De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development

Abstract

Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtained a 12-Gb transcriptome dataset of pummelo through a mixture of RNA from seven tissues using Illumina pair-end sequencing, assembled into 57,212 unigenes with an average length of 1010 bp. The annotation and classification results showed that a total of 39,584 unigenes had similar hits to the known proteins of four public databases, and 31,501 were classified into 55 Gene Ontology (GO) functional sub-categories. The search for putative molecular markers among 57,212 unigenes identified 10,276 simple sequence repeats (SSRs) and 64,720 single nucleotide polymorphisms (SNPs). High-quality primers of 1174 SSR loci were designed, of which 88.16% were localized to nine chromosomes of sweet orange. Of 100 SSR primers that were randomly selected for testing, 87 successfully amplified clear banding patterns. Of these primers, 29 with a mean PIC (polymorphic information content) value of 0.52 were effectively applied for phylogenetic analysis. Of the 20 SNP primers, 14 primers, including 54 potential SNPs, yielded target amplifications, and 46 loci were verified via Sanger sequencing. This new dataset will be a valuable resource for molecular biology studies of pummelo and provides reliable information regarding SNP and SSR marker development, thus expediting the breeding program of pummelo.

De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development

“…bungeanum , followed by the di-type motifs. This finding is similar to the results reported for pummelo 28 and cotton 29 . Two hundred and six SSRs were present in the compound types, meaning they contained stretches of two or more different repeats.…”

Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery

“…NGS technologies can be used to develop abundant SSR or SNP markers with high efficiency and accuracy [62]. In this study, we screened 1595 SSRs of 2–6 bp in length from unigene sequences >1000 bp in length.…”

Genetic diversity of Herpetospermum caudigerum (Ser.) Baill using AFLP and chloroplast microsatellites

“…Haplotype H1 was found in a single population (2800 m). Of the haplotype H2 samples, 67% (16) and 33% (8) belonged to the 3000 m population and the 3300 m population, respectively (Table 6). Overall, H2 was the most frequent haplotype (34.3%), followed by haplotypes H5 (27.1%) and H1 (25.7%), whereas the frequency of the other four haplotypes was only 12.9% ( Table 6).…”

“…To date, several DNA-based molecular marker techniques, such as simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP) and single nucleotide polymorphism (SNP) have been utilized to identify the genetic diversity of plant species [15][16][17]. Most molecular markers have the advantage of being non-tissue-specific, relatively abundant, suitable for early rapid assessment, and less susceptible to environmental impacts [18].…”