ArticleMolecular genetics and genomics : MGG2016
De novo assembly and characterization of the leaf, bud, and fruit transcriptome from the vulnerable tree Juglans mandshurica for the development of 20 new microsatellite markers using Illumina sequencing.
Article in Molecular genetics and genomics : MGG, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 60 citations in OpenAlex.
- Integrated endogenous hormones and transcriptome analysis contribute to fruit development related gene mining in Eriobotrya japonica.Scientific reports · 2025Article
- Genome-wide identification analysis of the 4-Coumarate: CoA ligase (4CL) gene family expression profiles in Juglans regia and its wild relatives J. Mandshurica resistance and salt stress.BMC plant biology · 2024Article
- Characterisation of theBiodiversity data journal · 2024Article
- A Multiplex PCR System of Novel Microsatellite Loci for Population Genetic Application in Walnuts.Plants (Basel, Switzerland) · 2023Article
- De Novo Transcriptome Profiling for the Generation and Validation of Microsatellite Markers, Transcription Factors, and Database Development forInternational journal of molecular sciences · 2023Article
- Genome-wide identification, characterization, and expression pattern of the late embryogenesis abundant (LEA) gene family in Juglans regia and its wild relatives J. mandshurica.BMC plant biology · 2023Article
- Article
- Genetic Diversity and Structure of Persian Walnut (Plants (Basel, Switzerland) · 2022Article
- Genetic Diversity ofFrontiers in plant science · 2022Article
- Flower Development of HeterodichogamousFrontiers in plant science · 2021Article
- De novo assembly and Transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics.BMC plant biology · 2020Article
- Review
- Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut.PloS one · 2020Article
- Population genetic structure and adaptive differentiation of iron walnutEcology and evolution · 2019Article
- A new triterpene from the green walnut husks of Juglans mandshurica Maxim.Journal of natural medicines · 2019Article
- Development and Characterization of EST-SSR Markers From RNA-Seq Data inFrontiers in plant science · 2019Article
- The Phytogeographic History of Common Walnut in China.Frontiers in plant science · 2018Article
- A rapid and cost-effective approach for the development of polymorphic microsatellites in non-model species using paired-end RAD sequencing.Molecular genetics and genomics : MGG · 2017Article
- Characterization of the Lycium barbarum fruit transcriptome and development of EST-SSR markers.PloS one · 2017Article
- Article
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Manchurian walnut (Juglans mandshurica Maxim.) is a vulnerable, temperate deciduous tree valued for its wood and nut, but transcriptomic and genomic data for the species are very limited. Next generation sequencing (NGS) has made it possible to develop molecular markers for this species rapidly and efficiently. Our goal is to use transcriptome information from RNA-Seq to understand development in J. mandshurica and develop polymorphic simple sequence repeats (SSRs, microsatellites) to understand the species' population genetics. In this study, more than 47.7 million clean reads were generated using Illumina sequencing technology. De novo assembly yielded 99,869 unigenes with an average length of 747 bp. Based on sequence similarity search with known proteins, a total of 39,708 (42.32 %) genes were identified. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) identified 15,903 (16.9 %) unigenes. Further, we identified and characterized 63 new transcriptome-derived microsatellite markers. By testing the markers on 4 to 14 individuals from four populations, we found that 20 were polymorphic and easily amplified. The number of alleles per locus ranged from 2 to 8. The observed and expected heterozygosity per locus ranged from 0.209 to 0.813 and 0.335 to 0.842, respectively. These twenty microsatellite markers will be useful for studies of population genetics, diversity, and genetic structure, and they will undoubtedly benefit future breeding studies of this walnut species. Moreover, the information uncovered in this research will also serve as a useful genetic resource for understanding the transcriptome and development of J. mandshurica and other Juglans species.
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