Integrative analyses of long and short-read RNA sequencing reveal the spliced isoform regulatory network of seedling growth dynamics in upland cotton

IF 3.9 4区 生物学 Q1 GENETICS & HEREDITY Functional & Integrative Genomics Pub Date : 2024-09-04 DOI:10.1007/s10142-024-01420-0
Kashif Shahzad, Meng Zhang, Iqra Mubeen, Xuexian Zhang, Liping Guo, Tingxiang Qi, Juanjuan Feng, Huini Tang, Xiuqin Qiao, Jianyong Wu, Chaozhu Xing
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Abstract

The polyploid genome of cotton has significantly increased the transcript complexity. Recent advances in full-length transcript sequencing are now widely used to characterize the complete landscape of transcriptional events. Such studies in cotton can help us to explore the genetic mechanisms of the cotton seedling growth. Through long-read single-molecule RNA sequencing, this study compared the transcriptomes of three yield contrasting genotypes of upland cotton. Our analysis identified different numbers of spliced isoforms from 31,166, 28,716, and 28,713 genes in SJ48, Z98, and DT8 cotton genotypes, respectively, most of which were novel compared to previous cotton reference transcriptomes, and showed significant differences in the number of exon structures and coding sequence length due to intron retention. Quantification of isoform expression revealed significant differences in expression in the root and leaf of each genotype. An array of key isoform target genes showed protein kinase or phosphorylation functions, and their protein interaction network contained most of the circadian oscillator proteins. Spliced isoforms from the GIGANTEA (GI) protien were differentially regulated in each genotype and might be expected to regulate translational activities, including the sequence and function of target proteins. In addition, these spliced isoforms generate diurnal expression profiles in cotton leaves, which may alter the transcriptional regulatory network of seedling growth. Silencing of the novel spliced GI isoform Gh_A02G0645_N17 significantly affected biomass traits, contributed to variable growth, and increased transcription of the early flowering pathway gene ELF in cotton. Our high-throughput hybrid sequencing results will be useful to dissect functional differences among spliced isoforms in the polyploid cotton genome.

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长短线程 RNA 测序的综合分析揭示了陆地棉幼苗生长动态的剪接同工酶调控网络。
棉花的多倍体基因组大大增加了转录本的复杂性。目前,全长转录本测序技术的最新进展已被广泛用于描述转录事件的全貌。对棉花的此类研究有助于我们探索棉花幼苗生长的遗传机制。通过长线程单分子 RNA 测序,本研究比较了三种产量对比强烈的陆地棉基因型的转录组。我们的分析分别从 SJ48、Z98 和 DT8 棉花基因型的 31,166 个、28,716 个和 28,713 个基因中发现了不同数量的剪接异构体,其中大部分与以往的棉花参考转录组相比都是新的,并且由于内含子的保留,外显子结构的数量和编码序列的长度都有显著差异。对同工酶表达量的定量分析显示,各基因型在根部和叶片中的表达量存在显著差异。一系列关键的同工酶目标基因显示了蛋白激酶或磷酸化功能,其蛋白相互作用网络包含了大多数昼夜节律振荡蛋白。来自 GIGANTEA(GI)原蛋白的剪接异构体在每种基因型中都受到不同的调控,可能会调控翻译活动,包括目标蛋白的序列和功能。此外,这些剪接异构体在棉花叶片中产生昼夜表达谱,这可能会改变幼苗生长的转录调控网络。沉默新的剪接 GI 异构体 Gh_A02G0645_N17 会显著影响棉花的生物量性状,导致生长多变,并增加早花途径基因 ELF 的转录。我们的高通量杂交测序结果将有助于剖析多倍体棉花基因组中剪接异构体的功能差异。
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来源期刊
CiteScore
3.50
自引率
3.40%
发文量
92
审稿时长
2 months
期刊介绍: Functional & Integrative Genomics is devoted to large-scale studies of genomes and their functions, including systems analyses of biological processes. The journal will provide the research community an integrated platform where researchers can share, review and discuss their findings on important biological questions that will ultimately enable us to answer the fundamental question: How do genomes work?
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