The whole-genome survey of Acer griseum,its polymorphic simple sequence repeats development and application

Background:Acer griseum Pax is an endangered species endemic to China with both ornamental and economic value.However,the lack of information on its genome size and characteristics hinders further work at the genome level.Methods:This paper applied bioinformatics methods to predict the characteristics and patterns of the A.griseum genome,providing an important basis for formulating its whole-genome sequencing scheme.This study also characterized the simple sequence repeats(SSRs)of A.griseum,laying the foundation for the development and application of genome-wide SSR markers.In this study,PE150 sequencing was performed by the BGI MGISEQ platform,and the sequence files were analyzed by the K-mer method to estimate the characteristic information by GCE software.Results:The genome size was finally determined to be 739.63 Mb,its heterozygosity ratio was 1.33%,and the repetition ratio was 65.68%.A total of 825,960 SSR loci were identified in the assembled genome sequence,and primers were successfully designed for 526,020 loci.To verify the effectiveness of these primers,100 pairs of primers were randomly selected and synthesized,and 81 pairs successfully amplified the target fragments.Fourteen pairs of primers with good polymorphism were selected for principal component analysis of 31 A.griseum individuals from two populations,showing favorable heterozygosity and PIC values.According to the findings,these SSRs might identify genetic variations based on geographic areas.Conclusion:It is suggested that Illumina+PacBio assembly strategy should be used for whole-genome sequencing due to the high heterozygosity rate and high repetition rate of the genome.In addition,the SSR primers designed in batches in this study laid a foundation for the in-depth study of population structure and population maintenance mechanism of A.griseum,which is helpful for the effective conservation and sustainable utilization of this germplasm resource.

Chromosome-level genome assembly of the glass catfish(Kryptopterus vitreolus)reveals molecular clues to its transparent phenotype

Glass catfish(Kryptopterus vitreolus)are notable in the aquarium trade for their highly transparent body pattern.This transparency is due to the loss of most reflective iridophores and light-absorbing melanophores in the main body,although certain black and silver pigments remain in the face and head.To date,however,the molecular mechanisms underlying this transparent phenotype remain largely unknown.To explore the genetic basis of this transparency,we constructed a chromosome-level haplotypic genome assembly for the glass catfish,encompassing 32 chromosomes and 23344 protein-coding genes,using PacBio and Hi-C sequencing technologies and standard assembly and annotation pipelines.Analysis revealed a premature stop codon in the putative albinism-related tyrp1b gene,encoding tyrosinase-related protein 1,rendering it a nonfunctional pseudogene.Notably,a synteny comparison with over 30 other fish species identified the loss of the endothelin-3(edn3b)gene in the glass catfish genome.To investigate the role of edn3b,we generated edn3b^(−/−)mutant zebrafish,which exhibited a remarkable reduction in black pigments in body surface stripes compared to wild-type zebrafish.These findings indicate that edn3b loss contributes to the transparent phenotype of the glass catfish.Our high-quality chromosome-scale genome assembly and identification of key genes provide important molecular insights into the transparent phenotype of glass catfish.These findings not only enhance our understanding of the molecular mechanisms underlying transparency in glass catfish,but also offer a valuable genetic resource for further research on pigmentation in various animal species.

Construction of a chromosome-level genome assembly for genome-wide identification of growth-related quantitative trait loci in Sinocyclocheilus grahami(Cypriniformes,Cyprinidae)

The Dianchi golden-line barbel,Sinocyclocheilus grahami(Regan,1904),is one of the“Four Famous Fishes”of Yunnan Province,China.Given its economic value,this species has been artificially bred successfully since 2007,with a nationally selected breed(“S.grahami,Bayou No.1”)certified in 2018.For the future utilization of this species,its growth rate,disease resistance,and wild adaptability need to be improved,which could be achieved with the help of molecular markerassisted selection(MAS).In the current study,we constructed the first chromosome-level genome of S.grahami,assembled 48 pseudo-chromosomes,and obtained a genome size of 1.49 Gb.We also performed QTL-seq analysis of S.grahami using the highest and lowest bulks(i.e.,largest and smallest size)in both a sibling and random population.We screened two quantitative trait loci(QTLs)(Chr3,14.9-39.1 Mb and Chr17,4.1-27.4 Mb)as major growth-related locations.Several candidate genes(e.g.,map2k5,stat1,phf21a,sox6,and smad6)were also identified,with functions related to growth,such as cell differentiation,neuronal development,skeletal muscle development,chondrogenesis,and immunity.These results built a solid foundation for in-depth MAS studies on the growth traits of S.grahami.