Starfruit (Averrhoa carambola L.) is an important fruit for Malaysian export and great attention has been made to improve starfruit fruit quality at Malaysian Agricultural Research and Development Institute (MARDI). T...Starfruit (Averrhoa carambola L.) is an important fruit for Malaysian export and great attention has been made to improve starfruit fruit quality at Malaysian Agricultural Research and Development Institute (MARDI). The current study used next generation sequencing (NGS) technologies to develop starfruit simple sequence repeat (SSR) from 2 varieties namely B11 and B17 using Illumina HiSeq. The pre-processed reads were de novo assembled to generate approximately 75,000 and 74,000 scaffolds respectively. Total genome size for B11 and B17 were around 345 Mbp and 342 Mbp based on K-mer distribution analysis. In-silico microsatellite mining of each variety has identified more than 17,000 SSR in B11 and B17 respectively. Dinucleotides were the most abundant, accounting for more than 70% of all SSR and repeat motif GA (49%) was most common. A total of 239 SSR primer pairs were designed from contigs larger than 350 nucleotides and tested for amplification. The 30 polymorphic SSRs were used to DNA fingerprint of 12 starfruit hybrids. Polymorphism information content (PIC) ranged from 0.1411 to 0.6838, with an average of 0.3919. The Unweighted Pair-Group Method for Arithmetic Averages (UPGMA) dendrogram clustered 12 starfruit accessions into 2 groups.展开更多
Baccaurea motleyana(rambai)is underutilized fruits that are native to Malaysia,Indonesia and Thailand.In this study,a total of 54,779 unigenes identified from rambai transcriptome were used for simple sequence repeat(...Baccaurea motleyana(rambai)is underutilized fruits that are native to Malaysia,Indonesia and Thailand.In this study,a total of 54,779 unigenes identified from rambai transcriptome were used for simple sequence repeat(SSR)analysis by MIcroSAtellite(MISA).A total of 20,420 SSRs were found to be distributed within 37.27%of the total number of unigenes.Mononucleotide repeats represented the main type,accounting for 64.04%,followed by trinucleotide repeats(20.28%)and dinucleotide repeats(19.94%).Gene annotation to seven databases has a success ratio of 68.53%(National Center for Biotechnology Information(NCBI)protein sequences),53.68%(NCBI nucleotide sequences),27.43%(Kyoto Encyclopedia of Genes and Genome Ortholog),56.0%(SwissProt),52.44%(Protein family),53.99%(Gene Ontology)and 26.44%(Kluster of Orthologous Group).Further rambai SSRs were randomly selected and validated to B.motleyana(rambai),B.macrocarpa(tampoi),B.polyneura(jentik-jentik),B.ramiflora(pupor)and B.scortechinii(setambun).展开更多
文摘Starfruit (Averrhoa carambola L.) is an important fruit for Malaysian export and great attention has been made to improve starfruit fruit quality at Malaysian Agricultural Research and Development Institute (MARDI). The current study used next generation sequencing (NGS) technologies to develop starfruit simple sequence repeat (SSR) from 2 varieties namely B11 and B17 using Illumina HiSeq. The pre-processed reads were de novo assembled to generate approximately 75,000 and 74,000 scaffolds respectively. Total genome size for B11 and B17 were around 345 Mbp and 342 Mbp based on K-mer distribution analysis. In-silico microsatellite mining of each variety has identified more than 17,000 SSR in B11 and B17 respectively. Dinucleotides were the most abundant, accounting for more than 70% of all SSR and repeat motif GA (49%) was most common. A total of 239 SSR primer pairs were designed from contigs larger than 350 nucleotides and tested for amplification. The 30 polymorphic SSRs were used to DNA fingerprint of 12 starfruit hybrids. Polymorphism information content (PIC) ranged from 0.1411 to 0.6838, with an average of 0.3919. The Unweighted Pair-Group Method for Arithmetic Averages (UPGMA) dendrogram clustered 12 starfruit accessions into 2 groups.
文摘Baccaurea motleyana(rambai)is underutilized fruits that are native to Malaysia,Indonesia and Thailand.In this study,a total of 54,779 unigenes identified from rambai transcriptome were used for simple sequence repeat(SSR)analysis by MIcroSAtellite(MISA).A total of 20,420 SSRs were found to be distributed within 37.27%of the total number of unigenes.Mononucleotide repeats represented the main type,accounting for 64.04%,followed by trinucleotide repeats(20.28%)and dinucleotide repeats(19.94%).Gene annotation to seven databases has a success ratio of 68.53%(National Center for Biotechnology Information(NCBI)protein sequences),53.68%(NCBI nucleotide sequences),27.43%(Kyoto Encyclopedia of Genes and Genome Ortholog),56.0%(SwissProt),52.44%(Protein family),53.99%(Gene Ontology)and 26.44%(Kluster of Orthologous Group).Further rambai SSRs were randomly selected and validated to B.motleyana(rambai),B.macrocarpa(tampoi),B.polyneura(jentik-jentik),B.ramiflora(pupor)and B.scortechinii(setambun).
