The pen shell(Atrina pectinata) is a large wedge-shaped bivalve, which belongs to family Pinnidae. Due to its large and nutritious adductor muscle, it is the popular seafood with high commercial value in Asia-Pacific ...The pen shell(Atrina pectinata) is a large wedge-shaped bivalve, which belongs to family Pinnidae. Due to its large and nutritious adductor muscle, it is the popular seafood with high commercial value in Asia-Pacific countries. However, limiting genomic and transcriptomic data have hampered its genetic investigations. In this study, the transcriptome of A. pectinata was deeply sequenced using Illumina pair-end sequencing technology. After assembling, a total of 127263 unigenes were obtained. Functional annotation indicated that the highest percentage of unigenes(18.60%) was annotated on GO database, followed by 18.44% on PFAM database and 17.04% on NR database. There were 270 biological pathways matched with those in KEGG database. Furthermore, a total of 23452 potential simple sequence repeats(SSRs) were identified, of them the most abundant type was mono-nucleotide repeats(12902, 55.01%), which was followed by di-nucleotide(8132, 34.68%), tri-nucleotide(2010, 8.57%), tetra-nucleotide(401, 1.71%), and penta-nucleotide(7, 0.03%) repeats. Sixty SSRs were selected for validating and developing genic SSR markers, of them 23 showed polymorphism in a cultured population with the average observed and expected heterozygosities of 0.412 and 0.579, respectively. In this study, we established the first comprehensive transcript dataset of A. pectinata genes. Our results demonstrated that RNA-Seq is a fast and cost-effective method for genic SSR development in non-model species.展开更多
The recent breakthroughs in next-generation sequencing technologies, such as those of Roche 454,Illumina/Solexa, and ABI SOLID, have dramatically reduced the cost of producing short reads of the genome of new species....The recent breakthroughs in next-generation sequencing technologies, such as those of Roche 454,Illumina/Solexa, and ABI SOLID, have dramatically reduced the cost of producing short reads of the genome of new species. The huge volume of reads, along with short read length, high coverage, and sequencing errors, poses a great challenge to de novo genome assembly. However, the paired-end information provides a new solution to these problems. In this paper, we review and compare some current assembly tools, including Newbler, CAP3, Velvet,SOAPdenovo, AllPaths, Abyss, IDBA, PE-Assembly, and Telescoper. In general, we compare the seed extension and graph-based methods that use the overlap/lapout/consensus approach and the de Bruijn graph approach for assembly. At the end of the paper, we summarize these methods and discuss the future directions of genome assembly.展开更多
基金the grants from Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, P. R. China (No. 2016LMFS-B02)the Key Research and Development Program of Shandong Province (No. 2016GSF115012)+1 种基金Basic Scientific Research Fund of YSFRI (No. 2060302201516054)Natural Science Foundation of Shandong Province (No. ZR2016 CQ32)
文摘The pen shell(Atrina pectinata) is a large wedge-shaped bivalve, which belongs to family Pinnidae. Due to its large and nutritious adductor muscle, it is the popular seafood with high commercial value in Asia-Pacific countries. However, limiting genomic and transcriptomic data have hampered its genetic investigations. In this study, the transcriptome of A. pectinata was deeply sequenced using Illumina pair-end sequencing technology. After assembling, a total of 127263 unigenes were obtained. Functional annotation indicated that the highest percentage of unigenes(18.60%) was annotated on GO database, followed by 18.44% on PFAM database and 17.04% on NR database. There were 270 biological pathways matched with those in KEGG database. Furthermore, a total of 23452 potential simple sequence repeats(SSRs) were identified, of them the most abundant type was mono-nucleotide repeats(12902, 55.01%), which was followed by di-nucleotide(8132, 34.68%), tri-nucleotide(2010, 8.57%), tetra-nucleotide(401, 1.71%), and penta-nucleotide(7, 0.03%) repeats. Sixty SSRs were selected for validating and developing genic SSR markers, of them 23 showed polymorphism in a cultured population with the average observed and expected heterozygosities of 0.412 and 0.579, respectively. In this study, we established the first comprehensive transcript dataset of A. pectinata genes. Our results demonstrated that RNA-Seq is a fast and cost-effective method for genic SSR development in non-model species.
基金supported in part by the National Natural Science Foundation of China (Nos.61232001,61128006,and 61073036)
文摘The recent breakthroughs in next-generation sequencing technologies, such as those of Roche 454,Illumina/Solexa, and ABI SOLID, have dramatically reduced the cost of producing short reads of the genome of new species. The huge volume of reads, along with short read length, high coverage, and sequencing errors, poses a great challenge to de novo genome assembly. However, the paired-end information provides a new solution to these problems. In this paper, we review and compare some current assembly tools, including Newbler, CAP3, Velvet,SOAPdenovo, AllPaths, Abyss, IDBA, PE-Assembly, and Telescoper. In general, we compare the seed extension and graph-based methods that use the overlap/lapout/consensus approach and the de Bruijn graph approach for assembly. At the end of the paper, we summarize these methods and discuss the future directions of genome assembly.
