Evolution and Adaptation of Baboon and Mandrill Revealed by Genome Sequencing

Ye Yin

Evolution and Adaptation of Baboon and Mandrill Revealed by Genome Sequencing

Ye Yin

Abstract

Evolution and Adaptation of Baboon and Mandrill Revealed by Genome Sequencing AcademicBaboon (genus Papio) and mandrill (Mandrillus sphinx) are closely related with human beings in phylogenetic relationships, which can serve as unique models for primate evolutionary studies as well as human diseases researches. However, genetic researches and genomic resources of baboon and mandrill are limited, especially comparing to chimpanzee and gorilla. Thus genome sequencing of baboon and mandrill was carried out here for constructing reference genomes of these remarkable Old World monkeys. With the process of sampling, DNA extraction and sequencing, 414 Gb and 426 Gb raw sequencing data of different libraries were generated for baboon and mandrill respectively using the second generation sequencing platform. Then, genome assembly was carried out based on the sequencing data of both species. The genome assembly of baboon was 3.11 Gb with contig N50 to be 21,659, and scaffold N50 to be 1,070,645, and the genome assembly of mandrill was 2.88 Gb with contig N50 to be 20,483, and scaffold N50 to be 3,564,730. With the assembled genomes, repeat contents were first annotated to be 42.3% and 40.4% respectively for baboon and mandrill. After masking the repeat content in the genomes, evidence based and ab-initial gene annotation were combined together to predict 23,867 genes in baboon and 21,906 genes in mandrill. Searching 3,023 BUSCO (Benchmarking Universal Single-Copy Orthologs) genes against the predicted genes, the completeness of the genes were estimated to be 97% (baboon) and 98% (mandrill). This comprehensive assembly and complete gene sets provides new biological insight into genetic diversity, structural variation, behavioral characteristic. Comparative genomic analysis among primates was conducted to reveal the synteny between primates and also the gene family evolution of contraction and expansion especially in baboon and mandrill. There were 9,930, 11,418,14,318 gene pairs between baboon and mandrill, macaque and baboon, human and macaque. In baboon and mandrill lineage, there were 545 expanded and 618 contracted gene families, expanded genes were significantly enriched in biosynthetic process, structural constituent of ribosome, nucleosomal DNA binding, G-protein coupled receptor activity, olfactory receptor activity, glucose catabolic process, peptidyl-prolyl isomerization, as well as carbon fixation in photosynthetic organisms and electron transport chain pathway. Molecular mechanisms of adaptation for baboon and mandrill including immune, language competence and olfactory character were also investigated through comparative genomics. Through this study, genomic resources were provided for primate species, and comprehensive insights of adaptation and evolution were also provided for better understanding of baboon and mandrill.

Originalsprog	Engelsk

Forlag	Department of Biology, Faculty of Science, University of Copenhagen
Status	Udgivet - 2019

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@phdthesis{def5211801974befb3c0c717b9f6eb75,

title = "Evolution and Adaptation of Baboon and Mandrill Revealed by Genome Sequencing",

abstract = "Evolution and Adaptation of Baboon and Mandrill Revealed by Genome Sequencing AcademicBaboon (genus Papio) and mandrill (Mandrillus sphinx) are closely related with human beings in phylogenetic relationships, which can serve as unique models for primate evolutionary studies as well as human diseases researches. However, genetic researches and genomic resources of baboon and mandrill are limited, especially comparing to chimpanzee and gorilla. Thus genome sequencing of baboon and mandrill was carried out here for constructing reference genomes of these remarkable Old World monkeys. With the process of sampling, DNA extraction and sequencing, 414 Gb and 426 Gb raw sequencing data of different libraries were generated for baboon and mandrill respectively using the second generation sequencing platform. Then, genome assembly was carried out based on the sequencing data of both species. The genome assembly of baboon was 3.11 Gb with contig N50 to be 21,659, and scaffold N50 to be 1,070,645, and the genome assembly of mandrill was 2.88 Gb with contig N50 to be 20,483, and scaffold N50 to be 3,564,730. With the assembled genomes, repeat contents were first annotated to be 42.3% and 40.4% respectively for baboon and mandrill. After masking the repeat content in the genomes, evidence based and ab-initial gene annotation were combined together to predict 23,867 genes in baboon and 21,906 genes in mandrill. Searching 3,023 BUSCO (Benchmarking Universal Single-Copy Orthologs) genes against the predicted genes, the completeness of the genes were estimated to be 97% (baboon) and 98% (mandrill). This comprehensive assembly and complete gene sets provides new biological insight into genetic diversity, structural variation, behavioral characteristic. Comparative genomic analysis among primates was conducted to reveal the synteny between primates and also the gene family evolution of contraction and expansion especially in baboon and mandrill. There were 9,930, 11,418,14,318 gene pairs between baboon and mandrill, macaque and baboon, human and macaque. In baboon and mandrill lineage, there were 545 expanded and 618 contracted gene families, expanded genes were significantly enriched in biosynthetic process, structural constituent of ribosome, nucleosomal DNA binding, G-protein coupled receptor activity, olfactory receptor activity, glucose catabolic process, peptidyl-prolyl isomerization, as well as carbon fixation in photosynthetic organisms and electron transport chain pathway. Molecular mechanisms of adaptation for baboon and mandrill including immune, language competence and olfactory character were also investigated through comparative genomics. Through this study, genomic resources were provided for primate species, and comprehensive insights of adaptation and evolution were also provided for better understanding of baboon and mandrill.",

author = "Ye Yin",

year = "2019",

language = "English",

publisher = "Department of Biology, Faculty of Science, University of Copenhagen",

