Erratum to“Targeted Genotyping of a Whole-Gene Repertoire by an Ultrahigh-Multiplex and Flexible HD-Marker Approach”[Engineering 13(2022)186–196]

There was a mistake in affiliation a,the correct one should be“MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Center,Ocean University of China,Qingdao 266003,China”as updated above;Affiliations c and d should be reversed:Affiliation c should be“Laboratory for Marine Fisheries Science and Food Production Processes,Pilot Qingdao National Laboratory for Marine Science and Technology,Qingdao 266237,China,”and the affiliation d should be“Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering,Sanya Oceanographic Institution,Ocean University of China,Sanya 572000,China.”

Targeted Genotyping of a Whole-Gene Repertoire by an Ultrahigh-Multiplex and Flexible HD-Marker Approach

Targeted genotyping is an extremely powerful approach for the detection of known genetic variations that are biologically or clinically important.However,for non-model organisms,large-scale target geno-typing in a cost-effective manner remains a major challenge.To address this issue,we present an ultrahigh-multiplex,in-solution probe array-based high-throughput diverse marker genotyping(HD-Marker)approach that is capable of targeted genotyping of up to 86000 loci,with coverage of the whole gene repertoire,in what is a 27-fold and six-fold multiplex increase in comparison with the conventional Illumina GoldenGate and original HD-Marker assays,respectively.We perform extensive analyses of var-ious ultrahigh-multiplex levels of HD-Marker(30 k-plex,56 k-plex,and 86 k-plex)and show the power and excellent performance of the proposed method with an extremely high capture rate(about 96%)and genotyping accuracy(about 96%).With great advantages in terms of cost(as low as 0.0006 USD per geno-type)and high technical flexibility,HD-Marker is a highly efficient and powerful tool with broad appli-cation potential for genetic,ecological,and evolutionary studies of non-model organisms.

A bacterial symbiont in the gill of the marine scallop Argopecten irradians irradians metabolizes dimethylsulfoniopropionate

Microbial lysis of dimethylsulfoniopropionate(DMSP)is a key step in marine organic sulfur cycling and has been recently demonstrated to play an important role in mediating interactions between bacteria,algae,and zooplankton.To date,microbes that have been found to lyse DMSP are largely confined to free‐living and surface‐attached bacteria.In this study,we report for the first time that a symbiont(termed“Rhodobiaceae bacterium HWgs001”)in the gill of the marine scallop Argopecten irradians irradians can lyse and metabolize DMSP.Analysis of 16S rRNA gene sequences suggested that HWgs001 accounted for up to 93%of the gill microbiota.Microscopic observations suggested that HWgs001 lived within the gill tissue.Unlike symbionts of other bivalves,HWgs001 belongs to Alphaproteobacteria rather than Gammaproteobacteria,and no genes for carbon fixation were identified in its small genome.Moreover,HWgs001 was found to possess a dddP gene,responsible for the lysis of DMSP to acrylate.The enzymatic activity of dddP was confirmed using the heterologous expression,and in situ transcription of the gene in scallop gill tissues was demonstrated using reverse‐transcription PCR.Together,these results revealed a taxonomically and functionally unique symbiont,which represents the first‐documented DMSP‐metabolizing symbiont likely to play significant roles in coastal marine ecosystems.

Fine‑mapping and association analysis of candidate genes for papilla number in sea cucumber,Apostichopus japonicus

The papilla number is one of the most economically important traits of sea cucumber in the China marketing trade.However,the genetic basis for papilla number diversity in holothurians is still scarce.In the present study,we conducted genomewide association studies(GWAS)for the trait papilla number of sea cucumbers utilizing a set of 400,186 high-quality SNPs derived from 200 sea cucumbers.Two significant trait-associated SNPs that passed Bonferroni correction(P<1.25E−7)were located in the intergenic region near PATS1 and the genic region of EIF4G,which were reported to play a pivotal role in cell growth and proliferation.The fine-mapping regions around the top two lead SNPs provided precise causative loci/genes related to papilla formation and cellular activity,including PPP2R3C,GBP1,and BCAS3.Potential SNPs with P<1E−4 were acquired for the following GO and KEGG enrichment analysis.Moreover,the two lead SNPs were verified in another population of sea cucumber,and the expressive detection of three potential candidate genes PATS1,PPP2R3C,and EIF4G that near or cover the two lead SNPs was conducted in papilla tissue of TG(Top papilla number group)and BG(Bottom papilla number group)by qRT-PCR.We found the significantly higher expression profile of PATS1(3.34-fold),PPP2R3C(4.90-fold),and EIF4G(4.23-fold)in TG,implying their potential function in papilla polymorphism.The present results provide valuable information to decipher the phenotype differences of the papilla trait and will provide a scientific basis for selective breeding in sea cucumbers.

