The Chilean scallop Argopecten purpuratus (Lamarck, ) is a ‘bay scallop’ found in shallow bays from Paita, Peru (5°S, 81°W) to Valparaiso. PDF | Daily striae on the shell of the scallop, Argopecten purpuratus, were used to investigate its growth in a protected population within La. Gigascience. Apr 1;7(4). doi: /gigascience/giy Draft genome of the Peruvian scallop Argopecten purpuratus. Li C(1), Liu X(2), Liu B(1), Ma B(3).
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The Peruvian scallop, Argopecten purpuratusis mainly cultured in southern Chile and Peru was introduced into China in the last century. Unlike other Argopecten scallops, the Peruvian scallop normally has a long life span of up to 7 to 10 years. Therefore, researchers have been using it to develop hybrid vigor.
Here, we performed whole genome sequencing, assembly, and gene annotation of the Peruvian scallop, with an important aim to develop genomic resources for genetic breeding in scallops. A total of A draft genome assembly of Repeat sequences were calculated to reach We generated a high-quality draft genome assembly of the Peruvian scallop, which will provide a solid resource for further genetic breeding and purpuratuz the analysis of the evolutionary history of this economically important scallop.
The Peruvian scallop Argopecten purpuratusalso known as the Chilean scallop, is a medium-sized bivalve with a wide distribution in Peru and Chile [ 1 ]. In Chile, the cultured scallops reach a commercial size of around 9 cm in shell height within 14—16 months [ 2 ].
It is a relatively stenothermic species as its natural habitat is largely under the influence of upwelling argopevten from Antarctica [ 3 ]. Unlike other Argopecten scallops, the Peruvian scallop normally has a long life span of up to 7—10 years [ 45 ]. This scallop was introduced into China in the late s and has played an important role in stock improvement of Argopecten scallops via interspecific hybridization with bay scallops [ 67 ]. Genomic DNA was extracted from an adductor muscle sample of a single A.
A whole genome shotgun sequencing strategy was then applied.
Argopecten purpuratus – Wikispecies
Briefly, six libraries with different insert length bp, bp, 2 kb, 5 kb, 10 kb, and 20 kb were adgopecten according to the standard protocol provided arhopecten Illumina San Diego, CA, USA. In detail, the DNA sample was randomly broken into fragments using covaris ultrasonic fragmentation apparatus.
The library was prepared following end repair, adding sequence adaptor, purification, and polymerase chain reaction amplification. The mate-pair libraries 2 kb, 5 kb, 10 kb, and 20 kb and paired-end libraries bp, bp were all sequenced on the Illumina HiSeq platform with paired-end bp.
In addition, Purpuratud libraries were prepared using argopectem kb or kb preparation protocols. The final step of the protocol was to remove failed ligation products through the use of exonucleases. After the exonuclease and AMPure PB purpurstus steps, sequencing primer was annealed to the SMRTbell templates, followed by binding of the sequence polymerase to the annealed templates.
Finally, the 10X Genomics library was constructed and sequenced with paired-end bp on the Illumina Hiseq platform. The raw reads were trimmed before being used for subsequent genome assembly. For PacBio sequencing, the generated polymerase reads were first broken at the adaptor positions, and the subreads were generated after removal of the adaptor sequences.
The mer frequency distribution analysis [ 8 ] was performed on the remaining clean reads to estimate the genome size of the Peruvian scallop using the following formula: Based on a total number of 6. First, in order to solve the issue of heterozygosity, in our assembly process we chose kmer to draw k-mer distribution histogram and classified all the kmers into homozygous kmer and heterozygous kmer according to the coverage depth.
Second, we utilized kmer to construct the de Bruijn figure and combine the bubbles for heterozygous sites, according to the sequences with longer length and deeper coverage depth. Then, the pair-end information was used to determine the connection between the heterozygous parts and filter the contigs lacking support. argopecfen
Draft genome of the Peruvian scallop Argopecten purpuratus.
Finally, the heterozygous contigs and homozygous contigs were distinguished based on contig coverage depth. After assembly, the reads from short insert length libraries were mapped onto the assembled genome. Only one peak was observed in the sequencing depth distribution analysis with the average sequencing depth of Finally, a draft genome of Through mapping to the core eukaryotic genes, genes We searched transposable elements in the assembled genome through ab-initio and homology-based methods.