}

TY - BOOK

T1 - Evolution and Adaptation of Baboon and Mandrill Revealed by Genome Sequencing

AU - Yin, Ye

PY - 2019

Y1 - 2019

N2 - Evolution and Adaptation of Baboon and Mandrill Revealed by Genome Sequencing AcademicBaboon (genus Papio) and mandrill (Mandrillus sphinx) are closely related with human beings in phylogenetic relationships, which can serve as unique models for primate evolutionary studies as well as human diseases researches. However, genetic researches and genomic resources of baboon and mandrill are limited, especially comparing to chimpanzee and gorilla. Thus genome sequencing of baboon and mandrill was carried out here for constructing reference genomes of these remarkable Old World monkeys. With the process of sampling, DNA extraction and sequencing, 414 Gb and 426 Gb raw sequencing data of different libraries were generated for baboon and mandrill respectively using the second generation sequencing platform. Then, genome assembly was carried out based on the sequencing data of both species. The genome assembly of baboon was 3.11 Gb with contig N50 to be 21,659, and scaffold N50 to be 1,070,645, and the genome assembly of mandrill was 2.88 Gb with contig N50 to be 20,483, and scaffold N50 to be 3,564,730. With the assembled genomes, repeat contents were first annotated to be 42.3% and 40.4% respectively for baboon and mandrill. After masking the repeat content in the genomes, evidence based and ab-initial gene annotation were combined together to predict 23,867 genes in baboon and 21,906 genes in mandrill. Searching 3,023 BUSCO (Benchmarking Universal Single-Copy Orthologs) genes against the predicted genes, the completeness of the genes were estimated to be 97% (baboon) and 98% (mandrill). This comprehensive assembly and complete gene sets provides new biological insight into genetic diversity, structural variation, behavioral characteristic. Comparative genomic analysis among primates was conducted to reveal the synteny between primates and also the gene family evolution of contraction and expansion especially in baboon and mandrill. There were 9,930, 11,418,14,318 gene pairs between baboon and mandrill, macaque and baboon, human and macaque. In baboon and mandrill lineage, there were 545 expanded and 618 contracted gene families, expanded genes were significantly enriched in biosynthetic process, structural constituent of ribosome, nucleosomal DNA binding, G-protein coupled receptor activity, olfactory receptor activity, glucose catabolic process, peptidyl-prolyl isomerization, as well as carbon fixation in photosynthetic organisms and electron transport chain pathway. Molecular mechanisms of adaptation for baboon and mandrill including immune, language competence and olfactory character were also investigated through comparative genomics. Through this study, genomic resources were provided for primate species, and comprehensive insights of adaptation and evolution were also provided for better understanding of baboon and mandrill.

AB - Evolution and Adaptation of Baboon and Mandrill Revealed by Genome Sequencing AcademicBaboon (genus Papio) and mandrill (Mandrillus sphinx) are closely related with human beings in phylogenetic relationships, which can serve as unique models for primate evolutionary studies as well as human diseases researches. However, genetic researches and genomic resources of baboon and mandrill are limited, especially comparing to chimpanzee and gorilla. Thus genome sequencing of baboon and mandrill was carried out here for constructing reference genomes of these remarkable Old World monkeys. With the process of sampling, DNA extraction and sequencing, 414 Gb and 426 Gb raw sequencing data of different libraries were generated for baboon and mandrill respectively using the second generation sequencing platform. Then, genome assembly was carried out based on the sequencing data of both species. The genome assembly of baboon was 3.11 Gb with contig N50 to be 21,659, and scaffold N50 to be 1,070,645, and the genome assembly of mandrill was 2.88 Gb with contig N50 to be 20,483, and scaffold N50 to be 3,564,730. With the assembled genomes, repeat contents were first annotated to be 42.3% and 40.4% respectively for baboon and mandrill. After masking the repeat content in the genomes, evidence based and ab-initial gene annotation were combined together to predict 23,867 genes in baboon and 21,906 genes in mandrill. Searching 3,023 BUSCO (Benchmarking Universal Single-Copy Orthologs) genes against the predicted genes, the completeness of the genes were estimated to be 97% (baboon) and 98% (mandrill). This comprehensive assembly and complete gene sets provides new biological insight into genetic diversity, structural variation, behavioral characteristic. Comparative genomic analysis among primates was conducted to reveal the synteny between primates and also the gene family evolution of contraction and expansion especially in baboon and mandrill. There were 9,930, 11,418,14,318 gene pairs between baboon and mandrill, macaque and baboon, human and macaque. In baboon and mandrill lineage, there were 545 expanded and 618 contracted gene families, expanded genes were significantly enriched in biosynthetic process, structural constituent of ribosome, nucleosomal DNA binding, G-protein coupled receptor activity, olfactory receptor activity, glucose catabolic process, peptidyl-prolyl isomerization, as well as carbon fixation in photosynthetic organisms and electron transport chain pathway. Molecular mechanisms of adaptation for baboon and mandrill including immune, language competence and olfactory character were also investigated through comparative genomics. Through this study, genomic resources were provided for primate species, and comprehensive insights of adaptation and evolution were also provided for better understanding of baboon and mandrill.

UR - https://rex.kb.dk/primo-explore/fulldisplay?docid=KGL01012004263&context=L&vid=NUI&search_scope=KGL&tab=default_tab&lang=da_DK

M3 - Ph.D. thesis

BT - Evolution and Adaptation of Baboon and Mandrill Revealed by Genome Sequencing

PB - Department of Biology, Faculty of Science, University of Copenhagen

ER -