The long intergenic non-coding RNA (lincRNA) landscape of the soybean genome

Long intergenic non-coding RNAs (lincRNAs; 长链基因间非编码RNAs) are emerging as important regulators of diverse biological processes. However, our understanding of lincRNA abundance and function remains very limited especially for agriculturally important plants. Soybean is a major legume crop plant (豆科作物) providing over a half of global oilseed (含油种子) production. Moreover, soybean can form symbiotic relationships (共生关系) with Rhizobium bacteria (根瘤菌) to fix atmospheric nitrogen (大气氮). Soybean has a complex paleopolyploid (古多倍体) genome and exhibits many vegetative and floral development complexities. Soybean cultivars have photoperiod (光周期) requirements restricting its use and productivity. Molecular regulators of these legume-specific developmental processes remain enigmatic (似谜的). Long non-coding RNAs may play important regulatory roles in soybean growth and development. In this study over one billion RNAseq read pairs from 37 samples representing nine tissues were used to discover 6,018 lincRNA loci. The lincRNAs were shorter than protein-coding transcripts, had lower expression levels and more sample specific expression. Few of the loci were found to be conserved in two other legume species (chickpea 鹰嘴豆 and Medicago 苜蓿), but almost two hundred homeologous (部分同源的) lincRNA in the soybean genome were detected. Protein-coding gene-lincRNA co-expression analysis suggested an involvement (参与) of lincRNAs in stress response, signal transduction and developmental processes. Positional analysis (位置分析) of lincRNA loci implicated involvement in transcriptional regulation. lincRNA expression from centromeric regions (着丝粒区) was observed especially in actively dividing tissues (分裂组织) suggesting possible roles in cell division. Integration of publically available genome-wide association data with the lincRNA map of the soybean genome uncovered 23 lincRNAs potentially associates with agronomic traits (农艺性状).

长链基因间非编码RNA（lincRNA）在植物不同生物过程中起重要调控作用。然而，我们对于lincRNA在植物基因组上的丰度和功能还了解得不多，尤其是在农业上重要的植物。大豆是一种主要的豆科作物，其提供了超过一半的全球含油种子产量。此外，大豆可以和根瘤菌形成共生关系以固定大气中的氮。大豆有一个复杂的古多倍体基因组，并且存在生长和花发育等复杂问题。大豆栽培种由于光周期的条件需要因而限制了其应用和产量。这些大豆特异性的发育过程中的分子调控机制仍然是个谜团。长链非编码RNA可能在大豆的生长和发育中起着重要的调控作用。本文基于大豆9个不同部位的组织37个样本的RNA-seq测序数据鉴定了共6,018个lincRNA位点。这些lincRNA比蛋白编码的转录本长度更短，并且具有更低的表达量和更高的样本特异性表达。很少有lincRNA位点在大豆和其它两个豆类植物鹰嘴豆和苜蓿之间存在保守性，但作者还是在大豆基因组中鉴定到了大约200个部分同源的lincRNA。蛋白编码基因和lincRNA之间共表达分析显示lincRNAs会参与胁迫响应、信号转导及发育进程。lincRNA位点的位置分析暗示lincRNA可能会参与转录调控。着丝粒区的lincRNA表达水平在分裂组织中比较活跃，表明lincRNA可能参与了细胞分裂。整合公共发表的全基因组关联数据和大豆的lincRNA图谱，本文发现了23个lincRNAs潜在的与大豆的农艺性状相关联。

通讯：Prem L. Bhalla (https://www.findanexpert.unimelb.edu.au/display/person12992#tab-research)

个人简介：旁遮普大学本硕博。

doi: https://doi.org/10.1104/pp.17.01657