Whole genome re-sequencing and development of SSR markers in oriental melon

Song, Woon-Ho; Chung, Sang-Min

doi:10.5010/jpb.2019.46.2.071

Cited by 7 publications

(5 citation statements)

References 23 publications

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“…The Characteristics of SSR. With the rapid development of sequencing technology, more and more transcriptome data of Chinese herbal medicines such as S. miltiorrhiza, Dendrobium catenatum, Polygonatum Mill., and G. uralensis had been released [28], which provided feasibility and practical basis for developing genomic-SSR [29], EST-SSR, SNP [8][9][10], InDel [30], and KASP molecular markers. In this study, a total of 165,912 SSR loci with a frequency of 25.86% were identified from 435,858 unigenes of P. sibiricum transcriptome under the MISA screening conditions.…”

Section: Discussionmentioning

confidence: 99%

SSR Loci Analysis in Transcriptome and Molecular Marker Development in Polygonatum sibiricum

Yang

Jiang

Wang³

et al. 2022

BioMed Research International

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To study the SSR loci information and develop molecular markers, a total of 435,858 unigenes in transcriptome of Polygonatum sibiricum were used to explore SSR. The distribution frequency of SSR and the basic characteristics of repeat motifs were analyzed using MISA software, and SSR primers were designed by Primer 3.0 software and then validated by PCR. Moreover, the gene function analysis of SSR Unigene was obtained by Blast. The results showed that 112,728 SSR loci were found in the transcriptome of Polygonatum sibiricum, which distributed in 435,858 unigenes with a distribution frequency of 25.86%. Mo-nucleotide and Di-nucleotide repeat were the main types, accounted for 83.83% of all SSRs. The repeat motifs of A/T and AC/GT were the predominant repeat types of Mo-nucleotide and Di-nucleotide, respectively. A total of 113,305 pairs of SSR primers with the potential to produce polymorphism were designed for maker development. One hundred and fifty-four of the 500 randomly selected primers not only produced fragments with expected molecular size but also had high polymorphism, which could accurately separate the tested varieties. The gene function of unigenes containing SSR was mostly related to the molecular function of Polygonatum sibiricum. The SSR markers in transcriptome of Polygonatum sibiricum show rich type, strong specificity, and high potential of polymorphism, which will benefit the candidate gene mining and marker-assisted breeding. The developed markers can also provide technical methods for molecular identification of intraspecific species of Polygonatum Mill. and maker-assisted breeding of superior varieties of Polygonatum Mill.

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Section: Discussionmentioning

confidence: 99%

SSR Loci Analysis in Transcriptome and Molecular Marker Development in Polygonatum sibiricum

Yang

Jiang

Wang³

et al. 2022

BioMed Research International

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“…A comparison of the published genome sizes of plants suggests that the A. venetum genome is relatively small, indicating that future genome assembly and annotation should be relatively simple. We have completed the genome survey of A. cannabinum and found its genome to be 239.02 Mbp in size, which is smaller than that of A. venetum [32] .…”

Section: Discussionmentioning

confidence: 99%

Genome survey and SSR analysis of Apocynum venetum

Song

Chen

et al. 2019

Bioscience Reports

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Apocynum venetum is an eco-economic plant that exhibits high stress resistance. In the present paper, we carried out a whole-genome survey of A. venetum in order to provide a foundation for its whole-genome sequencing. High-throughput sequencing technology (Illumina NovaSep) was first used to measure the genome size of A. venetum, and bioinformatics methods were employed for the evaluation of the genome size, heterozygosity ratio, repeated sequences, and GC content in order to provide a foundation for subsequent whole-genome sequencing. The sequencing analysis results indicated that the preliminary estimated genome size of A. venetum was 254.40 Mbp, and its heterozygosity ratio and percentage of repeated sequences were 0.63 and 40.87%, respectively, indicating that it has a complex genome. We used k-mer = 41 to carry out a preliminary assembly and obtained contig N50, which was 3841 bp with a total length of 223949699 bp. We carried out further assembly to obtain scaffold N50, which was 6196 bp with a total length of 227322054 bp. We performed simple sequence repeat (SSR) molecular marker prediction based on the A. venetum genome data and identified a total of 101918 SSRs. The differences between the different types of nucleotide repeats were large, with mononucleotide repeats being most numerous and hexanucleotide repeats being least numerous. We recommend the use of the ‘2+3’ (Illumina+PacBio) sequencing combination to supplement the Hi-C technique and resequencing technique in future whole-genome research in A. venetum.

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“…The PacBio platform were used for whole genome sequencing the A. cannabinum genome. Table1 represents total sequencing volume was 117.13 G, and the coverage was 490.04 X based on calculations of the genome size (239.02 M) estimated from a survey (41). In addition, the Illumina platform was used for the sequencing of a constructed second-generation small fragment library.…”

Section: Sequencing Data Statisticsmentioning

confidence: 99%

Whole-genome Sequencing and Analysis of Apocynum Cannabinum

2023

JEMOA

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Background Apocynum cannabinum is an important plant resource from the Apocynaceae family. However, the lack of complete genome information has severely impeded research progress of molecular biology research in this plant. Whole-genome sequencing can provide an in-depth understanding of species growth, development, and evolutionary origin, and is the most effective method for scientifically exploring the ecological and economic value of a plant. Methods and results In this study, we employed Illumina HiSeq, single-molecule real-time sequencing, 10X genomics linked reads, and chromatin interaction (Hi-C), a new assembly technique, to successfully assemble the whole draft genome for A. cannabinum (260 Mb). The super-scaffold N50 genome size from the Hi-C assisted assembly was 21.16 Mb and was anchored to 11 chromosomes, resulting in a high-quality reference genome at the chromosome level (2n = 2x = 22). We further annotated, analyzed, and predicted 22,793 protein-coding genes, of which the functions of 95.6% were already annotated, 92.3% contained conserved protein domains, and 78.7% were aligned to known metabolic pathways. Conclusion’s: This high-quality A. cannabinum genome can be used to analyze growth and development and evaluate gene evolution at the genome level, as well as assist in the comparative genomics and genetic modification of other important medicinal plants in Apocynaceae. Comparative analysis of the gene families showed that A. cannabinum speciated around 35.8 (27.0–46.9) million years ago.

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Whole genome re-sequencing and development of SSR markers in oriental melon

Cited by 7 publications

References 23 publications

SSR Loci Analysis in Transcriptome and Molecular Marker Development in Polygonatum sibiricum

SSR Loci Analysis in Transcriptome and Molecular Marker Development in Polygonatum sibiricum

Genome survey and SSR analysis of Apocynum venetum

Whole-genome Sequencing and Analysis of Apocynum Cannabinum

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