Thiyagarajan, V. | Search bioRxiv

bioRxiv2024

Purifying selection and intraspecies recombination may drive the speciation in Crassostrea: evidence from complete mitochondria sequence of Crassostrea hongkongensis and comparative genomic analysis

Repeat dynamics and recombination play a crucial role during the evolution of the mitochondrial genome in plants and animals. However, this phenomenon has got less attention within Crassostrea, a complex marine species found worldwide having high commercial value as well as efficient carbon neutralizer. During this study, we characterized the whole mitochondrial genomes of C. hongkongensis retrieved from transcriptome data (GenBank acc. no. MZ073671). The current mitochondrial genome (18,616 bp) was composed of a non-coding control region (D-loop region), 2 ribosomal RNA (rRNA genes), 12 protein-coding genes (PCGs), and 23 transfer RNA (tRNA). Furthermore, comparative genomics analysis revealed that the present isolate is closely related to the Chinese isolate (NC_011518) with 99.82% similarity. Microsatellite analysis within the mitochondrial genome revealed its bias towards mononucleotide repeat A/T, di-nucleotide AG followed by AT and AC, trinucleotide AAT followed by AAG, ATC, and ATG. The recombination analysis deciphered the lack of interspecific recombination, but the presence of intraspecific recombination within ND1, ND2, and ND4L of Crassostrea species. Selection pressure analysis revealed the presence of purifying selection within maximum genes which drive the evolution of the species.

evolutionary biology↗

bioRxiv2023

Genome-wide and chromosomal microsatellite marker landscape analysis within the genus Crassostrea

Microsatellite is a classical codominant marker frequently used to study genetics and evolution of living entities as well as molecular breeding in commercially important species. Although it has a tremendous application in oyster aquaculture, the lack of knowledge about its type, distribution pattern, and comparative analysis is limited. Thus, in this study, we conducted a genome-wide as well as chromosomal microsatellite landscape analysis within the genus Crassostrea. The genome-wide microsatellites number varied from 169432-212368, with relative abundance (RA) and relative density (RD) ranging from 310.18-336.5 loci/Mb and 7553.4-8793.42 bp/Mb, respectively. About 14.99-16.75% of total microsatellites were considered compound microsatellites having cRA and cRD, 21.78-25.5 loci/Mb, and 1332.81-1694.54 bp/Mb, respectively. The mononucleotide microsatellites were predominant followed by di and tetranucleotide. The RA and RD of the SSRs revealed no correlation with genome size but a significant correlation with GC content. However, the number of SSRs showed a significant relationship with the genome size but no relation with GC content. In contrast, the incidence of cSSR was positively associated with genome size and GC content. Finally, 29 cSSR loci were developed and validated in C. hongkonensis using one wild population followed by its cross-species amplification. The allele number (Ne), observed heterozygosity (Ho), expected heterozygosity (He), inbreeding co-efficient (Fis), the polymorphic information content (PIC), ranged from 2-10, 0.092-0.897, 0.0001-1, 0.088-0.828, respectively. The present study elucidated microsatellite evolution within the Crassostrea genome and the loci developed can be utilized for brood stock analysis, parentage assignment, and construction of linkage map of the respective species.

genomics↗