl2 has been lost in Heuchera parviflora, Tiarella polyphylla, M. rossii and O. rupifraga but presents in the reference genome of Penthorum chinense. Seven cp hotspot regions (trnH-psbA, trnR-atpA, atpI-rps2, rps2-rpoC2, petN-psbM, rps4-trnT and rpl33-rps18) were identified between Oresitrophe and Mukdenia, while four hotspots (trnQ-psbK, trnR-atpA, trnS-psbZ and rpl33-rps18) were identified within Oresitrophe. In addition, 24 polymorphic cpSSR loci were found between Oresitrophe and Mukdenia. Most importantly, we successfully developed 126 intergeneric polymorphic gSSR markers between Oresitrophe and Mukdenia, as well as 452 intrageneric ones within Oresitrophe. Twelve randomly selected intergeneric gSSRs have shown that these two genera exhibit a significant genetic structure.ConclusionsIn this study, we conducted genome skimming for Oresitrophe rupifraga and Mukdenia rossii. Using these data, we were able to not only assemble their complete chloroplast genomes, but also develop abundant genetic resources (cp hotspots, cpSSRs, polymorphic gSSRs). The genomic patterns and genetic resources presented here will contribute to further studies on population genetics, phylogeny and conservation biology in Saxifragaceae.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4633-x) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data

et al. 2018

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“…A total of 27 danshen plants were genotyped using 10 SSR molecular markers to analyze the genetic diversity existing between and within the seven S. miltiorrhiza cultivars ( Table S2 ). Danshen SSR genotyping analysis method used established by Dr. Qi ZC [ 56 , 57 ].…”

Section: Methodsmentioning

confidence: 99%

Core Microbiome of Medicinal Plant Salvia miltiorrhiza Seed: A Rich Reservoir of Beneficial Microbes for Secondary Metabolism?

Chen

Yan

et al. 2018

IJMS

128

102

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Seed microbiome includes special endophytic or epiphytic microbial taxa associated with seeds, which affects seed germination, plant growth, and health. Here, we analyzed the core microbiome of 21 Salvia miltiorrhiza seeds from seven different geographic origins using 16S rDNA and ITS amplicon sequencing, followed by bioinformatics analysis. The whole bacterial microbiome was classified into 17 microbial phyla and 39 classes. Gammaproteobacteria (67.6%), Alphaproteobacteria (15.6%), Betaproteobacteria (2.6%), Sphingobacteria (5.0%), Bacilli (4.6%), and Actinobacteria (2.9%) belonged to the core bacterial microbiome. Dothideomycetes comprised 94% of core fungal microbiome in S. miltiorrhiza seeds, and another two dominant classes were Leotiomycetes (3.0%) and Tremellomycetes (2.0%). We found that terpenoid backbone biosynthesis, degradation of limonene, pinene, and geraniol, and prenyltransferases, were overrepresented in the core bacterial microbiome using phylogenetic examination of communities by reconstruction of unobserved states (PICRUSt) software. We also found that the bacterial genera Pantoea, Pseudomonas, and Sphingomonas were enriched core taxa and overlapped among S. miltiorrhiza, maize, bean, and rice, while a fungal genus, Alternaria, was shared within S. miltiorrhiza, bean, and Brassicaceae families. These findings highlight that seed-associated microbiomeis an important component of plant microbiomes, which may be a gene reservoir for secondary metabolism in medicinal plants.

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“…Different methods may be applied for genotyping in plants. Microsatellite (Martins et al, 2013a;Ru et al, 2017;Qi et al, 2017) and DNA barcodes (Cameron & Fu, 2006;Qi et al, 2013) have been used for genotyping Smilax species and have shown phylogenetic relationships between different Smilax species. Additionally, Sulistyaningsih et al (2018) used the DNA barcode rbcL for phylogenetic analysis of Smilax spp.…”

Section: Molecular Barcode Sequencesmentioning

confidence: 99%

“…Morphological and molecular barcode analysis are lacking for S. purhampuy in Ecuador, despite its medicinal use. Phylogenetic analysis of the Smilax genus includes microsatellites (Martins et al, 2013a;Ru et al, 2017;Qi et al, 2017) which are also informative tools for genetic diversity and gene flow studies. Other methods for the phylogenetic analysis of plants includes DNA barcodes, which may be used as a complementary tool in the taxonomic identification of the species; for instance, the plastid genome regions atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer, and trnH-psbA spacer have been tested as universal plant barcodes (CBOL Plant Working Group, 2009).…”

Section: Introductionmentioning

confidence: 99%

Molecular barcode and morphological analysis of Smilax purhampuy Ruiz, Ecuador

Soledispa

Santos-Ordóñez

Miranda

et al. 2021

PeerJ

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Smilax plants are distributed in tropical, subtropical, and temperate regions in both hemispheres of the world. They are used extensively in traditional medicines in a number of countries. However, morphological and molecular barcodes analysis, which may assist in the taxonomic identification of species, are lacking in Ecuador. In order to evaluate the micromorphological characteristics of these plants, cross sections of Smilax purhampuy leaves were obtained manually. The rhizome powder, which is typically used in traditional medicines, was analyzed for micromorphological characteristics. All samples were clarified with 1% sodium hypochlorite. Tissues were colored with 1% safranin in water and were fixed with glycerinated gelatin. DNA was extracted from the leaves using a modified CTAB method for molecular barcode characterization and PCR was performed using primers to amplify the different loci including the plastid genome regions atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer; and the nuclear DNA sequence ITS2. A DNA sequence similarity search was performed using BLAST in the GenBank nr database and phylogenetic analysis was performed using the maximum likelihood method according to the best model identified by MEGAX using a bootstrap test with 1,000 replicates. Results showed that the micromorphological evaluation of a leaf cross section depicted a concave arrangement of the central vein, which was more pronounced in the lower section and had a slight protuberance. The micromorphological analysis of the rhizome powder allowed the visualization of a group of cells with variable sizes in the parenchyma and revealed thickened xylematic vessels associated with other elements of the vascular system. Specific amplicons were detected in DNA barcoding for all the barcodes tested except for the trnH–psbA spacer. BLAST analysis revealed that the Smilax species was predominant in all the samples for each barcode; therefore, the genus Smilax was confirmed through DNA barcode analysis. The barcode sequences psbK-psbI, atpF-atpH, and ITS2 had a better resolution at the species level in phylogenetic analysis than the other barcodes we tested.

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Development of microsatellite loci in Mediterranean sarsaparilla (Smilax aspera; Smilacaceae) using transcriptome data

Cited by 8 publications

References 12 publications

Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data

Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data

Core Microbiome of Medicinal Plant Salvia miltiorrhiza Seed: A Rich Reservoir of Beneficial Microbes for Secondary Metabolism?

Molecular barcode and morphological analysis of Smilax purhampuy Ruiz, Ecuador

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