Glutathione S-transferase genes in scallops and their diverse expression patterns after exposure to PST-producing dinoflagellates

The glutathione S-transferases(GSTs)are a superfamily of enzymes that function in cellular protection against toxic substances and oxidative stress.Bivalves could accumulate high concentration of paralytic shellfish toxins(PSTs)from harmful algae.To understand the possible involvement of GSTs in protecting bivalves during PST accumulation and metabolism,the GST genes were systemically analyzed in two cultured scallops,Azumapecten farreri and Mizuhopecten yessoensis,which were reported for PST deposition during harmful algae bloom.A total of 35 and 37 GSTs were identified in A.farreri(AfGSTs)and M.yessoensis(MyGSTs)genome,respectively,and the expansion of the sigma class from the cytosolic subfamily was observed.In both scallop species,sigma class GSTs showed higher expression than other members.The high GSTs expression was detected mainly during/after larvae stages and in the two most toxic organs,hepatopancreas and kidney.After ingesting PST-producing dinoflagellates,all the regulated AfGSTs in the hepatopancrcas were from the sigma class,but with opposite regulation pattern between Alexandrium catenella and A.minutum exposure.In scallop kidneys,where PSTs transformed into higher toxicity,more AfGSTs were regulated than in the hepatopancreas,and most of them were from the sigma class,with similar regulation pattern between A.catenella and A.minutum exposure.In M.yessoensis exposed to A.catenella,MyGST-σ2 was the only up-regulated MyGST in both hepatopancreas and kidney.Our results suggested the possible diverse function of scallop GSTs and the importance of sigma class in the defense against PSTs,which would contribute to the adaptive evolution of scallops in marine environments.

High-resolution linkage and quantitative trait locus mapping using an interspecific cross between Argopecten irradians irradians(♀) and A. purpuratus (♂)

The bay scallop and Peruvian scallop are economically important species.Interspecific hybrids of these two scallops outperformed both of their parent species in multiple growth traits but exhibited decreased fertility,which provides good models for the study of heterosis and species divergence.Genetic mapping serves as a chromosomal-level framework to investigate the molecular mechanisms of hybridization and introgression.In this study,high-resolution linkage maps were constructed for the bay and Peruvian scallops with an interspecific hybrid family.The linkage map of the bay scallop covered over 98.9% of the whole genome with 2994 mapped markers and the average marker interval of 0.32 cM.For the Peruvian scallop,1585 markers were mapped with the average maker interval of 0.51 cM,covering 97.7% of the genome.Both the two linkage maps have 16 linkage groups,corresponding to the haploid chromosome number of the two species.Approximately,54.5% of markers exhibited significant deviation from the expected Mendelian ratio of segregation,lending in sights into the intrinsic incompatibility between the two species.QTLs related to growth and shell coloration were detected,which could explain 13.1%and 74.9% of the phenotypic variance,respectively.This represents important information for further evaluation.These findings are an important addition to the genomic resources for scallop genetic studies,and are especially useful for investigations on genomic incompatibility for hybridization,genome evolution of closely related species,and genetic enhancement programs in aquaculture.

Adaptive Bird-like Genome Miniaturization During the Evolution of Scallop Swimming Lifestyle

Genome miniaturization drives key evolutionary innovations of adaptive traits in vertebrates,such as the flight evolution of birds.However,whether similar evolutionary processes exist in invertebrates remains poorly understood.Derived from the second-largest animal phylum,scallops are a special group of bivalve molluscs and acquire the evolutionary novelty of the swimming lifestyle,providing excellent models for investigating the coordinated genome and lifestyle evolution.Here,we show for the first time that genome sizes of scallops exhibit a generally negative correlation with locomotion activity.To elucidate the co-evolution of genome size and swimming lifestyle,we focus on the Asian moon scallop(Amusium pleuronectes)that possesses the smallest known scallop genome while being among scallops with the highest swimming activity.Whole-genome sequencing of A.pleuronectes reveals highly conserved chromosomal macrosynteny and microsynteny,suggestive of a highly contracted but not degenerated genome.Genome reduction of A.pleuronectes is facilitated by significant inactivation of transposable elements,leading to reduced gene length,elevated expression of genes involved in energy-producing pathways,and decreased copy numbers and expression levels of biomineralization-related genes.Similar evolutionary changes of relevant pathways are also observed for bird genome reduction with flight evolution.The striking mimicry of genome miniaturization underlying the evolution of bird flight and scallop swimming unveils the potentially common,pivotal role of genome size fluctuation in the evolution of novel lifestyles in the animal kingdom.