Nature

A molecular cell atlas of mouse lemur, an emerging model primate

L Liza Shapiro A Andriamahery Razafindrakoto H Hajanirina Noëline Ravelonjanahary P Patricia Wright A Anne D. Yoder C Cathy V. Williams R Robert Schopler U Ute Radespiel J Jean-Michel Verdier C Corinne Lautier E E. Christopher Kirk R Rebecca Lewis A Astrid Gillich Z Zicheng Zhao E Elias Godoy J Jérémy Terrien J Jacques Epelbaum D Dita Gratzinger K Katherine Lucot T Thomas Montine J Jessica D’Addabbo I Isaac Bakerman P Patricia Nguyen A Aaron Kershner K Karim Mrouj P Philip Beachy T Thomas H. Ambrosi M Malachia Hoover A Alina Alam C Charles Chan S SoRi Jang A Avin Veerakumar P Peng Li A Andrea R. Yung C Connor V. Duffy S Song-Lin Ding E Ed S. Lein S Silvana Konermann L Liqun Luo T Trygve E. Bakken J Justus M. Kebschull R Rebecca D. Hodge T Taichi Isobe M Michael F. Clarke B Biter Bilen J Jean Farup A Andoni Urtasun J Jengmin Kang M Ming Chen B BaoXiang Li V Varun Ramanan Subramaniam S Shravani Mukherjee A Aditi Swarup L Lily Kim B Bronwyn Scott A Ahmad Al-Moujahed A Albert Y. Wu D Douglas Vollrath N Nicholas Schaum A Amanda L. Wiggenhorn T Tony Wyss-Coray J Jonathan Z. Long Y Yin Liu A Ahmad Nabhan G Gabriel Loeb S Shengda Lin H Honor Paine D Deviana Burhan A Aris Taychameekiatchai B Bruce Wang F F. Hernán Espinoza C Christin Kuo R Ross Metzger Z Zhen Qi R Rebecca Culver K Kerwyn C. Huang P Patrick Neuhöfer C Charles A. Chang Y Yan Hang S Seung K. Kim H Hannah N. W. Weinstein P Paul Allegakoen F Franklin W. Huang S Sivakamasundari S Song Eun Lee H Hannah K. Frank S Scott D. Boyd W Wan-Jin Lu A Ankit Baghel W William Kong C Carly Israel A Ashley Maynard M Michelle Tan Y Youcef Ouadah J Jalal Baruni T Timothy Ting-Hsuan Wu R Robert C. Jones S Spyros Darmanis S Sheela Crasta J Jia Yan A Aditi Agrawal S Shelly Huynh B Brian Yu J James Webber W Weilun Tan S Saba Nafees Z Zhengda Li M Michael F. Z. Wang R Roozbeh Dehghannasiri J Julia Olivieri J Julia Salzman L Lisbeth A. Guethlein P Peter Parham Q Qiuyu Jing J Jane Antony G Geoff Stanley J Jinxurong Yang W Winston Koh S Sheng Wang S Snigdha Agarwal K Kyle Awayan E Erin McGeever V Venkata N. P. Vemuri P Pranav V. Lalgudi C Camille Ezran S Shixuan Liu S Stephen Chang J Jingsi Ming O Olga Botvinnik L Lolita Penland A Alexander Tarashansky A Antoine de Morree K Kyle J. Travaglini J Jia Zhao G Gefei Wang K Kazuteru Hasegawa H Hosu Sin R Rene Sit J Jennifer Okamoto R Rahul Sinha Y Yue Zhang C Caitlin J. Karanewsky J Jozeph L. Pendleton M Maurizio Morri M Martine Perret F Fabienne Aujard L Lubert Stryer S Steven Artandi M Margaret T. Fuller I Irving L. Weissman T Thomas A. Rando J James E. Ferrell B Bo Wang I Iwijn De Vlaminck C Can Yang K Kerriann M. Casey M Megan A. Albertelli A Angela Oliveira Pisco J Jim Karkanias N Norma Neff A Angela Ruohao Wu S Stephen R. Quake M Mark A. Krasnow

Abstract

Abstract Mouse lemurs are the smallest and fastest reproducing primates, as well as one of the most abundant, and they are emerging as a model organism for primate biology, behaviour, health and conservation. Although much has been learnt about their ecology and phylogeny in Madagascar and their physiology, little is known about their cellular and molecular biology. Here we used droplet-based and plate-based single-cell RNA sequencing to create Tabula Microcebus, a transcriptomic atlas of 226,000 cells from 27 mouse lemur organs opportunistically obtained from four donors clinically and histologically characterized. Using computational cell clustering, integration and expert cell annotation, we define and biologically organize more than 750 lemur molecular cell types and their full gene expression profiles. This includes cognates of most classical human cell types, including stem and progenitor cells, and differentiating cells along the developmental trajectories of spermatogenesis, haematopoiesis and other adult tissues. We also describe dozens of previously unidentified or sparsely characterized cell types. We globally compare expression profiles to define the molecular relationships of cell types across the body, and explore primate cell and gene expression evolution by comparing lemur transcriptomes to those of human, mouse and macaque. This reveals cell-type-specific patterns of primate specialization and many cell types and genes for which the mouse lemur provides a better human model than mouse1. The atlas provides a cellular and molecular foundation for studying this model primate and establishes a general approach for characterizing other emerging model organisms.

