De novo transcriptome analysis of the Siberian apricot (Prunus sibirica L.) and search for potential SSR markers by 454 pyrosequencing

Dong, Shuang-Lin; Liu, Yulin; Niu, Jun; Ning, Yu; Lin, Senjie; Zhang, Zhixiang

doi:10.1016/j.gene.2014.04.031

Cited by 31 publications

(38 citation statements)

References 49 publications

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“…The (AG/CT)n dinucleotides (68.73%) was the most abundant in dinucleotide SSR units, followed by (AT/AT)n dinucleotides (24.76%) and (AC/GT)n dinucleotides (6.41%). However, GC dinucleotide repeats are relatively rare in the present study (only 0.10%), which was very similar to previous reports (Dong et al, 2014;Jain et al, 2014;Zhou et al, 2012). In trinucleotide SSR units, the (AAG/CTT)n trinucleotides were the richest SSR loci repeats (37.19%), followed by (ATC/ATG)n trinucleotides (14.86%), (AAT/ATT)n trinucleotides (12.96%), (ACC/GGT)n trinucleotides (7.59%), (AAC/GTT)n trinucleotides (7.30%), (AGG/CCT)n trinucleotides (7.26%), and (AGC/CTG)n trinucleotides (7.18%).…”

Section: Resultssupporting

confidence: 93%

Development of RNA-Seq SSR Markers and Application to Genetic Relationship Analysis among Sea Buckthorn Germplasm

Li¹,

Ruan²,

Wang³

et al. 2017

J. Amer. Soc. Hort. Sci.

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Sea buckthorn (Hippophae rhamnoides) is an ecologically and economically valuable species that has been widely cultivated as a new berry crop rich in nutritional and medicinal compounds. RNA Sequencing (RNA-Seq) simple sequence repeat (SSR) markers were developed to evaluate the genetic relationships among 91 plants of 31 cultivars from two subspecies, mongolica and sinensis, as well as intraspecific hybrids between them. A total of 7540 RNA-Seq SSRs were identified as potential molecular markers, in which AG/CT (27.57%) was the most abundant unit type. AT/AT (9.93%), and AAG/CTT (11.95%) are the other main repeat motifs. A total of 110 primer pairs were randomly selected for validation of amplification. Seventeen SSR loci, located in genes encoding metabolic processes and cellulose synthases, were identified to be polymorphic among different sea buckthorn cultivars. These SSR loci generated 48 alleles, ranging from 2 to 5 per locus. Cluster analysis based on the proportion of shared alleles and unweighted pair group method with arithmetic average (UPGMA) algorithm divided all the genotypes into two main groups, with all of the ssp. sinensis cultivars (native to China) and hybrids in one group and ssp. mongolica cultivars (introduced from Russia) in the other group, which was in good agreement with their taxonomic classification. The RNA-Seq SSRs developed in this study have a potential use in the conservation of sea buckthorn germplasm and marker-assisted breeding (MAB).

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Section: Resultssupporting

confidence: 93%

Development of RNA-Seq SSR Markers and Application to Genetic Relationship Analysis among Sea Buckthorn Germplasm

Li¹,

Ruan²,

Wang³

et al. 2017

J. Amer. Soc. Hort. Sci.

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“…The transcripts of the pool (85,766 fragments) were classified into the three GO main categories of biological process, cellular component, and molecular function with numbers 65,119 (41%), 46,225 (29.11%), and 47,477 (29.89%), respectively. The present findings are in agreement with previous results; Dong et al (2014) reported the highest assignments of transcripts of embryos of Siberian apricot to biological processes (54,667, 40.72%), followed by cellular components (51,551, 38.40%) and molecular functions (28,039, 20.88%). Similarly, GO assignment of transcripts sequenced from buds, leaves, stems, flowers, fruit pulp, and seeds of commercial apricot resulted in maximum hits to biological processes, followed by cellular components and molecular function (Bai et al, 2016).…”

Section: Discussionsupporting

confidence: 94%

De novo transcriptome assembly and SSR markerdevelopment in apricot (Prunus armeniaca)

