A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing

First author: Bo Wang; Affiliations: Cold Spring Harbor Laboratory (冷泉港实验室): New York, USA

Corresponding author: Doreen Ware

Maize and sorghum are both important crops with similar overall plant architectures, but they have key differences, especially in regard to their inflorescences (花序). To better understand these two organisms at the molecular level, we compared expression profiles of both protein-coding and noncoding transcripts in 11 matched tissues using single-molecule, long-read, deep RNA sequencing. This comparative analysis revealed large numbers of novel isoforms in both species. Evolutionarily young genes were likely to be generated in reproductive tissues (生殖组织) and usually had fewer isoforms than old genes. We also observed similarities and differences in alternative splicing patterns and activities, both among tissues and between species. The maize subgenomes exhibited no bias in isoform generation; however, genes in the B genome were more highly expressed in pollen tissue, whereas genes in the A genome were more highly expressed in endosperm. We also identified a number of splicing events conserved between maize and sorghum. In addition, we generated comprehensive and high-resolution maps of poly(A) sites, revealing similarities and differences in mRNA cleavage between the two species. Overall, our results reveal considerable splicing and expression diversity between sorghum and maize, well beyond what was reported in previous studies, likely reflecting the differences in architecture between these two species.

玉米和高粱是两个非常重要的经济作物，具有相似的植株结构，但也存在关键的差异，尤其是两者的花序不同。为了进一步从分子水平理解这两个物种之间的差异，本文对玉米和高粱11对匹配组织进行了三代RNA深度测序，综合比较蛋白编码和非编码转录本的表达谱。转录组比较研究揭示了两个物种中大量新的基因转录异构体。进化上比较年轻的基因往往会在生殖组织中产生，与进化上古老的基因相比具有更少的异构体。作者在不同组织间和不同物种间均观察到了可变剪切模式和活性的异同点。玉米的亚基因不存在异构体偏性，然而在B套基因组上的基因更偏向于在花粉组织中表达，而在A套基因组上的基因更偏向于在胚乳组织中表达。作者还鉴定了玉米和高粱高度保守的剪切事件。另外，作者构建了这两个物种高分辨率的poly(A)位点图谱，显示了这两个物种在mRNA剪切上的异同点。综上，本文的研究揭示了在玉米和高粱之间存在很大的剪切和表达多样性，远远超过了之前研究的预期，可能反映了这两个物种在植物结构上的差异。

通讯：Doreen Ware (https://www.cshl.edu/research/faculty-staff/doreen-ware/)

研究方向：植物基因组演化和作物遗传改良。

doi: 10.1101/gr.227462.117

Journal: Genome Research

Published in Advance: 30 April, 2018

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