Insights into hominid evolution from the gorilla genome sequence
1Wellcome Trust Sanger Insitute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
2Bioinformatics Research Center, Aarhus University, C.F. Møllers Allé 8, 8000 Aarhus C, Denmark
3Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
4European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
5Department of Genetic Medicine and Development, University of Geneva Medical School, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
6Institut de Biologia Evolutiva (UPF-CSIC), 08003 Barcelona, Catalonia, Spain
7Institucio Catalana de Recerca i Estudis Avançats, ICREA, 08010 Barcelona, Spain
8Department of Zoology, University of Cambridge, Downing St, Cambridge, CB2 3EJ, UK
9University of Cambridge, Department of Oncology, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
10Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
11Howard Hughes Medical Institute, University of Washington, Seattle, Washington, 20815-6789, USA
12Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
13Department of Anthropology, Yale University, 10 Sachem Street, New Haven, Connecticut 06511, USA
14The Genome Institute at Washington University, Washington University School of Medicine, Saint Louis, Missouri 63108, USA
15MRC Functional Genomics Unit, University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK
16Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
17Comparative Genomics Unit, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892-2152, USA
18Max Planck Institute for Evolutionary Anthropology, Primatology Department, Deutscher Platz 6, Leipzig 04103, Germany
19Children’s Hospital Oakland Research Institute, Oakland, California 94609, USA
20San Diego Zoo’s Institute for Conservation Research, Escondido, California 92027, USA
Humans share many elements of their anatomy and physiology with both gorillas and chimpanzees, and our similarity to these species was emphasised by Darwin and Huxley in the first evolutionary accounts of human origins1
. Molecular studies confirmed that we are closer to the African apes than to orangutans, and on average closer to chimpanzees than gorillas2
(). Subsequent analyses have explored functional differences between the great apes and their relevance to human evolution, assisted recently by reference genome sequences for chimpanzee3
. Here we provide a reference assembly and initial analysis of the gorilla genome sequence, establishing a foundation for the further study of great ape evolution and genetics.
Recent technological developments have dramatically reduced the costs of sequencing, but the assembly of a whole vertebrate genome remains a challenging computational problem. We generated a reference assembly from a single female western lowland gorilla (Gorilla gorilla gorilla
) named Kamilah, using 5.4 Gbp of capillary sequence combined with 166.8 Gbp of Illumina read pairs (see Methods Summary). Genes, transcripts and predictions of gene orthologues and paralogues were annotated by Ensembl5
, and additional analysis found evidence for 498 functional long (> 200 bp) intergenic RNA transcripts. summarizes the assembly and annotation properties. An assessment of assembly quality using finished fosmid sequences found that typical (N50) stretches of error-free sequence are 7.2 kbp in length, with errors tending to be clustered in repetitive regions. Outside RepeatMasked regions and away from contig ends, the total rate of single-base and indel errors is 0.13 per kbp. See Supplementary Information
for further details.
Assembly and annotation statistics
We also collected less extensive sequence data for three other gorillas, to enable a comparison of species within the Gorilla genus. Gorillas survive today only within several isolated and endangered populations whose evolutionary relationships are uncertain. In addition to Kamilah, our analysis included two western lowland gorillas, Kwanza (male) and EB(JC) (female), and one eastern lowland, Mukisi (male).