全长转录组分析揭示，野生蔗属 Saccharum spontaneum 亚基因组有助于甘蔗中的糖分积累。

The subgenome Saccharum spontaneum contributes to sugar accumulation in sugarcane as revealed by full-length transcriptomic analysis.

机构信息

State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China.

National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China.

出版信息

J Adv Res. 2023 Dec;54:1-13. doi: 10.1016/j.jare.2023.02.001. Epub 2023 Feb 11.

DOI:10.1016/j.jare.2023.02.001

PMID:36781019

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10703721/

Abstract

INTRODUCTION

Modern sugarcane cultivars (Saccharum spp. hybrids) derived from crosses between S. officinarum and S. spontaneum, with high-sugar traits and excellent stress tolerance inherited respectively. However, the contribution of the S. spontaneum subgenome to sucrose accumulation is still unclear.

OBJECTIVE

To compensate for the absence of a high-quality reference genome, a transcriptome analysis method is needed to analyze the molecular basis of differential sucrose accumulation in sugarcane hybrids and to find clues to the contribution of the S. spontaneum subgenome to sucrose accumulation.

METHODS

PacBio full-length sequencing was used to complement genome annotation, followed by the identification of differential genes between the high and low sugar groups using differential alternative splicing analysis and differential expression analysis. At the subgenomic level, the factors responsible for differential sucrose accumulation were investigated from the perspective of transcriptional and post-transcriptional regulation.

RESULTS

A full-length transcriptome annotated at the subgenomic level was provided, complemented by 263,378 allele-defined transcript isoforms and 139,405 alternative splicing (AS) events. Differential alternative splicing (DA) analysis and differential expression (DE) analysis identified differential genes between high and low sugar groups and explained differential sucrose accumulation factors by the KEGG pathways. In some gene models, different or even opposite expression patterns of alleles from the same gene were observed, reflecting the potential evolution of these alleles toward novel functions in polyploid sugarcane. Among DA and DE genes in the sucrose source-sink complex pathway, we found some alleles encoding sucrose accumulation-related enzymes derived from the S. spontaneum subgenome were differentially expressed or had DA events between the two contrasting sugarcane hybrids.

CONCLUSION

Full-length transcriptomes annotated at the subgenomic level could better characterize sugarcane hybrids, and the S. spontaneum subgenome was found to contribute to sucrose accumulation.

摘要

简介

现代甘蔗品种（甘蔗属杂种）来源于甘蔗和甘蔗之间的杂交，具有高糖特性和优良的应激耐受性。然而，甘蔗属亚基因组对蔗糖积累的贡献仍不清楚。

目的

为了弥补高质量参考基因组的缺失，需要一种转录组分析方法来分析甘蔗杂种中蔗糖积累差异的分子基础，并找到甘蔗属亚基因组对蔗糖积累贡献的线索。

方法

使用 PacBio 全长测序来补充基因组注释，然后使用差异剪接分析和差异表达分析来鉴定高糖组和低糖组之间的差异基因。在亚基因组水平上，从转录和转录后调控的角度研究了导致蔗糖积累差异的因素。

结果

提供了一个亚基因组水平注释的全长转录组，补充了 263378 个等位基因定义的转录异构体和 139405 个选择性剪接（AS）事件。差异选择性剪接（DA）分析和差异表达（DE）分析鉴定了高糖组和低糖组之间的差异基因，并通过 KEGG 途径解释了蔗糖积累差异的因素。在一些基因模型中，来自同一基因的等位基因表现出不同甚至相反的表达模式，反映了这些等位基因在多倍体甘蔗中向新功能进化的潜力。在蔗糖源库复合体途径的 DA 和 DE 基因中，我们发现一些来自甘蔗属亚基因组的编码蔗糖积累相关酶的等位基因在两个对照甘蔗杂种之间表现出差异表达或有 DA 事件。