College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China.
Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China.
BMC Biol. 2023 Jul 21;21(1):161. doi: 10.1186/s12915-023-01643-w.
Pennisetum giganteum (AABB, 2n = 4x = 28) is a C4 plant in the genus Pennisetum with origin in Africa but currently also grown in Asia and America. It is a crucial forage and potential energy grass with significant advantages in yield, stress resistance, and environmental adaptation. However, the mechanisms underlying these advantageous traits remain largely unexplored. Here, we present a high-quality genome assembly of the allotetraploid P. giganteum aiming at providing insights into biomass accumulation.
Our assembly has a genome size 2.03 Gb and contig N50 of 88.47 Mb that was further divided into A and B subgenomes. Genome evolution analysis revealed the evolutionary relationships across the Panicoideae subfamily lineages and identified numerous genome rearrangements that had occurred in P. giganteum. Comparative genomic analysis showed functional differentiation between the subgenomes. Transcriptome analysis found no subgenome dominance at the overall gene expression level; however, differentially expressed homoeologous genes and homoeolog-specific expressed genes between the two subgenomes were identified, suggesting that complementary effects between the A and B subgenomes contributed to biomass accumulation of P. giganteum. Besides, C4 photosynthesis-related genes were significantly expanded in P. giganteum and their sequences and expression patterns were highly conserved between the two subgenomes, implying that both subgenomes contributed greatly and almost equally to the highly efficient C4 photosynthesis in P. giganteum. We also identified key candidate genes in the C4 photosynthesis pathway that showed sustained high expression across all developmental stages of P. giganteum.
Our study provides important genomic resources for elucidating the genetic basis of advantageous traits in polyploid species, and facilitates further functional genomics research and genetic improvement of P. giganteum.
巨桉（AABB，2n=4x=28）是黍属 C4 植物，起源于非洲，但目前也在亚洲和美洲种植。它是一种重要的饲料和潜在能源草，在产量、抗逆性和环境适应性方面具有显著优势。然而，这些有利特征的机制在很大程度上仍未得到探索。在这里，我们展示了一个巨桉的高质量基因组组装，旨在为生物量积累提供见解。
我们的组装基因组大小为 2.03Gb，contig N50 为 88.47Mb，进一步分为 A 和 B 亚基因组。基因组进化分析揭示了 Panicoideae 亚科谱系的进化关系，并鉴定了巨桉中发生的许多基因组重排。比较基因组分析显示了亚基因组之间的功能分化。转录组分析发现整体基因表达水平没有亚基因组优势；然而，在两个亚基因组之间鉴定了差异表达的同系基因和同系特异性表达基因，表明 A 和 B 亚基因组之间的互补效应有助于巨桉的生物量积累。此外，C4 光合作用相关基因在巨桉中显著扩张，它们的序列和表达模式在两个亚基因组之间高度保守，这表明两个亚基因组都对巨桉高效的 C4 光合作用做出了巨大贡献，而且几乎是同等贡献。我们还鉴定了 C4 光合作用途径中的关键候选基因，这些基因在巨桉的所有发育阶段都表现出持续的高表达。
我们的研究为阐明多倍体物种有利特征的遗传基础提供了重要的基因组资源，并为进一步的功能基因组学研究和巨桉的遗传改良提供了便利。
