Figure 1.

Challenges in the study of satellite DNA (satDNA) sequences and the importance to fully understand the repetitive genomic fraction. SatDNAs can be found clustered at the centromeres, telomeres and forming interstitial heterochromatin (CH) blocks, as well as scattered (interspersed) throughout the chromosomes. The full characterization of satDNAs needs to be addressed in two levels: 1-Disclose satDNAs linear sequence and improve their representation in genome assemblies. Despite currently used sequencing strategies (e.g., next generation sequencing (NGS)) contributed for satDNA studies, the full characterization of these sequences will only be achieved by using sequencing technologies capable of long reads, bioinformatics pipelines suitable for highly repetitive sequences, together with other techniques (e.g., FISH, optical mapping). These strategies need to be directed to specific chromosome structures such as centromeres (centrOMICs) and telomeres (telOMICs), which harbor large amounts of satDNA. Important also is the integration of genomic data with sequence localization in the chromosomes, and their interaction with other components of the genome (chromosomics); 2- Clarify satDNAs function(s) in the genome by studying the satellite non-coding RNAs (satncRNA) and their interaction with other components and structures in the genome. In this field there is the need to develop adequate biology techniques to address repetitive sequences transcription study. The disclosure of satDNA sequences will help to better understand its genomic architecture ant its role in genome restructuring in evolution and disease.