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Article Details

Journal Nature
Volume / Issue Vol. 644, Issue 8075
Published August 07, 2025
Pages 173-184
ISSN 0028-0836
Publisher Nature Portfolio

Journal Info

Nature

Nature Portfolio
ISSN: 0028-0836 Health Sciences

Authors (163)

L

Liza Shapiro

A

Andriamahery Razafindrakoto

H

Hajanirina Noëline Ravelonjanahary

P

Patricia Wright

A

Anne D. Yoder

C

Cathy V. Williams

R

Robert Schopler

U

Ute Radespiel

J

Jean-Michel Verdier

C

Corinne Lautier

E

E. Christopher Kirk

R

Rebecca Lewis

A

Astrid Gillich

Z

Zicheng Zhao

E

Elias Godoy

J

Jérémy Terrien

J

Jacques Epelbaum

D

Dita Gratzinger

K

Katherine Lucot

T

Thomas Montine

J

Jessica D’Addabbo

I

Isaac Bakerman

P

Patricia Nguyen

A

Aaron Kershner

K

Karim Mrouj

P

Philip Beachy

T

Thomas H. Ambrosi

M

Malachia Hoover

A

Alina Alam

C

Charles Chan

S

SoRi Jang

A

Avin Veerakumar

P

Peng Li

A

Andrea R. Yung

C

Connor V. Duffy

S

Song-Lin Ding

E

Ed S. Lein

S

Silvana Konermann

L

Liqun Luo

T

Trygve E. Bakken

J

Justus M. Kebschull

R

Rebecca D. Hodge

T

Taichi Isobe

M

Michael F. Clarke

B

Biter Bilen

J

Jean Farup

A

Andoni Urtasun

J

Jengmin Kang

M

Ming Chen

B

BaoXiang Li

V

Varun Ramanan Subramaniam

S

Shravani Mukherjee

A

Aditi Swarup

L

Lily Kim

B

Bronwyn Scott

A

Ahmad Al-Moujahed

A

Albert Y. Wu

D

Douglas Vollrath

N

Nicholas Schaum

A

Amanda L. Wiggenhorn

T

Tony Wyss-Coray

J

Jonathan Z. Long

Y

Yin Liu

A

Ahmad Nabhan

G

Gabriel Loeb

S

Shengda Lin

H

Honor Paine

D

Deviana Burhan

A

Aris Taychameekiatchai

B

Bruce Wang

F

F. Hernán Espinoza

C

Christin Kuo

R

Ross Metzger

Z

Zhen Qi

R

Rebecca Culver

K

Kerwyn C. Huang

P

Patrick Neuhöfer

C

Charles A. Chang

Y

Yan Hang

S

Seung K. Kim

H

Hannah N. W. Weinstein

P

Paul Allegakoen

F

Franklin W. Huang

S

Sivakamasundari

S

Song Eun Lee

H

Hannah K. Frank

S

Scott D. Boyd

W

Wan-Jin Lu

A

Ankit Baghel

W

William Kong

C

Carly Israel

A

Ashley Maynard

M

Michelle Tan

Y

Youcef Ouadah

J

Jalal Baruni

T

Timothy Ting-Hsuan Wu

R

Robert C. Jones

S

Spyros Darmanis

S

Sheela Crasta

J

Jia Yan

A

Aditi Agrawal

S

Shelly Huynh

B

Brian Yu

J

James Webber

W

Weilun Tan

S

Saba Nafees

Z

Zhengda Li

M

Michael F. Z. Wang

R

Roozbeh Dehghannasiri

J

Julia Olivieri

J

Julia Salzman

L

Lisbeth A. Guethlein

P

Peter Parham

Q

Qiuyu Jing

J

Jane Antony

G

Geoff Stanley

J

Jinxurong Yang

W

Winston Koh

S

Sheng Wang

S

Snigdha Agarwal

K

Kyle Awayan

E

Erin McGeever

V

Venkata N. P. Vemuri

P

Pranav V. Lalgudi

C

Camille Ezran

S

Shixuan Liu

S

Stephen Chang

J

Jingsi Ming

O

Olga Botvinnik

L

Lolita Penland

A

Alexander Tarashansky

A

Antoine de Morree

K

Kyle J. Travaglini

J

Jia Zhao

G

Gefei Wang

K

Kazuteru Hasegawa

H

Hosu Sin

R

Rene Sit

J

Jennifer Okamoto

R

Rahul Sinha

Y

Yue Zhang

C

Caitlin J. Karanewsky

J

Jozeph L. Pendleton

M

Maurizio Morri

M

Martine Perret

F

Fabienne Aujard

L

Lubert Stryer

S

Steven Artandi

M

Margaret T. Fuller

I

Irving L. Weissman

T

Thomas A. Rando

J

James E. Ferrell

B

Bo Wang

I

Iwijn De Vlaminck

C

Can Yang

K

Kerriann M. Casey

M

Megan A. Albertelli

A

Angela Oliveira Pisco

J

Jim Karkanias

N

Norma Neff

A

Angela Ruohao Wu

S

Stephen R. Quake

M

Mark A. Krasnow

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