The Internet of Things (IoT) and Distributed ledger technology (DLT) have significantly changed our daily lives. Due to their distributed operational environment and naturally decentralized applications, the convergence of these two technologies indicates a more lavish arrangement for the future. This article develops a comprehensive survey to investigate and illustrate state-of-the-art DLT for various IoT use cases, from smart homes to autonomous vehicles and smart cities. We develop a novel framework for conducting a systematic and comprehensive review of DLT over IoT by extending the knowledge graph approach. With relevant insights from this review, we extract innovative and pragmatic techniques to DLT design that enable high-performance, sustainable, and highly scalable IoT systems. Our findings support designing an end-to-end IoT-native DLT architecture for the future that fully coordinates network-assisted functionalities.