Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity.
Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity.
复制标题
对单子叶盐生植物互花米草（Spartina alterniflora Loisel）进行转录组分析，揭示了与其盐适应相关的候选基因。
DOI：
10.1186/s12864-016-3017-3
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发表时间：
2016-08-19
期刊：
影响因子：
4.4
通讯作者：
Baisakh N
中科院分区：
文献类型：
--
作者：
Bedre R;Mangu VR;Srivastava S;Sanchez LE;Baisakh N
土壤盐分影响作物的生长和产量。植物对盐度的反应是通过一系列基因的协调调节和表达来进行生理生化调节的。近年来，盐生植物对盐的适应机制受到了生物学家的关注。互花米草是路易斯安那州原生的单子叶盐生植物，可以承受高达两倍海水强度的盐度。利用454/GS-FLX对互花草叶片和根系转录组进行了测序，分析了互花草适应盐度的分子机制。总共，770,690条平均长度为324 bp的高质量reads被从头组装成73,131条contigs（平均长度为577 bp），序列覆盖率为5.9X。大多数unigenes（95%）注释到具有已知功能的蛋白质上，与水稻基因的相似性超过90%。大约28%的独特基因被认为是互花葡萄球菌特有的。数字表达谱显示，盐胁迫下转运体、液泡质子泵成员和转录因子显著富集（P < 0.01），表明离子稳态和转录调控在盐胁迫下的适应过程中起着重要作用。在13份互花草材料中，共获得9457个单基因的10805个SSRs标记，并通过遗传多样性分析进行了验证。本研究通过对互花草转录组的研究，了解盐生植物在盐胁迫下的基因调控。互花草的转录组测序（对照和盐调控）为进一步的禾草基因发现研究提供了平台。这项研究和我们之前发表的研究表明，互花葡萄球菌是一个丰富的耐盐基因库，可以用来培育耐盐谷类作物，特别是水稻，这是全球重要的主要粮食作物。本文的在线版本（doi:10.1186/s12864-016-3017-3）包含补充材料，可供授权用户使用。
Soil salinity affects growth and yield of crop plants. Plants respond to salinity by physiological and biochemical adjustments through a coordinated regulation and expression of a cascade of genes. Recently, halophytes have attracted attention of the biologists to understand their salt adaptation mechanisms. Spartina alterniflora (smooth cordgrass) is a Louisiana native monocot halophyte that can withstand salinity up to double the strength of sea water. To dissect the molecular mechanisms underlying its salinity adaptation, leaf and root transcriptome of S. alterniflora was sequenced using 454/GS-FLX. Altogether, 770,690 high quality reads with an average length 324-bp were assembled de novo into 73,131 contigs (average 577-bp long) with 5.9X sequence coverage. Most unigenes (95 %) annotated to proteins with known functions, and had more than 90 % similarity to rice genes. About 28 % unigenes were considered specific to S. alterniflora. Digital expression profiles revealed significant enrichment (P < 0.01) of transporters, vacuolar proton pump members and transcription factors under salt stress, which suggested the role of ion homeostasis and transcriptional regulation in the salinity adaptation of this grass. Also, 10,805 SSRs markers from 9457 unigenes were generated and validated through genetic diversity analysis among 13 accessions of S. alterniflora. The present study explores the transcriptome of S. alterniflora to understand the gene regulation under salt stress in halophytes. The sequenced transcriptome (control and salt-regulated) of S. alterniflora provides a platform for further gene finding studies in grasses. This study and our previously published studies suggested that S. alterniflora is a rich reservoir of salt tolerance genes that can be used to develop salt tolerant cereal crops, especially rice, a major food crop of global importance. The online version of this article (doi:10.1186/s12864-016-3017-3) contains supplementary material, which is available to authorized users.