Complete Mitochondrial Genome Sequencing of a Burial from a Romano–Christian Cemetery in the Dakhleh Oasis, Egypt: Preliminary Indications

Abstract

The curse of ancient Egyptian DNA was lifted by a recent study which sequenced the mitochondrial genomes (mtGenome) of 90 ancient Egyptians from the archaeological site of Abusir el-Meleq. Surprisingly, these ancient inhabitants were more closely related to those from the Near East than to contemporary Egyptians. It has been accepted that the timeless highway of the Nile River seeded Egypt with African genetic influence, well before pre-Dynastic times. Here we report on the successful recovery and analysis of the complete mtGenome from a burial recovered from a remote Romano–Christian cemetery, Kellis 2 (K2). K2 serviced the ancient municipality of Kellis, a village located in the Dakhleh Oasis in the southwest desert in Egypt. The data were obtained by high throughput sequencing (HTS) performed independently at two ancient DNA facilities (Armed Forces DNA Identification Laboratory, Dover, DE, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA). These efforts produced concordant haplotypes representing a U1a1a haplogroup lineage. This result indicates that Near Eastern maternal influence previously identified at Abusir el-Meleq was also present further south, in ancient Kellis during the Romano–Christian period.

Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens

“…Modern human contamination in the mtDNA data, as assessed using ContamMix, was estimated at 0.6% (95% CI 0.08–1.8%) in CAP-Lib1 and 11.6% in CAP-Lib2 (95% CI 9.7–13.6%). The value for Lib1 is consistent with the rates observed in other ancient DNA studies [ 44 , 46 , 48 , 49 , 50 , 51 , 52 , 61 , 62 , 63 , 64 , 65 , 66 ]. Though the estimated contamination rate in Lib2 was somewhat higher, it had no effect on consensus calling for the endogenous molecules, as the same mtGenome profile was recovered from both libraries.…”

“…MtDNA haplotypes recently obtained from ancient human remains from sub-Saharan Africa belong only to haplogroup L subgroups [ 65 , 88 ]. However, nearly all of the remains excavated in the Northern part of the continent belong to Eurasian mtDNA lineages [ 63 , 67 , 74 , 89 , 90 ]. In fact, of the 114 mtDNA genomes now available from northern African ancient human remains, only one belongs to an African lineage (L3 observed in a skeleton from Abusir el-Meleq [ 74 ]).…”

Applications of Probe Capture Enrichment Next Generation Sequencing for Whole Mitochondrial Genome and 426 Nuclear SNPs for Forensically Challenging Samples

“…Next generation sequencing (NGS) has shown great promise in the analysis of DNA from degraded, limited, and mixed samples often encountered in forensic cases [ 1 , 2 , 3 ]. NGS platforms produce millions of reads for sequencing multiple samples in a single sequencing run, thereby making it possible for sequencing of the whole mitochondrial (mt) genome and proving valuable for analyzing nuclear single nucleotide polymorphism (SNPs) and short tandem repeats (STRs) [ 4 , 5 , 6 , 7 ].…”

Massive parallel sequencing in forensics: advantages, issues, technicalities, and prospects

“…Multiple different PCR strategies exist for amplifying the mitochondrial genome, whether it be in two long segments for whole genome amplification of good-quality DNA [58,59], multiple smaller fragments (~2 kb) for whole genome amplification in partially compromised samples [60], or many overlapping small amplicons for amplification of either the control region [61] or entire genome [62] in degraded samples. NGS analysis with any of these approaches can be carried out using either an enzymatic fragmentation system or by direct sequencing of the PCR products for those methods producing fragments of less than~500 bp.…”