De Novo Transcriptome Assembly and EST-SSR Marker Development and Application in Chrysosplenium macrophyllum

Xiang, Niyan; Lu, Bojie; Yuan, Tao; Yang, Tiange; Wu, Zhihua; Liu, Hong; Liu, Xing; Qin, Rui

doi:10.3390/genes14020279

Cited by 6 publications

(3 citation statements)

References 65 publications

(78 reference statements)

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“…SSRs are important molecular markers used in genetic diversity research and molecular breeding (Jin et al 2020). In G. longituba , mono‐nucleotide SSR repeats were the most abundant SSR type, which is consistent with previous results in Chrysosplenium macrophyllum (Xiang et al 2023), Amomum tsaoko (Ma et al 2022), and Ammopiptanthus mongolicus (Jin et al 2016). LncRNAs are a class of RNA transcripts with a length of more than 200 bp, which lack the ability to encode proteins.…”

Section: Discussionsupporting

confidence: 91%

Full‐length transcriptome sequencing provides new insights into the complexity of flavonoid biosynthesis in Glechoma longituba

Shan,

Xu,

Zhong

et al. 2023

Physiologia Plantarum

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Glechoma longituba has been frequently used in treating urolithiasis and cholelithiasis due to the presence of flavonoids, which are its major bioactive constituents. However, research on the molecular background of flavonoid biosynthesis in G. longituba is limited. In this study, we used single‐molecule real‐time combined with next‐generation sequencing technologies to construct the complete transcriptome of G. longituba. We identified 404,648 non‐redundant transcripts, including 249,697 coding sequences, 197,811 simple sequence repeats, 174,846 long noncoding RNA, and 176,554 coding RNA. Moreover, we functionally annotated 346,218 isoforms (85.56%) and identified 86,528 differentially expressed genes. We also identified 55 non‐redundant full‐length isoforms related to the flavonoid biosynthetic pathway. Pearson correlation analysis revealed that the expression levels of some key genes of the flavonoid biosynthesis pathway were significantly positively correlated with the flavonoid metabolites. Furthermore, we performed bioinformatics analysis (sequence and structural) of isoform_47029 (encoding flavanone 3‐hydroxylase) and isoform_53692 (encoding flavonol synthase) to evaluate their potential biological functions. Finally, we validated gene expression levels of 12 flavonoid‐related key enzyme genes using quantitative real‐time PCR. Overall, this study provides full‐length transcriptome information on G. longituba for the first time and valuable molecular resources for further research on the medicinal properties of this plant.

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Section: Discussionsupporting

confidence: 91%

Full‐length transcriptome sequencing provides new insights into the complexity of flavonoid biosynthesis in Glechoma longituba

Shan,

Xu,

Zhong

et al. 2023

Physiologia Plantarum

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“…cDNA libraries were constructed. A normalized cDNA library of A. heimuer was constructed using methods described by Venugopal et al [47][48][49][50] . Then, sequencing with an Illumina NovaSeq 6000 was performed to generate raw data.…”

Section: Rna Extraction and Transcriptome Sequencingmentioning

confidence: 99%

Transcriptome analysis and development of EST-SSR markers in the mushroom Auricularia heimuer

