PMID- 36854669
OWN - NLM
STAT- MEDLINE
DCOM- 20230615
LR  - 20240215
IS  - 1549-5469 (Electronic)
IS  - 1088-9051 (Print)
IS  - 1088-9051 (Linking)
VI  - 33
IP  - 3
DP  - 2023 Mar
TI  - Complete sequencing of a cynomolgus macaque major histocompatibility complex 
      haplotype.
PG  - 448-462
LID - 10.1101/gr.277429.122 [doi]
AB  - Macaques provide the most widely used nonhuman primate models for studying the 
      immunology and pathogenesis of human diseases. Although the macaque major 
      histocompatibility complex (MHC) region shares most features with the human 
      leukocyte antigen (HLA) region, macaques have an expanded repertoire of MHC class 
      I genes. Although a chimera of two rhesus macaque MHC haplotypes was first 
      published in 2004, the structural diversity of MHC genomic organization in 
      macaques remains poorly understood owing to a lack of adequate genomic reference 
      sequences. We used ultralong Oxford Nanopore and high-accuracy Pacific 
      Biosciences (PacBio) HiFi sequences to fully assemble the  approximately 5.2-Mb M3 haplotype of 
      an MHC-homozygous, Mauritian-origin cynomolgus macaque (Macaca fascicularis). The 
      MHC homozygosity allowed us to assemble a single MHC haplotype unambiguously and 
      avoid chimeric assemblies that hampered previous efforts to characterize this 
      exceptionally complex genomic region in macaques. The high quality of this new 
      assembly is exemplified by the identification of an extended cluster of six 
      Mafa-AG genes that contains a recent duplication with a highly similar  approximately 48.5-kb 
      block of sequence. The MHC class II region of this M3 haplotype is similar to the 
      previously sequenced rhesus macaque haplotype and HLA class II haplotypes. The 
      MHC class I region, in contrast, contains 13 MHC-B genes, four MHC-A genes, and 
      three MHC-E genes (vs. 19 MHC-B, two MHC-A, and one MHC-E in the previously 
      sequenced haplotype). These results provide an unambiguously assembled single 
      contiguous cynomolgus macaque MHC haplotype with fully curated gene annotations 
      that will inform infectious disease and transplantation research.
CI  - (c) 2023 Karl et al.; Published by Cold Spring Harbor Laboratory Press.
FAU - Karl, Julie A
AU  - Karl JA
AUID- ORCID: 0000-0002-4447-4721
AD  - Department of Pathology and Laboratory Medicine, School of Medicine and Public 
      Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.
FAU - Prall, Trent M
AU  - Prall TM
AUID- ORCID: 0000-0003-0635-4152
AD  - Department of Pathology and Laboratory Medicine, School of Medicine and Public 
      Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.
FAU - Bussan, Hailey E
AU  - Bussan HE
AUID- ORCID: 0000-0002-0961-7109
AD  - Department of Pathology and Laboratory Medicine, School of Medicine and Public 
      Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.
FAU - Varghese, Joshua M
AU  - Varghese JM
AUID- ORCID: 0000-0001-9777-0818
AD  - Department of Pathology and Laboratory Medicine, School of Medicine and Public 
      Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.
FAU - Pal, Aparna
AU  - Pal A
AD  - Department of Pathology and Laboratory Medicine, School of Medicine and Public 
      Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.
FAU - Wiseman, Roger W
AU  - Wiseman RW
AUID- ORCID: 0000-0002-7682-7085
AD  - Department of Pathology and Laboratory Medicine, School of Medicine and Public 
      Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.
AD  - Wisconsin National Primate Research Center, University of Wisconsin-Madison, 
      Madison, Wisconsin 53715, USA.
FAU - O'Connor, David H
AU  - O'Connor DH
AUID- ORCID: 0000-0003-2139-470X
AD  - Department of Pathology and Laboratory Medicine, School of Medicine and Public 
      Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA; 
      dhoconno@wisc.edu.
AD  - Wisconsin National Primate Research Center, University of Wisconsin-Madison, 
      Madison, Wisconsin 53715, USA.
LA  - eng
GR  - P51 OD011106/OD/NIH HHS/United States
GR  - T15 LM007359/LM/NLM NIH HHS/United States
GR  - T32 GM140935/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20230228
PL  - United States
TA  - Genome Res
JT  - Genome research
JID - 9518021
SB  - IM
MH  - Animals
MH  - Humans
MH  - Macaca fascicularis/genetics
MH  - Haplotypes
MH  - Macaca mulatta/genetics
MH  - *Major Histocompatibility Complex/genetics
MH  - Sequence Analysis, DNA/methods
MH  - Alleles
PMC - PMC10078292
EDAT- 2023/03/01 06:00
MHDA- 2023/06/15 06:42
PMCR- 2023/09/01
CRDT- 2023/02/28 23:35
PHST- 2022/10/24 00:00 [received]
PHST- 2023/02/21 00:00 [accepted]
PHST- 2023/06/15 06:42 [medline]
PHST- 2023/03/01 06:00 [pubmed]
PHST- 2023/02/28 23:35 [entrez]
PHST- 2023/09/01 00:00 [pmc-release]
AID - gr.277429.122 [pii]
AID - 10.1101/gr.277429.122 [doi]
PST - ppublish
SO  - Genome Res. 2023 Mar;33(3):448-462. doi: 10.1101/gr.277429.122. Epub 2023 Feb 28.