De novo transcriptome assembly of shrimp Palaemon serratus

Abstract

The shrimp Palaemon serratus is a coastal decapod crustacean with a high commercial value. It is harvested for human consumption. In this study, we used Illumina sequencing technology (HiSeq 2000) to sequence, assemble and annotate the transcriptome of P. serratus. RNA was isolated from muscle of adults individuals and, from a pool of larvae. A total number of 4 cDNA libraries were constructed, using the TruSeq RNA Sample Preparation Kit v2. The raw data in this study was deposited in NCBI SRA database with study accession number of SRP090769. The obtained data were subjected to de novo transcriptome assembly using Trinity software, and coding regions were predicted by TransDecoder. We used Blastp and Sma3s to annotate the identified proteins. The transcriptome data could provide some insight into the understanding of genes involved in the larval development and metamorphosis.SpecificationsOrganism/cell line/tissuePalaemon serratus/muscle adults individuals and pool of larvaeSexN/ASequencer or array typeIllumina HiSeq2000Data formatRaw or processedExperimental factorsDe novo transcriptome assembly of Palaemon serratus.Experimental featuresRNA was isolated from muscle of adults individuals and, from a pool of larvae. A total number of 4 cDNA libraries were constructed, using the TruSeq RNA Sample Preparation Kit v2. The obtained data were subjected to de novo transcriptome assembly using Trinity, and coding regions were predicted by TransDecoder. We used Blastp and Sma3s_v2 to annotate the identified proteins.ConsentN/ASample source locationArtabro Gulf (43° 22′00″N, 8°28′00′′’W) in the northwest of Spain.

Single-molecule long-read sequencing facilitates shrimp transcriptome research

“…Short-read sequencing (Illumina or 454) has been used to produce transcriptomes of some shrimp species, including L. vannamei 17 , 18 , 33 – 40 , Fenneropenaeus merguiensis 41 , 42 , Macrobrachium rosenbergii 43 , Triops newberryi 44 , T. longicaudatus 45 , Pandalus latirostris 46 , Fenneropenaeus chinensis 47 , Palaemon serratus 48 , and Penaeus monodon 49 . The average lengths of transcripts obtained in these studies were ~306–1,027 bp.…”

De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes

“…Genetic studies in P. serratus are scarce and mainly focused in its population genetics and cytogenetics. Solely one transcriptomic work is available for this species, providing data to study larval development and metamorphosis [19]. Regarding to sex determination in P. serratus, it is only known that heteromorphic sex chromosomes are absent [20].…”

Pan-genome of pear provides insights into the fruit quality traits differentiation between Asian and European pears

“…Extract high-quality full-length transcripts of ‘Yuluxiang’ pear were used for gene prediction model training based on Nanopore full-length transcriptome data of mixed tissues (leaves, flowers, sepals, stems, fruits, etc.). The raw sequencing data of Nanopore were filtered and obtained by Pychopper (https://github.com/friend0/pyChopper), then the filtered data were treated by the Pinfish (https://github.com/nanoporetech/pipeline-pinfish-analysis)package, Transdecoder (Perina et al, 2017), maker2 (Holt and Yandell, 2011), AUGUSTUS (Stanke et al, 2006) to train the gene prediction model of ‘Yuluxiang’ pear, and produced a standard .gff format file by EVM (Haas et al, 2008). Finally, the optimal alignment of genes function were inferred using diamond (Buchfink et al, 2015) against KEGG database (Kanehisa et al, 2012), E=1E-5, NCBI non redundant (NR) database (Pruitt et al, 2007), EggNOG (Huerta-Cepas et al, 2019), TrEMBL [205] (O’Donovan et al, 2002), InterPro (Mitchell et al, 2015), and SwissProt (Boeckmann et al, 2003) protein databases.…”