Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes

Abstract

IntroductionSorghum (Sorghum bicolor (L.) Moench) is an agriculturally and economically important staple crop that has immense potential as a bioenergy feedstock due to its relatively high productivity on marginal lands. To capitalize on and further improve sorghum as a potential source of sustainable biofuel, it is essential to understand the genomic mechanisms underlying complex traits related to yield, composition, and environmental adaptations.MethodsExpanding on a recently developed mapping population, we generated de novo genome assemblies for 10 parental genotypes from this population and identified a comprehensive set of over 24 thousand large structural variants (SVs) and over 10.5 million single nucleotide polymorphisms (SNPs).ResultsWe show that SVs and nonsynonymous SNPs are enriched in different gene categories, emphasizing the need for long read sequencing in crop species to identify novel variation. Furthermore, we highlight SVs and SNPs occurring in genes and pathways with known associations to critical bioenergy-related phenotypes and characterize the landscape of genetic differences between sweet and cellulosic genotypes.DiscussionThese resources can be integrated into both ongoing and future mapping and trait discovery for sorghum and its myriad uses including food, feed, bioenergy, and increasingly as a carbon dioxide removal mechanism.

Unlocking the Genetic Landscape: Enhanced Insights into Sweet Sorghum Genomes through Comprehensive superTranscriptomic Analysis

“…The total number of lncRNAs identified in maize (Wang et al, 2015;Lv et al, 2019), sorghum (Sun et al, 2020), rice (Zhou et al, 2021), and barley (Unver and Tombuloglu, 2020) ranged from 8000 to 23309 and showed that lncRNAs occupy the majority of total RNA. Recent studies on ten high-quality genome assemblies of diverse bioenergy sorghum genotypes reported similar results for lncRNAs (Voelker et al, 2023).…”

“…The total number of lncRNAs identified in maize (Wang et al, 2015;Lv et al, 2019), sorghum (Sun et al, 2020), rice (Zhou et al, 2021), and barley (Unver and Tombuloglu, 2020) ranged from 8000 to 23309, suggesting that lncRNAs can occupy the majority of total RNA. Recent studies on ten high-quality genome assemblies of diverse bioenergy sorghum genotypes reported similar results for lncRNAs (Voelker et al, 2023). The dispensable genes are major players contributing to variability, codes for various Transposable Elements (TEs), proteolytic enzymes, and regulators of biological processes;…”

“…The past studies on sorghum reported Transposable Elements (TEs) may play a role in gene content variation (Voelker et al, 2023) but they didn't reported other factors or processes, such as proteolysis and gene regulation, that could be more significant contributors to the observed variability in sorghum. We reported 301 genes that are exclusively located on sweet sorghum genomes which include hexokinases, core histones, cytochromes etc.…”

“…However, previous studies reported dispensable genes (63.6%) in sorghum when compared with rice, soybean, and Brachypodium sp ., suggesting that sorghum is more genetically diverse than other crops (Xin et al ., 2021) and Transposable Elements (TEs) could be major players in creating variability. The past studies on sorghum reported Transposable Elements (TEs) may play a role in gene content variation (Voelker et al ., 2023) but they didn’t reported other factors or processes, such as proteolysis and gene regulation, that could be more significant contributors to the observed variability in sorghum. We reported 301 genes that are exclusively located on sweet sorghum genomes which include hexokinases, core histones, cytochromes etc.…”

“…The Sweet Sorghum Reference Genome version 2.1 (SSRG), along with 14 published sorghum genomes, including one wild progenitor were retrieved from Phytozome [https://phytozome-next.jgi.doe.gov] and SorghumBase [https://www.sorghumbase.org] from past studies (Cooper et al ., 2019; Tao et al ., 2021; Voelker et al ., 2023). The pan-genome representing 390 diverse bioenergy sorghum accessions was downloaded from the ICRISAT repository [http://dataverse.icrisat.org] (Ruperao et al ., 2021).…”