Re-Assembling And Comparative Analysis Of G.Arboreum Chromosome 12 Identifies Chromosome Scale Mis-Assemblies In Its Sequenced Genome

Genome sequencing technologies continues to improve exponentially;but assembling genomes de novo remains an important challenge.One of the most difficult problems during de-novo genome assembly is the ordering and orientation of scaffolds to reconstruct the pseudo-chromosomes.The genome of cultivated G.arboreum was previously sequenced and assembled with 3,740 scaffolds that were anchored and oriented on 13 chromosomes by genetic map.However,different comparative analysis such as collinearity and synteny with the closely related species reported that draft sequenced genome of G.arboreum contains various mis-assemblies.To address this problem,we generated significantly correct high quality assembly of G.arboreum chromosome 12(A_A12)by combining both genetic map and reference assisted approaches.The current assembly of G.arboreum chromosome 12 has the total length of 94.64 Mb which comprised of 144 scaffolds and contained 3,361 protein coding genes,respectively.We found various major mis-assemblies in previous assembled chromosome 12 of G.arboreum particularly in anchoring and orienting of scaffolds into pseudo-molecule.Evaluation of results using the different comparative analysis such as collinearity,synteny and phylogeny study with the corresponding homologous chromosomes of G.raimondii and G.hirsutum also confirmed the significant improve quality of current chromosomal reassembly as compared to previous one.We also found that the divergence of G.hirsutum chromosome D12 from its proposed progenitor chromosome of G.raimondii was greater than that of G.hirsutum chromosome A12 from its G.arboreum progenitor chromosome.Additionally,a higher rate of gene losses has been found in the corresponding homologous chromosome 12 of tetraploid cotton than the diploid cotton.While the phylogenetic analysis based on the alignment of transcription factor related genes of five different families(ERF,bHLH,MYB,C2H2 and WRKY)from homologous chromosome 12 of G.raimondii,G.arboreum,and G.hirsutum revealed that genes from the same cotton species were not always clustered together but often scattered in different clades,showing that these genes were found homologous within three cotton species.This study offers the more accurate initial strategy towards the correction of mis-assemblies in cotton genome draft sequence that will provide more information on genome organization.