@article{149c248fa95449519dd8ccd4531fdb34,
title = "GENESPACE tracks regions of interest and gene copy number variation across multiple genomes",
abstract = "The development of multiple chromosome-scale reference genome sequences in many taxonomic groups has yielded a high-resolution view of the patterns and processes of molecular evolution. Nonetheless, leveraging information across multiple genomes remains a significant challenge in nearly all eukaryotic systems. These challenges range from studying the evolution of chromosome structure, to finding candidate genes for quantitative trait loci, to testing hypotheses about speciation and adaptation. Here, we present GENESPACE, which addresses these challenges by integrating conserved gene order and orthology to define the expected physical position of all genes across multiple genomes. We demonstrate this utility by dissecting presence–absence, copy-number, and structural variation at three levels of biological organization: spanning 300 million years of vertebrate sex chromosome evolution, across the diversity of the Poaceae (grass) plant family, and among 26 maize cultivars. The methods to build and visualize syntenic orthology in the GENESPACE R package offer a significant addition to existing gene family and synteny programs, especially in polyploid, outbred, and other complex genomes.",
author = "Lovell, {John T.} and Avinash Sreedasyam and Schranz, {M. Eric} and Melissa Wilson and Carlson, {Joseph W.} and Alex Harkess and David Emms and Goodstein, {David M.} and Jeremy Schmutz",
note = "Funding Information: The GENESPACE pipeline has been improved by advice and testing by A Healey, N Walden, V Scar-lett, R Walstead, S Carey, L Smith, J Vogel, J Willis, J Jenkins, T Juenger, and many others. Thanks to J Schnable, J Leebens-Mack, JG Monroe, CH Li, R Tarvin, and M Hufford for help refining the datasets and analyses presented in this manuscript. Thank you to Erich D Jarvis and the Vertebrate Genome Project members for advice and prepublication access to several genomes (budgerigar and dolphin). The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH1123. Visualization was inspired in part by MCScanX and pairwise {\textquoteleft}river{\textquoteright} plots generated by other software. The use of syntenic orthogroups was originally inspired by work developed by CoGe; similar syntenic homology approaches have been implemented by other software, including pSONIC. MAW{\textquoteright}s work on this was supported by the National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) grant R35GM124827. JTL would like to thank Ashley Lovell, our friends and family for their support, which allowed him to work on this project during the difficult past 2 years. Publisher Copyright: {\textcopyright} Lovell et al.",
year = "2022",
doi = "10.7554/ELIFE.78526",
language = "English (US)",
volume = "11",
journal = "eLife",
issn = "2050-084X",
publisher = "eLife Sciences Publications",
}