A Chromosome-level Reference Genome of African Oil Palm Provides Insights into Its Divergence and Stress Adaptation

The palm family(Arecaceae),consisting of2600 species,is the third most economically important family of plants.The African oil palm(Elaeis guineensis)is one of the most important palms.However,the genome sequences of palms that are currently available are still limited and fragmented.Here,we report a high-quality chromosome-level reference genome of an oil palm,Dura,assembled by integrating long reads with150 genome coverage.The assembled genome was 1.7 Gb in size,covering 94.5%of the estimated genome,of which 91.6%was assigned into 16 pseudochromosomes and 73.7%was repetitive sequences.Relying on the conserved synteny with oil palm,the existing draft genome sequences of both date palm and coconut were further assembled into chromosomal level.Transposon burst,particularly long terminal repeat retrotransposons,following the last whole-genome duplication,likely explains the genome size variation across palms.Sequence analysis of the VIRESCENS gene in palms suggests that DNA variations in this gene are related to fruit colors.Recent duplications of highly tandemly repeated pathogenesis-related proteins from the same tandem arrays play an important role in defense responses to Ganoderma.Whole-genome resequencing of both ancestral African and introduced oil palms in Southeast Asia reveals that genes under putative selection are notably associated with stress responses,suggesting adaptation to stresses in the new habitat.The genomic resources and insights gained in this study could be exploited for accelerating genetic improvement and understanding the evolution of palms.

Identification of novel Z/W chromosome-specific markers from the giant freshwater prawn Macrobrachium rosenbergii

The giant freshwater prawn(Macrobrachium rosenbergii)is a commercially cultured species in China.A sex chromosome-specific marker is crucial for sex identification and distinguishing sex chromosomes.Here,based on the results of reduced-representation genome sequencing and genome survey of M.rosenbergii,we identified steady sex-linked markers.Further nucleotide alignment analysis revealed 83.42%nucleotide similarity between the amplified W-and Z-chromosome fragments.qPCR confirmed that Z chromosome-specific fragments were present in males approximately twice as often compared to females.Similarly,the W chromosome-specific fragments were present in super females approximately twice as often compared to females.Our findings elucidate the ZW/ZZ sex determination type and contribute to exploring sex-related or sex-determining genes present on the sex chromosomes of M.rosenbergii.

Heritability of growth traits in the Asian seabass (Lates calcarifer)

Growth is an economically important trait in aquaculture.To improve growth trait of the Asian seabass(Lates calcarifer)we have been carrying out,since 2004,a selective breeding program.This study focuses on growth traits in the F2 fish generation,comprised of offspring from 23 mass crosses from 383 F_(1) brooders.Using genotyping analysis for 10 microsatellites from both brood stock and progeny we have reconstructed the pedigree of each mass-cross.For F_(2) generation at 90 days post hatch(dph),we have recorded body weight(BW)for 12,117 individuals and total length(TL),standard length(SL)and condition factor(K_(tl) and K_(sl))for 3530 individuals;and all five traits for 2136 individuals at 270 dph.At 90 dph the average BW was 46.88±20.95 g.Combining pedigree information,recorded growth traits and Restricted Maximum Likelihood method,we have estimated that the narrow sense heritability(h^(2))in F_(1) fish for BW,TL,SL,K_(tl) and K_(sl) was at,90 dph,0.12±0.03,0.11±0.03,0.10±0.03,0.20±0.04 and 0.11±0.03,respectively and,at 270 dph,0.34±0.07,0.32±0.07,0.30±0.06,0.13±0.04 and 0.11±0.04,respectively.At 90 dph the realised heritability for BW was 0.13.Comparing with F_(1) generation,the growth performance of F_(2) fish was increased by 14.4%.Heritability of growth traits will be useful for future genetic improvement programmes of the Asian seabass.