Development and characterization of genomic microsatellite markers in the tree species, Rhodoleia championii, R. parvipetala, and R. forrestii (Hamamelidaceae)

Huang, Yanshuang; Yin, Qianyi; Trương, Bá Vương; Meng, Kaikai; Chen, Sufang; Liao, Boyong; Fan, Qingxia

doi:10.1007/s11033-019-05106-w

Cited by 3 publications

(2 citation statements)

References 19 publications

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“…In some cases we detected a low efficiency of the primer design which could be attributed to the low coverage of our draft genome, leading to misassembly in the repetitive elements regions [ 58 , 59 ]. Nevertheless, the percentage of suitable primer pairs resulted in line with the one detected in previous SSR mining reports based on draft genome sequence obtained at low-coverage [ 60 , 61 , 62 ].…”

Section: Resultssupporting

confidence: 83%

Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

Martina

Acquadro

Barchi

et al. 2022

IJMS

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Anemone coronaria L. (2n = 2x = 16) is a perennial, allogamous, highly heterozygous plant marketed as a cut flower or in gardens. Due to its large genome size, limited efforts have been made in order to develop species-specific molecular markers. We obtained the first draft genome of the species by Illumina sequencing an androgenetic haploid plant of the commercial line “MISTRAL® Magenta”. The genome assembly was obtained by applying the MEGAHIT pipeline and consisted of 2 × 106 scaffolds. The SciRoKo SSR (Simple Sequence Repeats)-search module identified 401.822 perfect and 188.987 imperfect microsatellites motifs. Following, we developed a user-friendly “Anemone coronaria Microsatellite DataBase” (AnCorDB), which incorporates the Primer3 script, making it possible to design couples of primers for downstream application of the identified SSR markers. Eight genotypes belonging to eight cultivars were used to validate 62 SSRs and a subset of markers was applied for fingerprinting each cultivar, as well as to assess their intra-cultivar variability. The newly developed microsatellite markers will find application in Breeding Rights disputes, developing genetic maps, marker assisted breeding (MAS) strategies, as well as phylogenetic studies.

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Section: Resultssupporting

confidence: 83%

Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

Martina

Acquadro

Barchi

et al. 2022

IJMS

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“…The complete chloroplast genome contains all genes used to reconstruct the evolutionary history and provides more valuable and high‐quality information for evolutionary and phylogenetic analyses (Li et al, 2019). Complete chloroplast genome sequences are easily obtained due to the rapid development of large‐scale high‐throughput sequencing techniques, such as the Illumina and PacBio sequencing platforms (Huang et al, 2019; Kim et al, 2021; Lin et al, 2018; Yang et al, 2019; Ye et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

The complete chloroplast genomes of three Hamamelidaceae species: Comparative and phylogenetic analyses

Wang

Chen

Xie

et al. 2022

Ecology and Evolution

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Hamamelidaceae is an important group that represents the origin and early evolution of angiosperms. Its plants have many uses, such as timber, medical, spice, and ornamental uses. In this study, the complete chloroplast genomes of Loropetalum chinense (R. Br.) Oliver, Corylopsis glandulifera Hemsl., and Corylopsis velutina Hand.‐Mazz. were sequenced using the Illumina NovaSeq 6000 platform. The sizes of the three chloroplast genomes were 159,402 bp (C. glandulifera), 159,414 bp (C. velutina), and 159,444 bp (L. chinense), respectively. These chloroplast genomes contained typical quadripartite structures with a pair of inverted repeat (IR) regions (26,283, 26,283, and 26,257 bp), a large single‐copy (LSC) region (88,134, 88,146, and 88,160 bp), and a small single‐copy (SSC) region (18,702, 18,702, and 18,770 bp). The chloroplast genomes encoded 132–133 genes, including 85–87 protein‐coding genes, 37–38 tRNA genes, and 8 rRNA genes. The coding regions were composed of 26,797, 26,574, and 26,415 codons, respectively, most of which ended in A/U. A total of 37–43 long repeats and 175–178 simple sequence repeats (SSRs) were identified, and the SSRs contained a higher number of A + T than G + C bases. The genome comparison showed that the IR regions were more conserved than the LSC or SSC regions, while the noncoding regions contained higher variability than the gene coding regions. Phylogenetic analyses revealed that species in the same genus tended to cluster together. Chunia Hung T. Chang, Mytilaria Lecomte, and Disanthus Maxim. may have diverged early and Corylopsis Siebold & Zucc. was closely related to Loropetalum R. Br. This study provides valuable information for further species identification, evolution, and phylogenetic studies of Hamamelidaceae plants.

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Genome-wide discovery of single- and multi-locus simple sequence repeat markers and their characterization in Dendrocalamus strictus: a commercial polyploid bamboo species of India

Rohilla,

Ginwal,

Rana

et al. 2023

Genet Resour Crop Evol

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Development and characterization of genomic microsatellite markers in the tree species, Rhodoleia championii, R. parvipetala, and R. forrestii (Hamamelidaceae)

Cited by 3 publications

References 19 publications

Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

The complete chloroplast genomes of three Hamamelidaceae species: Comparative and phylogenetic analyses

Genome-wide discovery of single- and multi-locus simple sequence repeat markers and their characterization in Dendrocalamus strictus: a commercial polyploid bamboo species of India

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