<i>De novo</i> assembly, gene annotation, and simple sequence repeat marker development using Illumina paired-end transcriptome sequences in the pearl oyster <i>Pinctada maxima</i>

Deng, Yuewen; Lei, Qiannan; Tian, Qunli; Xie, Shouqi; Du, Xiaodong; Li, Junhui; Wang, Liqun; Xiong, Yi

doi:10.1080/09168451.2014.936351

Cited by 31 publications

(16 citation statements)

References 42 publications

(46 reference statements)

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“…This is also the first transcriptome report in echiuran worms. In the obtained transcriptome of U. unicinctus , the assembly of the 53,874,422 clean reads produced 52,093 unique sequences with an average size of 738 bp which is comparable with other studies generating transcriptome data [ 29 – 31 ]. The number of protein-coding genes in the U. unicinctus genome is unknown; however, if we assume general conservation based on estimates for the representative of the phylum Annelida Capitella teleta (32,415 genes; JGI annotation pipeline), ~83 % of protein-coding genes (26,889) were assembled in this study.…”

Section: Discussionsupporting

confidence: 78%

Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis

Liu

Zhang

et al. 2015

BMC Genomics

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BackgroundUrechis unicinctus, an echiuran worm inhabiting the U-shaped burrows in the coastal mud flats, is an important commercial and ecological invertebrate in Northeast Asian countries, which has potential applications in the study of animal evolution, coastal sediment improvement and marine drug development. Furthermore, the worm can tolerate and utilize well-known toxicant-sulfide. However, knowledge is limited on the molecular mechanism of U. unicinctus responding to sulfide due to deficiency of its genetic information.MethodsIn this study, we performed Illumina sequencing to obtain the first Urechis unicinctus transcriptome data. Sequenced reads were assembled and then annotated using blast searches against Nr, Nt, Swiss-Prot, KEGG and COG. The clean tags from four digital gene expression (DGE) libraries were mapped to the U. unicinctus transcriptome. DGE analysis and functional annotation were then performed to reveal its response to sulfide. The expressions of 12 candidate genes were validated using quantitative real-time PCR. The results of qRT-PCR were regressed against the DGE analysis, with a correlation coefficient and p-value reported for each of them.ResultsHere we first present a draft of U. unicinctus transcriptome using the Illumina HiSeqTM 2000 platform and 52,093 unique sequences were assembled with the average length of 738 bp and N50 of 1131 bp. About 51.6 % of the transcriptome were functionally annotated based on the databases of Nr, Nt, Swiss-Prot, KEGG and COG. Then based on the transcriptome, the digital gene expression analysis was conducted to examine the transcriptional response to sulfide during 6, 24 and 48 h exposure, and finally 1705, 1181 and 1494 tag-mapped genes were identified as differentially expressed genes in the 6-h, 24-h and 48-h libraries, then were further subjected to pathway analyses.ConclusionsIn the DGE database of U. unicinctus, the alterations in certain known sulfide-related pathways indicate similar changes in response to sulfide. For more than 80 % of the identified pathway members, this is the first report on their association with sulfide stress, among which glycolysis pathway and PIDD involving pathways were unique and discussed in details, and were thought to play important roles in the sulfide tolerance of U. unicinctus. All the results are helpful to explain the mechanism of sulfide tolerance and detoxification.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2094-z) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 78%

Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis

Liu

Zhang

et al. 2015

BMC Genomics

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“…We calculated N50 by adding long contigs to short contigs until the summed length exceeded 50% of the total length of all contigs. The Trinity de novo assembler used in this study has been shown to outperform other top assemblers and is widely used across a variety of taxa [ 27 , 28 , 29 , 30 ].…”

Section: Resultsmentioning

confidence: 99%

De novo Transcriptome Generation and Annotation for Two Korean Endemic Land Snails, Aegista chejuensis and Aegista quelpartensis, Using Illumina Paired-End Sequencing Technology

