Unveiling the Genomic Symphony: Identification Cultivar-Specific Genes and Enhanced Insights on Sweet Sorghum Genomes Through Comprehensive superTranscriptomic Analysis

IF 2.1 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY
Shinde Nikhil, Habeeb Shaikh Mohideen, Raja Natesan Sella
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Abstract

Sorghum (Sorghum bicolor (L.) Moench) is a multipurpose crop grown for food, fodder, and bioenergy production. Its cultivated varieties, along with their wild counterparts, contribute to the core genetic pool. Despite the availability of several re-sequenced sorghum genomes, a variable portion of sorghum genomes is not reported during reference genome assembly and annotation. The present analysis used 223 publicly available RNA-seq datasets from seven sweet sorghum cultivars to construct superTranscriptome. This approach yielded 45,864 Representative Transcript Assemblies (RTAs) that showcased intriguing Presence/Absence Variation (PAV) across 15 published sorghum genomes. We found 301 superTranscripts were exclusive to sweet sorghum, including 58 de novo genes encoded core and linker histones, zinc finger domains, glucosyl transferases, cellulose synthase, etc. The superTranscriptome added 2,802 new protein-coding genes to the Sweet Sorghum Reference Genome (SSRG), of which 559 code for different transcription factors (TFs). Our analysis revealed that MULE-like transposases were abundant in the sweet sorghum genome and could play a hidden role in the evolution of sweet sorghum. We observed large deletions in the D locus and terminal deletions in four other NAC encoding loci in the SSRG compared to its wild progenitor (353) suggesting non-functional NAC genes contributed to trait development in sweet sorghum. Moreover, superTranscript-based methods for Differential Exon Usage (DEU) and Differential Gene Expression (DGE) analyses were more accurate than those based on the SSRG. This study demonstrates that the superTranscriptome can enhance our understanding of fundamental sorghum mechanisms, improve genome annotations, and potentially even replace the reference genome.

Abstract Image

揭开基因组交响乐的神秘面纱:通过全面的超转录组分析鉴定栽培品种特异基因并加深对甜高粱基因组的了解
高粱(Sorghum bicolor (L.) Moench)是一种多用途作物,用于生产粮食、饲料和生物能源。高粱的栽培品种及其野生品种为核心基因库做出了贡献。尽管已经有了几个重新测序的高粱基因组,但在参考基因组的组装和注释过程中,高粱基因组的不同部分并没有被报告。本分析利用来自 7 个甜高粱栽培品种的 223 个公开可用的 RNA-seq 数据集构建了 superTranscriptome。这种方法产生了 45,864 个代表性转录本组装(RTA),展示了 15 个已发表的高粱基因组中耐人寻味的存在/不存在变异(PAV)。我们发现 301 个超级转录本是甜高粱独有的,其中包括 58 个编码核心和连接组蛋白、锌指结构域、葡糖基转移酶、纤维素合成酶等的新基因。超级转录组为甜高粱参考基因组(SSRG)增加了 2,802 个新的蛋白质编码基因,其中 559 个编码不同的转录因子(TFs)。我们的分析表明,甜高粱基因组中存在大量类似 MULE 的转座酶,它们可能在甜高粱的进化过程中扮演着隐秘的角色。与甜高粱的野生祖先(353)相比,我们在 SSRG 中观察到 D 基因座的大量缺失和其他四个 NAC 编码基因座的末端缺失,这表明非功能性 NAC 基因对甜高粱的性状发展起到了促进作用。此外,基于超级转录本的差异外显子使用(DEU)和差异基因表达(DGE)分析方法比基于 SSRG 的分析方法更为准确。这项研究表明,超级转录组可以增强我们对高粱基本机制的了解,改进基因组注释,甚至有可能取代参考基因组。
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来源期刊
Journal of Molecular Evolution
Journal of Molecular Evolution 生物-进化生物学
CiteScore
5.50
自引率
2.60%
发文量
36
审稿时长
3 months
期刊介绍: Journal of Molecular Evolution covers experimental, computational, and theoretical work aimed at deciphering features of molecular evolution and the processes bearing on these features, from the initial formation of macromolecular systems through their evolution at the molecular level, the co-evolution of their functions in cellular and organismal systems, and their influence on organismal adaptation, speciation, and ecology. Topics addressed include the evolution of informational macromolecules and their relation to more complex levels of biological organization, including populations and taxa, as well as the molecular basis for the evolution of ecological interactions of species and the use of molecular data to infer fundamental processes in evolutionary ecology. This coverage accommodates such subfields as new genome sequences, comparative structural and functional genomics, population genetics, the molecular evolution of development, the evolution of gene regulation and gene interaction networks, and in vitro evolution of DNA and RNA, molecular evolutionary ecology, and the development of methods and theory that enable molecular evolutionary inference, including but not limited to, phylogenetic methods.
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