Development of genic SSR marker resources from RNA-seq data in Camellia japonica and their application in the genus Camellia

Li, Qingyuan; Su, Xiaojun; Ma, Huanhuan; Du, Kun; Yang, Min; Chen, Baolin; Fu, Shao Ping; Fu, Tianjing; Xiang, Conglin; Zhao, Qing; Xu, Lin

doi:10.1038/s41598-021-89350-w

Cited by 20 publications

(20 citation statements)

References 36 publications

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“…Except for mono-repeats, the most abundant SSRs were tri-nucleotide repeats (54.5 and 64.5%), then di-nucleotide repeats (35.95 and 28.2%) in P. phaseoloides and P. m. lobata transcripts, respectively. This is consistent with the observation that tri-SSRs are generally the most frequently occurring SSRs found in genic SSRs, followed by di-SSRs [ 58 , 67 ]; however, there are exceptions as with Camellia japonica [ 68 ]. Among all the tri-nucleotides, AAG/CTT was found to be the most frequent motif, consistent with recent studies [ 69 – 71 ].…”

Section: Discussionsupporting

confidence: 89%

Identification of Pueraria spp. through DNA barcoding and comparative transcriptomics

2022

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Background Kudzu is a term used generically to describe members of the genus Pueraria. Kudzu roots have been used for centuries in traditional Chinese medicine in view of their high levels of beneficial isoflavones including the unique 8-C-glycoside of daidzein, puerarin. In the US, kudzu is seen as a noxious weed causing ecological and economic damage. However, not all kudzu species make puerarin or are equally invasive. Kudzu remains difficult to identify due to its diverse morphology and inconsistent nomenclature. Results We have generated sequences for the internal transcribed spacer 2 (ITS2) and maturase K (matK) regions of Pueraria montana lobata, P. montana montana, and P. phaseoloides, and identified two accessions previously used for differential analysis of puerarin biosynthesis as P. lobata and P. phaseoloides. Additionally, we have generated root transcriptomes for the puerarin-producing P. m. lobata and the non-puerarin producing P. phaseoloides. Within the transcriptomes, microsatellites were identified to aid in species identification as well as population diversity. Conclusions The barcode sequences generated will aid in fast and efficient identification of the three kudzu species. Additionally, the microsatellites identified from the transcriptomes will aid in genetic analysis. The root transcriptomes also provide a molecular toolkit for comparative gene expression analysis towards elucidation of the biosynthesis of kudzu phytochemicals.

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Section: Discussionsupporting

confidence: 89%

Identification of Pueraria spp. through DNA barcoding and comparative transcriptomics

2022

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“…We generated the first draft for genome sequence of A. coronaria , and we report on the massive microsatellite loci identification following its genome-wide survey. Microsatellite—alias simple sequence repeats (SSR)-markers, are co-dominantly inherited, ubiquitous, highly polymorphic, and have found large application in plant breeding and phylogenetic studies because of their simple application through conventional PCR protocols [ 10 , 11 , 12 , 13 , 14 , 15 , 16 ]. Unlike single nucleotide polymorphisms (SNPs), which have become the gold standard among molecular markers, SSRs show the advantage of being multi-allelic and highly informative, characterized by a certain level of transferability between related specie [ 17 , 18 , 19 , 20 ], and are easily and automatically scorable.…”

Section: Introductionmentioning

confidence: 99%

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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“…Tetranucleotide repeats were most abundant followed by di- and trinucleotide repeats. Genic SSRs are especially helpful in assaying functional diversity and marker-assisted selection (MAS) in plants ( Li et al, 2021 ). Therefore, we also mined SSRs in the protein-coding sequences of M. oleifera and identified 3,362 SSRs in 31,056 protein-coding genes, with the trinucleotide repeats being most abundant ( Table 2 ).…”

Section: Resultsmentioning

confidence: 99%

De novo Whole-Genome Assembly of Moringa oleifera Helps Identify Genes Regulating Drought Stress Tolerance

et al. 2021

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Abiotic stresses, especially drought stress, are responsible for heavy losses in productivity, which in turn poses an imminent threat for future food security. Understanding plants’ response to abiotic stress at the molecular level is crucially important for mitigating the impacts of climate change. Moringa oleifera is an important multipurpose plant with medicinal and nutritional properties and with an ability to grow in low water conditions, which makes the species an ideal candidate to study the regulatory mechanisms that modulate drought tolerance and its possible use in agroforestry system. In the present communication, we report whole-genome sequencing (WGS) of this species and assemble about 90% of the genome of M. oleifera var. Bhagya into 915 contigs with a N50 value of 4.7 Mb and predicted 32,062 putative protein-coding genes. After annotating the genome, we have chosen to study the heat shock transcription factor (HSF) family of genes to analyze their role in drought tolerance in M. oleifera. We predicted a total of 21 HSFs in the M. oleifera genome and carried out phylogenetic analyses, motif identification, analysis of gene duplication events, and differential expression of the HSF-coding genes in M. oleifera. Our analysis reveals that members of the HSF family have an important role in the plant’s response to abiotic stress and are viable candidates for further characterization.

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Development of genic SSR marker resources from RNA-seq data in Camellia japonica and their application in the genus Camellia

Cited by 20 publications

References 36 publications

Identification of Pueraria spp. through DNA barcoding and comparative transcriptomics

Identification of Pueraria spp. through DNA barcoding and comparative transcriptomics

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

De novo Whole-Genome Assembly of Moringa oleifera Helps Identify Genes Regulating Drought Stress Tolerance

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