Kang

Patnaik

Hwang

et al. 2016

IJMS

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Aegista chejuensis and Aegista quelpartensis (Family-Bradybaenidae) are endemic to Korea, and are considered vulnerable due to declines in their population. The limited genetic resources for these species restricts the ability to prioritize conservation efforts. We sequenced the transcriptomes of these species using Illumina paired-end technology. Approximately 257 and 240 million reads were obtained and assembled into 198,531 and 230,497 unigenes for A. chejuensis and A. quelpartensis, respectively. The average and N50 unigene lengths were 735.4 and 1073 bp, respectively, for A. chejuensis, and 705.6 and 1001 bp, respectively, for A. quelpartensis. In total, 68,484 (34.5%) and 77,745 (33.73%) unigenes for A. chejuensis and A. quelpartensis, respectively, were annotated to databases. Gene Ontology terms were assigned to 23,778 (11.98%) and 26,396 (11.45) unigenes, for A. chejuensis and A. quelpartensis, respectively, while 5050 and 5838 unigenes were mapped to 117 and 124 pathways in the Kyoto Encyclopedia of Genes and Genomes database. In addition, we identified and annotated 9542 and 10,395 putative simple sequence repeats (SSRs) in unigenes from A. chejuensis and A. quelpartensis, respectively. We designed a list of PCR primers flanking the putative SSR regions. These microsatellites may be utilized for future phylogenetics and conservation initiatives.

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“…The detailed reaction system and process were done according to Deng et al (2014). The PCR products were separated on 8% (w/v) polyacrylamide gels using Takara 20 bp DNA ladder marker by silver staining.…”

Section: Dna Isolation Ssr Amplification and Validationmentioning

confidence: 99%

“…SSRs markers can be generated using several techniques without single locus isolation, such as employing oligonucleotide primers (Zietkiewicz et al, 1994), SAMPL (Witsenboer et al, 1997) and transcriptome SSRs (Guo et al, 2015). When compared with genomic SSRs, transcriptome SSRs are more efficient Marguerat and Bähler, 2010;Deng et al, 2014) with relatively higher transferability (Varshney et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

Development of SSR Markers Using RNA-Seq Approach and Genetic Diversity of Two Populations of Asian Moon Scallop Amusium pleuronectes

Wang¹,

Zhao²,

Deng³

et al. 2017

IJAB

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In this study, we obtained a batch of simple sequence repeats (SSRs) from the transcriptome data of Asian moon scallop Amusium pleuronectes and analyzed the distribution and frequency of these SSRs. A total of 7,315 SSRs were obtained from 159,521 unigenes. Bioinformatics tools were employed to design appropriate primers. A total of 4,038 SSR loci had flanking sequences suitable for polymerase chain reaction primer design. One hundred SSR primers were validated and the rate of successful amplification was 78.0%. Fourteen randomly chosen primer pairs were amplified in Beibu Bay population (BP) and Hainan Baimajing population (HP). The number of alleles at each locus ranged from 2 to 3 in two populations, with mean values of 2.214 and 2.143, respectively. The observed heterozygosity, expected heterozygosity and polymorphism information content of BP were 0.463, 0.646 and 0.281, respectively, while those of HP were 0.309, 0.320 and 0.259, respectively. The developed SSR markers will be helpful for further studies on population genetics, genetic linkage construction and chromosome linkage mapping in the species.

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De novo assembly, gene annotation, and simple sequence repeat marker development using Illumina paired-end transcriptome sequences in the pearl oyster Pinctada maxima

Abstract: (2014) Denovo assembly, gene annotation, and simple sequence repeat marker development using Illumina paired-end transcriptome sequences in the pearl oyster Pinctadamaxima,

Cited by 31 publications

References 42 publications

Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis

Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis

De novo Transcriptome Generation and Annotation for Two Korean Endemic Land Snails, Aegista chejuensis and Aegista quelpartensis, Using Illumina Paired-End Sequencing Technology

Development of SSR Markers Using RNA-Seq Approach and Genetic Diversity of Two Populations of Asian Moon Scallop Amusium pleuronectes

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