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Reconstructed 3D ultrasound volume provides more context information compared to a sequence of 2D scanning frames, which is desirable for various clinical applications such as ultrasound-guided prostate biopsy. Nevertheless, 3D volume reconstruction from freehand 2D scans is a very challenging problem, especially without the use of external tracking devices. Recent deep learning based methods demonstrate the potential of directly estimating inter-frame motion between consecutive ultrasound frames. However, such algorithms are specific to particular transducers and scanning trajectories associated with the training data, which may not be generalized to other image acquisition settings. In this paper, we tackle the data acquisition difference as a domain shift problem and propose a novel domain adaptation strategy to adapt deep learning algorithms to data acquired with different transducers. Specifically, feature extractors that generate transducer-invariant features from different datasets are trained by minimizing the discrepancy between deep features of paired samples in a latent space. Our results show that the proposed domain adaptation method can successfully align different feature distributions while preserving the transducer-specific information for universal freehand ultrasound volume reconstruction.