Emergence and evolution of Hominidae-speciﬁc codin...

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Genome Biology and Evolution

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10.1093/gbe/evw132

Genome Biology and Evolution
gbe.oxfordjournals.org
Genome Biol Evol (2016) doi: 10.1093/gbe/evw132
First published online: June 11, 2016

Emergence and evolution of Hominidae-specificcoding and noncoding genomic sequences
123232Morteza Mahmoudi Saber , , Isaac Adeyemi Babarinde , , Nilmini Hettiarachchi , and213

Naruya Saitou , , ,*+ Author Affiliations↵ *Corresponding Author: Naruya Saitou, Division of Population Genetics, National Instituteof Genetics, Yata 1111, Mishima, 411-8540, Japan, TEL/FAX +81-55-981-6790/6789, Email:saitounr@nig.ac.jp
Received October 2, 2015.
Revision received February 10, 2016.
Revision received May 10, 2016.
Accepted May 31, 2016.

Abstract
Family Hominidae, which includes humans and great apes, is recognized
for unique complex social behavior and intellectual abilities. Despite theincreasing genome data, however, the genomic origin of its phenotypic
uniqueness has remained elusive. Clade-specific genes and highly
conserved noncoding sequences (HCNSs) are among the high-potential
evolutionary candidates involved in driving clade-specific characters andphenotypes. On this premise, we analyzed whole genome sequences alongwith gene orthology data retrieved from major DNA databases to findHominidae-specific genes and HCNSs. We discovered that Down syndrome
critical region 4 (DSCR4) is the only experimentally verified gene uniquely
present in Hominidae. DSCR4 has no structural homology to any known
protein and was inferred to have emerged in several steps throughLTR/ERV1, LTR/ERVL retrotransposition, and transversion. Using thegenomic distance as neutral evolution threshold, we identified 1,658
Hominidae-specific HCNSs. Polymorphism coverage and derived allele
frequency analysis of Hominidae-specific HCNSs showed that these HCNSs
are under purifying selection, indicating that they may harbor importantfunctions. They are overrepresented in promoters/untranslated regions, inclose proximity of genes involved in sensory perception of sound anddevelopmental process, and also showed a significantly lower nucleosome
occupancy probability. Interestingly, many ancestral sequences of the
Hominidae-specific HCNSs showed very high evolutionary rates. Thissuggests that new functions emerged through some kind of positive
selection, and then purifying selection started to operate to keep thesefunctions.
Key words
DSCR4

Hominidae

conserved noncoding sequences

lineage-specific genes

accelerated evolution© The Author(s) 2016. Published by Oxford University Press on behalf of the Society for
Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits
unrestricted reuse, distribution, and reproduction in any medium, provided the original work
is properly cited.

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