A new rhesus macaque assembly and annotation for next-generation sequencing analyses

Aleksey V. Zimin; Adam S. Cornish; Mnirnal D. Maudhoo; Robert M. Gibbs; Xiongfei Zhang; Sanjit Pandey; Daniel T. Meehan; Kristin Wipfler; Steven E. Bosinger; Zachary P. Johnson; Gregory K. Tharp; Guillaume Marçais; Michael Roberts; Betsy Ferguson; Howard S. Fox; Todd Treangen; Steven L. Salzberg; James A. Yorke; Robert B. Norgren

doi:10.1186/1745-6150-9-20

A new rhesus macaque assembly and annotation for next-generation sequencing analyses

Aleksey V. Zimin, Adam S. Cornish, Mnirnal D. Maudhoo, Robert M. Gibbs, Xiongfei Zhang, Sanjit Pandey, Daniel T. Meehan, Kristin Wipfler, Steven E. Bosinger, Zachary P. Johnson, Gregory K. Tharp, Guillaume Marçais, Michael Roberts, Betsy Ferguson, Howard S. Fox, Todd Treangen, Steven L. Salzberg, James A. Yorke, Robert B. Norgren

Oregon National Primate Research Center

Research output: Contribution to journal › Article › peer-review

131 Scopus citations

Abstract

BACKGROUND: The rhesus macaque (Macaca mulatta) is a key species for advancing biomedical research. Like all draft mammalian genomes, the draft rhesus assembly (rheMac2) has gaps, sequencing errors and misassemblies that have prevented automated annotation pipelines from functioning correctly. Another rhesus macaque assembly, CR_1.0, is also available but is substantially more fragmented than rheMac2 with smaller contigs and scaffolds. Annotations for these two assemblies are limited in completeness and accuracy. High quality assembly and annotation files are required for a wide range of studies including expression, genetic and evolutionary analyses.

RESULTS: We report a new de novo assembly of the rhesus macaque genome (MacaM) that incorporates both the original Sanger sequences used to assemble rheMac2 and new Illumina sequences from the same animal. MacaM has a weighted average (N50) contig size of 64 kilobases, more than twice the size of the rheMac2 assembly and almost five times the size of the CR_1.0 assembly. The MacaM chromosome assembly incorporates information from previously unutilized mapping data and preliminary annotation of scaffolds. Independent assessment of the assemblies using Ion Torrent read alignments indicates that MacaM is more complete and accurate than rheMac2 and CR_1.0. We assembled messenger RNA sequences from several rhesus tissues into transcripts which allowed us to identify a total of 11,712 complete proteins representing 9,524 distinct genes. Using a combination of our assembled rhesus macaque transcripts and human transcripts, we annotated 18,757 transcripts and 16,050 genes with complete coding sequences in the MacaM assembly. Further, we demonstrate that the new annotations provide greatly improved accuracy as compared to the current annotations of rheMac2. Finally, we show that the MacaM genome provides an accurate resource for alignment of reads produced by RNA sequence expression studies.

CONCLUSIONS: The MacaM assembly and annotation files provide a substantially more complete and accurate representation of the rhesus macaque genome than rheMac2 or CR_1.0 and will serve as an important resource for investigators conducting next-generation sequencing studies with nonhuman primates.

REVIEWERS: This article was reviewed by Dr. Lutz Walter, Dr. Soojin Yi and Dr. Kateryna Makova.

Original language	English (US)
Pages (from-to)	20
Number of pages	1
Journal	Biology direct
Volume	9
Issue number	1
DOIs	https://doi.org/10.1186/1745-6150-9-20
State	Published - 2014

ASJC Scopus subject areas

Immunology
Ecology, Evolution, Behavior and Systematics
Modeling and Simulation
General Biochemistry, Genetics and Molecular Biology
General Agricultural and Biological Sciences
Applied Mathematics

Access to Document

10.1186/1745-6150-9-20

Cite this

Zimin, A. V., Cornish, A. S., Maudhoo, M. D., Gibbs, R. M., Zhang, X., Pandey, S., Meehan, D. T., Wipfler, K., Bosinger, S. E., Johnson, Z. P., Tharp, G. K., Marçais, G., Roberts, M., Ferguson, B., Fox, H. S., Treangen, T., Salzberg, S. L., Yorke, J. A., & Norgren, R. B. (2014). A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biology direct, 9(1), 20. https://doi.org/10.1186/1745-6150-9-20

Zimin, AV, Cornish, AS, Maudhoo, MD, Gibbs, RM, Zhang, X, Pandey, S, Meehan, DT, Wipfler, K, Bosinger, SE, Johnson, ZP, Tharp, GK, Marçais, G, Roberts, M, Ferguson, B, Fox, HS, Treangen, T, Salzberg, SL, Yorke, JA & Norgren, RB 2014, 'A new rhesus macaque assembly and annotation for next-generation sequencing analyses', Biology direct, vol. 9, no. 1, pp. 20. https://doi.org/10.1186/1745-6150-9-20

