Comparative transcriptome in large-scale human and cattle populations

Yuelin Yao; Shuli Liu; Charley Xia; Yahui Gao; Zhangyuan Pan; Oriol Canela-Xandri; Ava Khamseh; Konrad Rawlik; Sheng Wang; Bingjie Li; Yi Zhang; Erola Pairo-Castineira; Kenton D’Mellow; Xiujin Li; Ze Yan; Cong jun Li; Ying Yu; Shengli Zhang; Li Ma; John B. Cole; Pablo J. Ross; Huaijun Zhou; Chris Haley; George E. Liu; Lingzhao Fang; Albert Tenesa

doi:10.1186/s13059-022-02745-4

Comparative transcriptome in large-scale human and cattle populations

Yuelin Yao, Shuli Liu, Charley Xia, Yahui Gao, Zhangyuan Pan, Oriol Canela-Xandri, Ava Khamseh, Konrad Rawlik, Sheng Wang, Bingjie Li, Yi Zhang, Erola Pairo-Castineira, Kenton D’Mellow, Xiujin Li, Ze Yan, Cong jun Li, Ying Yu, Shengli Zhang, Li Ma, John B. ColePablo J. Ross, Huaijun Zhou, Chris Haley, George E. Liu, Lingzhao Fang^*, Albert Tenesa

^*Corresponding author af dette arbejde

Center for Kvantitativ Genetik og Genomforskning, Aarhus

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

18 Citationer (Scopus)

Abstract

Background: Cross-species comparison of transcriptomes is important for elucidating evolutionary molecular mechanisms underpinning phenotypic variation between and within species, yet to date it has been essentially limited to model organisms with relatively small sample sizes. Results: Here, we systematically analyze and compare 10,830 and 4866 publicly available RNA-seq samples in humans and cattle, respectively, representing 20 common tissues. Focusing on 17,315 orthologous genes, we demonstrate that mean/median gene expression, inter-individual variation of expression, expression quantitative trait loci, and gene co-expression networks are generally conserved between humans and cattle. By examining large-scale genome-wide association studies for 46 human traits (average n = 327,973) and 45 cattle traits (average n = 24,635), we reveal that the heritability of complex traits in both species is significantly more enriched in transcriptionally conserved than diverged genes across tissues. Conclusions: In summary, our study provides a comprehensive comparison of transcriptomes between humans and cattle, which might help decipher the genetic and evolutionary basis of complex traits in both species.

Originalsprog	Engelsk
Artikelnummer	176
Tidsskrift	Genome Biology
Vol/bind	23
Nummer	1
ISSN	1474-7596
DOI	https://doi.org/10.1186/s13059-022-02745-4
Status	Udgivet - dec. 2022

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10.1186/s13059-022-02745-4

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Yao, Y., Liu, S., Xia, C., Gao, Y., Pan, Z., Canela-Xandri, O., Khamseh, A., Rawlik, K., Wang, S., Li, B., Zhang, Y., Pairo-Castineira, E., D’Mellow, K., Li, X., Yan, Z., Li, C. J., Yu, Y., Zhang, S., Ma, L., ... Tenesa, A. (2022). Comparative transcriptome in large-scale human and cattle populations. Genome Biology, 23(1), Artikel 176. https://doi.org/10.1186/s13059-022-02745-4

@article{d000f55fe992470d83bc2e081f808587,

title = "Comparative transcriptome in large-scale human and cattle populations",

abstract = "Background: Cross-species comparison of transcriptomes is important for elucidating evolutionary molecular mechanisms underpinning phenotypic variation between and within species, yet to date it has been essentially limited to model organisms with relatively small sample sizes. Results: Here, we systematically analyze and compare 10,830 and 4866 publicly available RNA-seq samples in humans and cattle, respectively, representing 20 common tissues. Focusing on 17,315 orthologous genes, we demonstrate that mean/median gene expression, inter-individual variation of expression, expression quantitative trait loci, and gene co-expression networks are generally conserved between humans and cattle. By examining large-scale genome-wide association studies for 46 human traits (average n = 327,973) and 45 cattle traits (average n = 24,635), we reveal that the heritability of complex traits in both species is significantly more enriched in transcriptionally conserved than diverged genes across tissues. Conclusions: In summary, our study provides a comprehensive comparison of transcriptomes between humans and cattle, which might help decipher the genetic and evolutionary basis of complex traits in both species.",

keywords = "Comparative transcriptome, Gene co-expression, Heritability enrichment, Inter-individual variability, RNA-seq",

