Genome Survey Sequencing of Luffa Cylindrica L. and Microsatellite High Resolution Melting (SSR-HRM) Analysis for Genetic Relationship of Luffa Genotypes

An, Jianyu; Yin, Mengqi; Zhang, Qin; Gong, Dongting; Jia, Xuchao; Guan, Yajing; Hu, Jin

doi:10.3390/ijms18091942

Cited by 19 publications

(6 citation statements)

References 38 publications

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“…Six classes of perfect SSRs were evaluated (from mono-to hexanucleotide) for their abundance in the assembled genome. Dinucleotides were the most abundant, in accordance with what has been previously reported in literature [30][31][32][33][34][35][36][37][38][39], representing 60.2% of the identified SSRs. Trinucleotides were the second most abundant class (23.7%), followed by tetranucleotides (6.8%).…”

Section: The Ssr Content Of the Poppy Anemone Draft Genomesupporting

confidence: 91%

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: The Ssr Content Of the Poppy Anemone Draft Genomesupporting

confidence: 91%

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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“…Recently, the genome survey sequencing by next-generation sequencing (NGS) has come out as a main, e cient and cost-effective scheme for generating a large scale of genetic and genomic information for different species [7][8][9][10][11]. Genome survey sequencing (GSS) based on the NGS platform has been proven utile in identifying genome-wide microsatellite markers in many non-model species especially [12][13]].…”

Section: Introductionmentioning

confidence: 99%

Genome survey sequencing and identification of genomic SSR markers for Batocera horsfieldi (Coleoptera: Cerambycidae)

Peng

Zhende

et al. 2021

Preprint

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The white-striped longhorn beetle Batocera horsfieldi (Coleoptera: Cerambycidae) is a polyphagous wood-boring pest that causes substantial damage to the lumber, fruit and nut industry. Here, next-generation sequencing was used to generate a whole genome survey dataset to provide fundamental information of its genome and develop genome-wide microsatellite markers for it. The genome size of B. horsfieldi was estimated as approximate 520 Mb by using K-mer analyses, and its heterozygosity ratio and repeat sequence ratio were 0.26% and 51.03%, respectively. The assembled genome was 528.56Mb with GC content of 35.40%. A total of 121750 microsatellite motifs were identified. The most frequent repeat motif was mononucleotide with a frequency of 85.84%, followed by 8.08% of dinonucleotide, 5.04% of trinonucleotide, 0.73% of tetranonucleotide, 0.20% of pentanonucleotide and 0.12% of hexanonucleotide motifs. The AT/AT, TA/TAand GA/TC repeats were the most abundant motifs of dinucleotide motifs, and AAT/ATT, TAA/TTA and ATA/TAT were the most abundant motifs of trinucleotide motifs, respectively. ninety six pairs of SSR primers were randomly selected for PCR amplification and agarose gel electrophoresis detection, among which 56 pairs of primers can be effectively amplified to obtain the target fragment. In summary, various candidate microsatellite markers were identified and characterized in this study using genome survey analysis.

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“…S1). Di-nucleotide microsatellites have been described as the most abundant in plant genomes, as in Carthamus tinctorius L. (Asteraceae) (Ambreen et al 2015), Luffa Cylindrica L. (An et al 2017), Sesamum indicum L. (Wei et al 2014), Cynara cardunculus L. (Portis et al 2016), and Pistacia vera L. (Motalebipour et al 2016).…”

Section: Resultsmentioning

confidence: 99%

Genome survey and development of 15 microsatellite molecular markers in Syagrus coronata (Martius) Beccari (Arecaceae) by next-generation sequencing

Barbosa

2018

Braz. J. Bot

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Syagrus coronata (Martius) Beccari belongs to the Arecaceae family, an economically and ecologically important species of palm tree. It grows in northeastern Brazil and has a widespread geographic distribution in the ''Caatinga'' (a seasonally dry tropical forest biome) and Atlantic forest domains (a rain forest biome). The aim of this study was to perform a genome survey and develop SSR markers using high-throughput sequencing. We obtained 78,231,881 million Illumina single-end and paired-end reads, and these reads were used to obtain contigs with a minimum of 500 nucleotides using Ray software. Mining of the SSRs was performed with Phobos software, while the primers were designed by Primer3. Thirty loci were analyzed, three of which were not amplified, 12 were monomorphic, and 15 were polymorphic. Five to 11 alleles per locus were observed, with the observed and expected heterozygosity at 0.06-0.63 and 0.73-0.88, respectively. Here, we report the first set of microsatellite markers developed for S. coronata, and their polymorphism levels indicate they can be used as powerful tools for evaluating genetic diversity and population structure, and thus contribute to conservation studies.

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Genome Survey Sequencing of Luffa Cylindrica L. and Microsatellite High Resolution Melting (SSR-HRM) Analysis for Genetic Relationship of Luffa Genotypes

Cited by 19 publications

References 38 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.

Genome survey sequencing and identification of genomic SSR markers for Batocera horsfieldi (Coleoptera: Cerambycidae)

Genome survey and development of 15 microsatellite molecular markers in Syagrus coronata (Martius) Beccari (Arecaceae) by next-generation sequencing

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