@article{158f642d413345a7ac4085de37aea8b5,

title = "A new rhesus macaque assembly and annotation for next-generation sequencing analyses",

abstract = "BACKGROUND: The rhesus macaque (Macaca mulatta) is a key species for advancing biomedical research. Like all draft mammalian genomes, the draft rhesus assembly (rheMac2) has gaps, sequencing errors and misassemblies that have prevented automated annotation pipelines from functioning correctly. Another rhesus macaque assembly, CR_1.0, is also available but is substantially more fragmented than rheMac2 with smaller contigs and scaffolds. Annotations for these two assemblies are limited in completeness and accuracy. High quality assembly and annotation files are required for a wide range of studies including expression, genetic and evolutionary analyses.RESULTS: We report a new de novo assembly of the rhesus macaque genome (MacaM) that incorporates both the original Sanger sequences used to assemble rheMac2 and new Illumina sequences from the same animal. MacaM has a weighted average (N50) contig size of 64 kilobases, more than twice the size of the rheMac2 assembly and almost five times the size of the CR_1.0 assembly. The MacaM chromosome assembly incorporates information from previously unutilized mapping data and preliminary annotation of scaffolds. Independent assessment of the assemblies using Ion Torrent read alignments indicates that MacaM is more complete and accurate than rheMac2 and CR_1.0. We assembled messenger RNA sequences from several rhesus tissues into transcripts which allowed us to identify a total of 11,712 complete proteins representing 9,524 distinct genes. Using a combination of our assembled rhesus macaque transcripts and human transcripts, we annotated 18,757 transcripts and 16,050 genes with complete coding sequences in the MacaM assembly. Further, we demonstrate that the new annotations provide greatly improved accuracy as compared to the current annotations of rheMac2. Finally, we show that the MacaM genome provides an accurate resource for alignment of reads produced by RNA sequence expression studies.CONCLUSIONS: The MacaM assembly and annotation files provide a substantially more complete and accurate representation of the rhesus macaque genome than rheMac2 or CR_1.0 and will serve as an important resource for investigators conducting next-generation sequencing studies with nonhuman primates.REVIEWERS: This article was reviewed by Dr. Lutz Walter, Dr. Soojin Yi and Dr. Kateryna Makova.",

author = "Zimin, {Aleksey V.} and Cornish, {Adam S.} and Maudhoo, {Mnirnal D.} and Gibbs, {Robert M.} and Xiongfei Zhang and Sanjit Pandey and Meehan, {Daniel T.} and Kristin Wipfler and Bosinger, {Steven E.} and Johnson, {Zachary P.} and Tharp, {Gregory K.} and Guillaume Mar{\c c}ais and Michael Roberts and Betsy Ferguson and Fox, {Howard S.} and Todd Treangen and Salzberg, {Steven L.} and Yorke, {James A.} and Norgren, {Robert B.}",

note = "Funding Information: This work was supported by National Institute of Health grant R24RR017444 (RN), P51OD011092 (BF) and P51 OD011132 (ZJ). We appreciate the helpful comments of Drs. Dave O{\textquoteright}Connor and Roger Wiseman on the rhesus MHC. We thank Jerilyn Pecotte of the Southwest National Primate Research Center for genomic DNA from the reference rhesus macaque. We appreciate the help of John Letaw, at the Oregon National Primate Research Center, and Tade Souaiaia, at the University of Southern California, for reviewing and suggesting improvements to the annotation file. At UNMC, we thank Brenda Morsey and Katy Emanuel for technical assistance with RNA isolation and Alok Dhar at the DNA Sequencing Core facility for library preparation and Illumina sequencing.",

year = "2014",

doi = "10.1186/1745-6150-9-20",

language = "English (US)",

volume = "9",

pages = "20",

journal = "Biology direct",

issn = "1745-6150",

publisher = "BioMed Central",

number = "1",

}

TY - JOUR

T1 - A new rhesus macaque assembly and annotation for next-generation sequencing analyses

AU - Zimin, Aleksey V.

AU - Cornish, Adam S.

AU - Maudhoo, Mnirnal D.

AU - Gibbs, Robert M.

AU - Zhang, Xiongfei

AU - Pandey, Sanjit

AU - Meehan, Daniel T.

AU - Wipfler, Kristin

AU - Bosinger, Steven E.

AU - Johnson, Zachary P.

AU - Tharp, Gregory K.

AU - Marçais, Guillaume

AU - Roberts, Michael

AU - Ferguson, Betsy

AU - Fox, Howard S.

AU - Treangen, Todd

AU - Salzberg, Steven L.

AU - Yorke, James A.

AU - Norgren, Robert B.

N1 - Funding Information: This work was supported by National Institute of Health grant R24RR017444 (RN), P51OD011092 (BF) and P51 OD011132 (ZJ). We appreciate the helpful comments of Drs. Dave O’Connor and Roger Wiseman on the rhesus MHC. We thank Jerilyn Pecotte of the Southwest National Primate Research Center for genomic DNA from the reference rhesus macaque. We appreciate the help of John Letaw, at the Oregon National Primate Research Center, and Tade Souaiaia, at the University of Southern California, for reviewing and suggesting improvements to the annotation file. At UNMC, we thank Brenda Morsey and Katy Emanuel for technical assistance with RNA isolation and Alok Dhar at the DNA Sequencing Core facility for library preparation and Illumina sequencing.

