Genoarchitecture and input–output organization of the mouse basal ganglia and thalamic parafascicular nucleus
The basal ganglia comprise interconnected subcortical nuclei essential for motor control, learning, emotion and cognition, yet how cell types relate to their circuit organization remains elusive. Here we show that spatial patterns of transcriptomic cell types in the basal ganglia and thalamic parafascicular nucleus relate to module-organized cortical inputs in the mouse. By co-registering genoarchitectural and connectivity datasets to the common coordinate framework, we delineate distinct three-dimensional subdivisions of these nuclei. Analyses of anterograde and retrograde viral tracing data and single-neuron reconstructions reveal that each subdivision receives convergent, modular and cell-type-specific cortical and subcortical inputs. Caudoputamen subdivisions primarily receive layer 5 intratelencephalic inputs from the entire isocortex, whereas smaller basal ganglia subdivisions receive ipsilateral layer 5 extratelencephalic inputs from limited cortical areas. The parafascicular nucleus subdivisions are connected with specific cortical modules and basal ganglia subdivisions. Our results suggest that combinatorial gene expression underlies a global map of parallel, modular and cell-type-specific basal ganglia and parafascicular nucleus subnetworks.
Authors
- Lauren Kruse (ORCID: https://orcid.org/0000-0002-3428-2443)
- Michael Kunst (ORCID: https://orcid.org/0000-0003-4159-8056)
- Leila Ahmadinia (ORCID: https://orcid.org/0009-0000-3892-0919)
- Quanxin Wang (ORCID: https://orcid.org/0000-0002-0007-7935)
- Nathan W. Gouwens (ORCID: https://orcid.org/0000-0001-8429-4090)
- Phil Lesnar (ORCID: https://orcid.org/0000-0002-2152-604X)
- Laila El-Hifnawi
- Cindy T. J. van Velthoven (ORCID: https://orcid.org/0000-0001-5120-4546)
- Staci A. Sorensen (ORCID: https://orcid.org/0000-0002-6799-2126)
- Xiuli Kuang (ORCID: https://orcid.org/0000-0001-7569-7605)
- Qingming Luo
- Hsien-Chi Kuo
- Xiangning Li (ORCID: https://orcid.org/0000-0002-3747-2824)
- Shenqin Yao (ORCID: https://orcid.org/0000-0003-2992-4752)
- Rachel Dalley (ORCID: https://orcid.org/0000-0001-7461-7845)
- Ying Wang (ORCID: https://orcid.org/0000-0002-9636-6300)
- Wenjie Xu (ORCID: https://orcid.org/0000-0002-5584-015X)
- Lydia Ng
- Yaoyao Li
- Zizhen Yao (ORCID: https://orcid.org/0000-0002-9361-5607)
- Hui Gong (ORCID: https://orcid.org/0000-0001-5519-6248)
- Ben Ouellette (ORCID: https://orcid.org/0000-0003-4913-554X)
- Anan Li
- Hongkui Zeng (ORCID: https://orcid.org/0000-0002-0326-5878)
- Matt Mallory
- Ashwin Bhandiwad (ORCID: https://orcid.org/0000-0002-6963-1594)
Institutions
- Allen Institute for Brain Science (US)
- Hainan University (CN)
- Wenzhou Medical University (CN)
- Suzhou Vocational Institute of Industrial Technology (CN)
- Suzhou Research Institute (CN)
- Allen Institute (US)
- State Key Laboratory of Digital Medical Engineering (CN)
- Hainan Medical University (CN)
Publication Details
- Journal
- Nature Neuroscience
- Published
- 2026-04-28
- DOI
- https://doi.org/10.1038/s41593-026-02253-9
- Primary Topic
- Neural dynamics and brain function
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Institute of Mental Health
- National Institute of Neurological Disorders and Stroke