Jiao,

Han,

Zhu

et al. 2024

Sci Rep

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Auricularia heimuer, the third most frequently cultivated edible mushroom species worldwide, has high medicinal value. However, a shortage of molecular marker hinders the efficiency and accuracy of genetic breeding efforts for A. heimuer. High-throughput transcriptome sequencing data are essential for gene discovery and molecular markers development. This study aimed to clarify the distribution of SSR loci across the A. heimuer transcriptome and to develop highly informative EST-SSR markers. These tools can be used for phylogenetic analysis, functional gene mining, and molecular marker-assisted breeding of A. heimuer. This study used Illumina high-throughput sequencing technology to obtain A. heimuer transcriptome data. The results revealed 37,538 unigenes in the A. heimuer transcriptome. Of these unigenes, 24,777 (66.01%) were annotated via comparison with the COG, Pfam, and NR databases. Overall, 2510 SSRs were identified from the unigenes, including 6 types of SSRs. The most abundant type of repeats were trinucleotides (1425, 56.77%), followed by mononucleotides (391, 15.58%) and dinucleotides (456, 18.17%). Primer pairs for 102 SSR loci were randomly designed for validity confirmation and polymorphism identification; this process yielded 53 polymorphic EST-SSR markers. Finally, 13 pairs of highly polymorphic EST-SSR primers were used to analyze the genetic diversity and population structure of 52 wild A. heimuer germplasms, revealing that the 52 germplasms could be divided into three categories. These results indicated that SSR loci were abundant in types, numbers, and frequencies, providing a potential basis for germplasm resource identification, genetic diversity analysis, and molecular marker-assisted breeding of A. heimuer.

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“…SSR isolation using WGS has been carried out on cultivated spinach (Spinacia oleracea) (Bhattarai et al 2021) and grape (Vitis vinifera) (Pei et al 2023). SSR isolation for transcriptome assembly has been carried out in crispa (Luctuca sativa) (Zhang et al 2021), oil palm (Zhou et al 2020), red ginger (Alpinia purpurata) (Vidya et al 2021), and golden saxifrage (Chrysosplenium alternifolium) (Xiang et al 2023).…”

Section: Introductionmentioning

confidence: 99%

Profile microsatellite mining of whole genome sequencing and transcriptomic assembly in dwarf and tall areca nut (Areca catechu) in Indonesia

ROMADHON,

SOBIR,

SUWARNO

et al. 2024

Biodiversitas

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Abstract. Romadhon MR, Sobir, Suwarno WB, Matra DD. 2024. Profile microsatellite mining of whole genome sequencing and transcriptomic assembly in dwarf and tall areca nut (Areca catechu L.) in Indonesia. Biodiversitas 25: 1081-1088. Areca nut (Areca catechu L.) has high diversity in fruit shape and flowering time. Two superior varieties are commonly cultivated in Indonesia, namely Betara areca nut (tall) and Emas areca nut (dwarf). Molecular level diversity from genomic and transcriptome of areca nut data is available at NCBI, but not yet for Indonesian areca nut. The research compared the results of SSR with two method approaches to detect genetic diversity in the plants accurately. This study aimed to compare the SSR motifs of Betara areca nut and Emas areca nut varieties from whole genome sequencing and transcriptome assembly. The research was conducted at the Leuwikopo Seed Centre Laboratory of the IPB University, Bogor, Indonesia. The methods used are Whole Genome Sequencing (WGS) and transcriptome assembly. A total number of identified SSRs from WGS approach from Betara areca nut of 95 SSRs and Emas areca nut of 95 SSRs, while Betara areca nut SSRs from transcriptome assembly of 466 SSRs and Emas areca nut of 357 SSRs. The percentage of contigs and transcripts from Betara areca nut containing SSR was 7.43% and 4.22%, respectively, while Emas areca nut was 8.06% and 2.04%, respectively. AT is the dominant SSR motif in WGS, while the GA motif dominates the transcriptome assembly results.

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De Novo Transcriptome Assembly and EST-SSR Marker Development and Application in Chrysosplenium macrophyllum

Cited by 6 publications

References 65 publications

Full‐length transcriptome sequencing provides new insights into the complexity of flavonoid biosynthesis in Glechoma longituba

Full‐length transcriptome sequencing provides new insights into the complexity of flavonoid biosynthesis in Glechoma longituba

Transcriptome analysis and development of EST-SSR markers in the mushroom Auricularia heimuer

Profile microsatellite mining of whole genome sequencing and transcriptomic assembly in dwarf and tall areca nut (Areca catechu) in Indonesia

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