PY - 2014

Y1 - 2014

N2 - BACKGROUND: The rhesus macaque (Macaca mulatta) is a key species for advancing biomedical research. Like all draft mammalian genomes, the draft rhesus assembly (rheMac2) has gaps, sequencing errors and misassemblies that have prevented automated annotation pipelines from functioning correctly. Another rhesus macaque assembly, CR_1.0, is also available but is substantially more fragmented than rheMac2 with smaller contigs and scaffolds. Annotations for these two assemblies are limited in completeness and accuracy. High quality assembly and annotation files are required for a wide range of studies including expression, genetic and evolutionary analyses.RESULTS: We report a new de novo assembly of the rhesus macaque genome (MacaM) that incorporates both the original Sanger sequences used to assemble rheMac2 and new Illumina sequences from the same animal. MacaM has a weighted average (N50) contig size of 64 kilobases, more than twice the size of the rheMac2 assembly and almost five times the size of the CR_1.0 assembly. The MacaM chromosome assembly incorporates information from previously unutilized mapping data and preliminary annotation of scaffolds. Independent assessment of the assemblies using Ion Torrent read alignments indicates that MacaM is more complete and accurate than rheMac2 and CR_1.0. We assembled messenger RNA sequences from several rhesus tissues into transcripts which allowed us to identify a total of 11,712 complete proteins representing 9,524 distinct genes. Using a combination of our assembled rhesus macaque transcripts and human transcripts, we annotated 18,757 transcripts and 16,050 genes with complete coding sequences in the MacaM assembly. Further, we demonstrate that the new annotations provide greatly improved accuracy as compared to the current annotations of rheMac2. Finally, we show that the MacaM genome provides an accurate resource for alignment of reads produced by RNA sequence expression studies.CONCLUSIONS: The MacaM assembly and annotation files provide a substantially more complete and accurate representation of the rhesus macaque genome than rheMac2 or CR_1.0 and will serve as an important resource for investigators conducting next-generation sequencing studies with nonhuman primates.REVIEWERS: This article was reviewed by Dr. Lutz Walter, Dr. Soojin Yi and Dr. Kateryna Makova.

AB - BACKGROUND: The rhesus macaque (Macaca mulatta) is a key species for advancing biomedical research. Like all draft mammalian genomes, the draft rhesus assembly (rheMac2) has gaps, sequencing errors and misassemblies that have prevented automated annotation pipelines from functioning correctly. Another rhesus macaque assembly, CR_1.0, is also available but is substantially more fragmented than rheMac2 with smaller contigs and scaffolds. Annotations for these two assemblies are limited in completeness and accuracy. High quality assembly and annotation files are required for a wide range of studies including expression, genetic and evolutionary analyses.RESULTS: We report a new de novo assembly of the rhesus macaque genome (MacaM) that incorporates both the original Sanger sequences used to assemble rheMac2 and new Illumina sequences from the same animal. MacaM has a weighted average (N50) contig size of 64 kilobases, more than twice the size of the rheMac2 assembly and almost five times the size of the CR_1.0 assembly. The MacaM chromosome assembly incorporates information from previously unutilized mapping data and preliminary annotation of scaffolds. Independent assessment of the assemblies using Ion Torrent read alignments indicates that MacaM is more complete and accurate than rheMac2 and CR_1.0. We assembled messenger RNA sequences from several rhesus tissues into transcripts which allowed us to identify a total of 11,712 complete proteins representing 9,524 distinct genes. Using a combination of our assembled rhesus macaque transcripts and human transcripts, we annotated 18,757 transcripts and 16,050 genes with complete coding sequences in the MacaM assembly. Further, we demonstrate that the new annotations provide greatly improved accuracy as compared to the current annotations of rheMac2. Finally, we show that the MacaM genome provides an accurate resource for alignment of reads produced by RNA sequence expression studies.CONCLUSIONS: The MacaM assembly and annotation files provide a substantially more complete and accurate representation of the rhesus macaque genome than rheMac2 or CR_1.0 and will serve as an important resource for investigators conducting next-generation sequencing studies with nonhuman primates.REVIEWERS: This article was reviewed by Dr. Lutz Walter, Dr. Soojin Yi and Dr. Kateryna Makova.

UR - http://www.scopus.com/inward/record.url?scp=85003348909&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85003348909&partnerID=8YFLogxK

U2 - 10.1186/1745-6150-9-20

DO - 10.1186/1745-6150-9-20

M3 - Article

C2 - 25319552

AN - SCOPUS:85003348909

SN - 1745-6150

VL - 9

SP - 20

JO - Biology direct

JF - Biology direct

IS - 1

ER -

A new rhesus macaque assembly and annotation for next-generation sequencing analyses

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this