author = "Yuelin Yao and Shuli Liu and Charley Xia and Yahui Gao and Zhangyuan Pan and Oriol Canela-Xandri and Ava Khamseh and Konrad Rawlik and Sheng Wang and Bingjie Li and Yi Zhang and Erola Pairo-Castineira and Kenton D{\textquoteright}Mellow and Xiujin Li and Ze Yan and Li, {Cong jun} and Ying Yu and Shengli Zhang and Li Ma and Cole, {John B.} and Ross, {Pablo J.} and Huaijun Zhou and Chris Haley and Liu, {George E.} and Lingzhao Fang and Albert Tenesa",

note = "Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = dec,

doi = "10.1186/s13059-022-02745-4",

language = "English",

volume = "23",

journal = "Genome Biology",

issn = "1474-7596",

publisher = "BioMed Central",

number = "1",

}

Yao, Y, Liu, S, Xia, C, Gao, Y, Pan, Z, Canela-Xandri, O, Khamseh, A, Rawlik, K, Wang, S, Li, B, Zhang, Y, Pairo-Castineira, E, D’Mellow, K, Li, X, Yan, Z, Li, CJ, Yu, Y, Zhang, S, Ma, L, Cole, JB, Ross, PJ, Zhou, H, Haley, C, Liu, GE, Fang, L & Tenesa, A 2022, 'Comparative transcriptome in large-scale human and cattle populations', Genome Biology, bind 23, nr. 1, 176. https://doi.org/10.1186/s13059-022-02745-4

TY - JOUR

T1 - Comparative transcriptome in large-scale human and cattle populations

AU - Yao, Yuelin

AU - Liu, Shuli

AU - Xia, Charley

AU - Gao, Yahui

AU - Pan, Zhangyuan

AU - Canela-Xandri, Oriol

AU - Khamseh, Ava

AU - Rawlik, Konrad

AU - Wang, Sheng

AU - Li, Bingjie

AU - Zhang, Yi

AU - Pairo-Castineira, Erola

AU - D’Mellow, Kenton

AU - Li, Xiujin

AU - Yan, Ze

AU - Li, Cong jun

AU - Yu, Ying

AU - Zhang, Shengli

AU - Ma, Li

AU - Cole, John B.

AU - Ross, Pablo J.

AU - Zhou, Huaijun

AU - Haley, Chris

AU - Liu, George E.

AU - Fang, Lingzhao

AU - Tenesa, Albert

PY - 2022/12

Y1 - 2022/12

N2 - Background: Cross-species comparison of transcriptomes is important for elucidating evolutionary molecular mechanisms underpinning phenotypic variation between and within species, yet to date it has been essentially limited to model organisms with relatively small sample sizes. Results: Here, we systematically analyze and compare 10,830 and 4866 publicly available RNA-seq samples in humans and cattle, respectively, representing 20 common tissues. Focusing on 17,315 orthologous genes, we demonstrate that mean/median gene expression, inter-individual variation of expression, expression quantitative trait loci, and gene co-expression networks are generally conserved between humans and cattle. By examining large-scale genome-wide association studies for 46 human traits (average n = 327,973) and 45 cattle traits (average n = 24,635), we reveal that the heritability of complex traits in both species is significantly more enriched in transcriptionally conserved than diverged genes across tissues. Conclusions: In summary, our study provides a comprehensive comparison of transcriptomes between humans and cattle, which might help decipher the genetic and evolutionary basis of complex traits in both species.

AB - Background: Cross-species comparison of transcriptomes is important for elucidating evolutionary molecular mechanisms underpinning phenotypic variation between and within species, yet to date it has been essentially limited to model organisms with relatively small sample sizes. Results: Here, we systematically analyze and compare 10,830 and 4866 publicly available RNA-seq samples in humans and cattle, respectively, representing 20 common tissues. Focusing on 17,315 orthologous genes, we demonstrate that mean/median gene expression, inter-individual variation of expression, expression quantitative trait loci, and gene co-expression networks are generally conserved between humans and cattle. By examining large-scale genome-wide association studies for 46 human traits (average n = 327,973) and 45 cattle traits (average n = 24,635), we reveal that the heritability of complex traits in both species is significantly more enriched in transcriptionally conserved than diverged genes across tissues. Conclusions: In summary, our study provides a comprehensive comparison of transcriptomes between humans and cattle, which might help decipher the genetic and evolutionary basis of complex traits in both species.

KW - Comparative transcriptome

KW - Gene co-expression

KW - Heritability enrichment

KW - Inter-individual variability

KW - RNA-seq

U2 - 10.1186/s13059-022-02745-4

DO - 10.1186/s13059-022-02745-4

M3 - Journal article

C2 - 35996157

AN - SCOPUS:85136200740

SN - 1474-7596

VL - 23

JO - Genome Biology

JF - Genome Biology

IS - 1

M1 - 176

ER -

Comparative transcriptome in large-scale human and cattle populations

Abstract

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