RESUMO
The mitochondrial genome of the long-spined black sea urchin, Diadema antillarum, was sequenced using Illumina next-generation sequencing technology. The complete mitogenome is 15,708 bp in length, containing two rRNA, 22 tRNA and 13 protein-coding genes, plus a noncoding control region of 133 bp. The nucleotide composition is 18.37% G, 23.79% C, 26.84% A and 30.99% T. The A + T bias is 57.84%. Phylogenetic analysis based on 12 complete mitochondrial genomes of sea urchins, including four species of the family Diadematidae, supported familial monophyly; however, the two Diadema species, D. antillarum and D. setosum were not recovered as sister taxa.
El genoma mitocondrial del erizo de mar negro de espinas largas, Diadema antillarum, se secuenció utilizando la tecnología de secuenciación de nueva generación de Illumina. El mitogenoma completo tiene un tamaño de 15,708 pb, que contiene dos ARNr, 22 ARNt y 13 genes codificadores de proteínas, además de una región de control no codificante de 133 pb. La composición de nucleótidos es 18.37% G, 23.79% C, 26.84% A y 30.99% T. El sesgo A+T es del 57.84%. El análisis filogenético basado en 12 genomas mitocondriales completos de erizos de mar, incluyendo cuatro especies de la familia Diadematidae, apoya la monofilia familiar. Sin embargo, las dos especies de Diadema en este estudio, D. antillarum y D. setosum no fueron identificadas como taxones hermanos.
RESUMO
Since the first Spanish settlers brought horses to America centuries ago, several local varieties and breeds have been established in the New World. These were generally a consequence of the admixture of the different breeds arriving from Europe. In some instances, local horses have been selectively bred for specific traits, such as appearance, endurance, strength, and gait. We looked at the genetics of two breeds, the Puerto Rican Non-Purebred (PRNPB) (also known as the "Criollo") horses and the Puerto Rican Paso Fino (PRPF), from the Caribbean Island of Puerto Rico. While it is reasonable to assume that there was a historic connection between the two, the genetic link between them has never been established. In our study, we started by looking at the genetic ancestry and diversity of current Puerto Rican horse populations using a 668 bp fragment of the mitochondrial DNA D-loop (HVR1) in 200 horses from 27 locations on the island. We then genotyped all 200 horses in our sample for the "gait-keeper" DMRT3 mutant allele previously associated with the paso gait especially cherished in this island breed. We also genotyped a subset of 24 samples with the Illumina Neogen Equine Community genome-wide array (65,000 SNPs). This data was further combined with the publicly available PRPF genomes from other studies. Our analysis show an undeniable genetic connection between the two varieties in Puerto Rico, consistent with the hypothesis that PRNPB horses represent the descendants of the original genetic pool, a mix of horses imported from the Iberian Peninsula and elsewhere in Europe. Some of the original founders of PRNRB population must have carried the "gait-keeper" DMRT3 allele upon arrival to the island. From this admixture, the desired traits were selected by the local people over the span of centuries. We propose that the frequency of the mutant "gait-keeper" allele originally increased in the local horses due to the selection for the smooth ride and other characters, long before the PRPF breed was established. To support this hypothesis, we demonstrate that PRNPB horses, and not the purebred PRPF, carry a signature of selection in the genomic region containing the DMRT3 locus to this day. The lack of the detectable signature of selection associated with the DMRT3 in the PRPF would be expected if this native breed was originally derived from the genetic pool of PRNPB horses established earlier and most of the founders already had the mutant allele. Consequently, selection specific to PRPF later focused on allels in other genes (including CHRM5, CYP2E1, MYH7, SRSF1, PAM, PRN and others) that have not been previously associated with the prized paso gait phenotype in Puerto Rico or anywhere else.
Assuntos
Cavalos , AnimaisRESUMO
The mitochondrial genome of the long-spined black sea urchin, Diadema antillarum, was sequenced using Illumina next-generation sequencing technology. The complete mitogenome is 15,708 bp in length, containing two rRNA, 22 tRNA and 13 protein-coding genes, plus a noncoding control region of 133 bp. The nucleotide composition is 18.37% G, 23.79% C, 26.84% A and 30.99% T. The A + T bias is 57.84%. Phylogenetic analysis based on 12 complete mitochondrial genomes of sea urchins, including four species of the family Diadematidae, supported familial monophyly; however, the two Diadema species, D. antillarum and D. setosum were not recovered as sister taxa.
RESUMO
BACKGROUND: The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for public data release. BGISEQ-500 sequence data and genotypes by an Illumina GWAS chip were cross-validated on multiple samples and additionally referenced to 1 sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. RESULTS: The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide polymorphisms, and microsatellites. To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population. CONCLUSIONS: Our results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces and cannot be ignored in future genetic and biomedical studies. These data will contribute a wealth of new information bringing forth a wealth of novel, endemic and medically related alleles.