Köse¹,

Çetinsağ²,

Gürcan³

2017

Turk J Agric For

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Apricot (Prunus armeniaca) is an important fruit crop worldwide. We have performed a de novo transcriptome assembly for 7 apricot accessions ('Stark Early Orange' (SEO), 'Hacıhaliloğlu' (HH), 'Perfection' , 'Iğdır' , 'Roxana' , 'Esen1' , and 'Esen2'), which yielded a total number of transcripts ranging from 30,363 for 'SEO' to 59,751 for 'Iğdır' . The pool of the reads produced from 7 accessions were assembled into 85,766 transcripts, with an average of 1165.69 nt. Functional annotation (Gene Ontology-GO and Kyoto Encyclopedia of Genes and Genomes-KEGG) was performed successfully for the transcripts. Simple sequence repeats (SSRs) were searched in the transcript pool and 14,722 di-, tri-tetra-, penta-, and hexanucleotide motif loci with a minimum of 5 repetitions for all motifs were identified. Primers were designed for 206 loci, and 72 of them were found to be polymorphic by amplifying diverse 24 apricot accessions, including 7 Plum Pox Virus (PPV)-resistant and 17 PPV-susceptible accessions. In order to test the amplification success of publicly available genomic SSRs (gSSRs) for diverse apricot accessions, an additional 88 published Prunus gSSRs were characterized amplifying the same 24 apricots and only 54 (62%) produced polymorphic bands. The new EST-SSRs could be a reliable source of primers for characterization and mapping studies of apricots, especially because they mostly flank easily scorable tri-and tetranucleotide repeats.

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“…Our results showed that 17,682 unigenes had no significant matches to any known genes and may represent novel transcribed sequences specific to A. fistulosum. Similar results have been observed in studies of other non-model plants (Du et al 2014;Zhu et al 2014;Wang et al 2015;Dong et al 2014). Additionally, the functions of the unigenes were classified by GO and COG annotations.…”

Section: Discussionsupporting

confidence: 84%

De novo assembly and characterization of the Welsh onion (Allium fistulosum L.) transcriptome using Illumina technology

Sun

Zhou

et al. 2015

Mol Genet Genomics

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Welsh onion (Allium fistulosum L.) has long been cultivated as a vegetable and spice for its flavor and aroma. However, transcriptomic and genomic data for A. fistulosum remain scarce. The goal of this study was to generate transcript sequences for functional genomic analyses, and identify genes potentially involved in sulfur, selenium, and vitamin metabolism. In total, 53,378,674 high-quality reads were generated, and de novo assembly resulted in 103,286 contigs and 53,837 unigenes. The average unigene length was 619 bp with an N50 of 832 bp. Similarity searches revealed that 36,155 sequences were similar to those of known proteins in public databases. Of these, 35,250 unigenes sequences were significantly similar to sequences in the NCBI non-redundant protein database and 22,804 were annotated in the Swiss-Prot database. Additionally, 13,125 and 26,660 unigenes were annotated in the Cluster of Orthologous Group and Gene Ontology databases, respectively. A total of 20,680 unigenes were classified into 128 pathways via functional annotation against the Kyoto Encyclopedia of Genes and Genomes pathway database. Key enzymes involved in sulfur and selenium metabolism were also identified. Additionally, our transcriptome revealed a number of unigenes encoding important enzymes involved in vitamin metabolism. We also identified 2014 simple sequence repeats in 1892 unigenes. This transcriptome analysis provides valuable information to further our understanding of the molecular mechanisms regulating the biosynthesis of organic sulfur compounds. The detected simple sequence repeats may facilitate marker-assisted selection in Welsh onion breeding experiments.

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De novo transcriptome analysis of the Siberian apricot (Prunus sibirica L.) and search for potential SSR markers by 454 pyrosequencing

Cited by 31 publications

References 49 publications

Development of RNA-Seq SSR Markers and Application to Genetic Relationship Analysis among Sea Buckthorn Germplasm

Development of RNA-Seq SSR Markers and Application to Genetic Relationship Analysis among Sea Buckthorn Germplasm

De novo transcriptome assembly and SSR markerdevelopment in apricot (Prunus armeniaca)

De novo assembly and characterization of the Welsh onion (Allium fistulosum L.) transcriptome using Illumina technology

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