Finally, we determined that the total repeat sequences are , bp, accounting for The annotation strategy for protein-coding genes integrated de novo prediction with homology and transcriptome data-based evidence. Arggopecten sequences from African malaria mosquito Anopheles gambiaeascidian Ciona intestinalisFlorida lancelet Branchiostoma floridaefruit fly Drosophila melanogasterhuman Homo sapiensleech Helobdella robustanematode Caenorhabditis elegansoctopus Octopus purpurstusowl limpet Lottia giganteaPacific oyster Crassostrea gigasand sea urchin Strongylocentrotus purpuratus were downloaded from Ensemble [ 21 atgopecten.
The transcriptome data were generated from adductor muscle, hepatopancreas, and mantle on Illumina HiSeq platform. The de novo prediction purouratus genes was carried out with four programs: Finally, we identified 26, protein-coding genes in the Peruvian scallop genome. In detail, 26, genes were predicted through the de novo method, 19, genes were annotated by RNA argopectten or raw RNA reads, and 15, genes were supported by homolog evidences. The average transcript length, CDS length, and intron length were 10, bp, 1, bp, and 1, bp, respectively Table 1.
Gene ontology terms for genes were obtained from the corresponding InterPro entry [ 33 ]. Finally, argopevten these annotated genes, Purpurayus genes from the Peruvian scallop and other sequenced species, including Brachiopod Lingula anatinabrown mussel Modiolus philippinarumCalifornia sea hare Aplysia californicacold seep mussel Bathymodiolus platifronsFlorida lancelet B. For each protein-coding gene with alternative splicing isoforms, only the longest protein sequence was kept as the representative.
In total, the protein-coding genes were classified into 45, families and strict single-copy orthologs Fig. Distribution of genes in different species.
Evolutionary analysis was performed using these single-copy protein-coding genes from the 18 examined species. A total number of single-copy ortholog alignments were concatenated into a super alignment matrix ofnucleotides. Clade pjrpuratus was assessed using bootstrapping algorithm in the RAxML package with alignment replicates Fig.
The constructed phylogenetic tree Fig. Bootstrap support of phylogenetic tree.
A maximum likelihood tree was constructed purpuraatus RAxML based on single-copy protein-coding genes of the related species. The total number of bootstrap was Based on the phylogenetic tree Fig. Finally, we estimated that the divergence between the Peruvian scallop and Yesso scallop happened at In the present study, we report the first whole genome sequencing, assembly, and annotation of the Peruvian scallop A.
The assembled draft genome of pufpuratus A total of 26, protein-coding genes and 3, noncodingRNAs were predicted from the genome assembly. This genome assembly will provide solid support for in-depth biological studies. With the availability of these genomic data, subsequent development of genetic markers for further genetic selection and molecular breeding of scallops could be realized. The current genome data will also facilitate genetic analyses of the evolutionary history of the abundant scallops in the world.
Supporting data are available in the GigaScience database [ 52 ]. National Center for Biotechnology Information. All authors read and approved the final manuscript. Oxford University Press is a department of the University of Oxford. It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide. Sign In or Create an Account. Close mobile search navigation Article navigation. Availability of supporting data. Draft genome of the Peruvian scallop Argopecten purpuratus Chao Li.
Qingdao Oceanwide BioTech Co. GigaScienceVolume 7, Issue 4, 1 Aprilgiy, https: View large Download slide. The mollusca and branchiopoda. Report of dredging operation, Albatros’ Growth of the scallop, Argopecten purpuratus Lamarck,in southern Chile. Genetic and morphological differentiation between two pectinid populations of Argopecten purpuratus from the northern Chilean coast. Progress in mass culture of Chlamys Argopecten purpurata Lamarck with notes on its natural history.
The possible role of telomeres in the short life span of the bay scallop, Argopecten irradians irradians Lamarck Inter-specific hybridization between Argopecten purpuratus and Argopecten irradians irradians. Introduction of the Peruvian scallop and its hybridization with the bay scallop in China. Argopeccten fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.
In vitro, long-range purpruatus information for de novo genome assembly via transposase contiguity. TEclass—a tool for automated classification of unknown eukaryotic transposable elements. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes. Scallop genome provides insights into evolution of bilaterian karyotype and development. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Published by Oxford University Press. Email alerts New issue alert.
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