De novo assembly and characterization of fruit transcriptome in Litchi chinensis Sonn and analysis of differentially regulated genes in fruit in response to shading.
De novo assembly and characterization of fruit transcriptome in Litchi chinensis Sonn and analysis of differentially regulated genes in fruit in response to shading.
复制标题
荔枝果实转录组的从头组装、表征及果实遮荫差异调控基因分析
DOI：
10.1186/1471-2164-14-552
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发表时间：
2013-08-14
期刊：
影响因子：
4.4
通讯作者：
Li J
中科院分区：
文献类型：
--
作者：
Li C;Wang Y;Huang X;Li J;Wang H;Li J
背景：荔枝（Litchi chinensis Sonn.）是热带和亚热带地区栽培的最重要的果树之一。然而，缺乏转录组和基因组信息阻碍了我们对荔枝坐果和果实发育的分子机制的理解。在果实发育早期，遮光会降低果实的生长，并导致果实脱落。本研究采用高通量RNA测序技术（RNA-Seq）对荔枝果实转录组进行从头组装和表征，并利用数字转录本丰度（DTA）分析技术对响应遮荫的差异表达基因进行研究。通过查询各种公共数据库来注释这些unigenes，其中发现34，029个unigenes与NCBI GenBank数据库中的基因同源，并且基于Swiss-Prot数据库中的已知蛋白质注释了22，945个unigenes。在进一步的正序分析中，5，885个单基因被分配有一个或多个基因本体论术语，10，234个命中与24个正序组分类簇（Clusters of Orthopathology Groups classification）比对，并且15，330个单基因被分类到266个京都基因和基因组途径百科全书（Encyclopedia of Genes and Genomes pathways）中。基于新组装的转录组，利用DTA分析技术研究了与遮荫胁迫相关的差异表达基因。总共有360万个和350万个高质量的标签分别从阴影和非阴影库中生成。多达1，039个unigenes被证明是显着差异调节。14个差异调节的unigene，这是随机选择的遮荫处理过程中进行更详细的表达比较，11被确定为可能参与荔枝幼果脱落的过程中。结论：组装的荔枝果实转录组提供了一个全球性的描述荔枝果实发育中表达的基因，并可以作为一个理想的仓库，为未来的功能特性的特定基因。DTA分析表明，有1000多个差异调节的unigene响应遮荫信号，其中一些可能参与了荔枝幼果的脱落过程，为荔枝器官脱落的分子机制提供了新的线索。
Background:Litchi (Litchi chinensis Sonn.) is one of the most important fruit trees cultivated in tropical and subtropical areas. However, a lack of transcriptomic and genomic information hinders our understanding of the molecular mechanisms underlying fruit set and fruit development in litchi. Shading during early fruit development decreases fruit growth and induces fruit abscission. Here, high-throughput RNA sequencing (RNA-Seq) was employed for the de novo assembly and characterization of the fruit transcriptome in litchi, and differentially regulated genes, which are responsive to shading, were also investigated using digital transcript abundance(DTA)profiling.Results:More than 53 million paired-end reads were generated and assembled into 57,050 unigenes with an average length of 601 bp. These unigenes were annotated by querying against various public databases, with 34,029 unigenes found to be homologous to genes in the NCBI GenBank database and 22,945 unigenes annotated based on known proteins in the Swiss-Prot database. In further orthologous analyses, 5,885 unigenes were assigned with one or more Gene Ontology terms, 10,234 hits were aligned to the 24 Clusters of Orthologous Groups classifications and 15,330 unigenes were classified into 266 Kyoto Encyclopedia of Genes and Genomes pathways. Based on the newly assembled transcriptome, the DTA profiling approach was applied to investigate the differentially expressed genes related to shading stress. A total of 3.6 million and 3.5 million high-quality tags were generated from shaded and non-shaded libraries, respectively. As many as 1,039 unigenes were shown to be significantly differentially regulated. Eleven of the 14 differentially regulated unigenes, which were randomly selected for more detailed expression comparison during the course of shading treatment, were identified as being likely to be involved in the process of fruitlet abscission in litchi.Conclusions:The assembled transcriptome of litchi fruit provides a global description of expressed genes in litchi fruit development, and could serve as an ideal repository for future functional characterization of specific genes. The DTA analysis revealed that more than 1000 differentially regulated unigenes respond to the shading signal, some of which might be involved in the fruitlet abscission process in litchi, shedding new light on the molecular mechanisms underlying organ abscission.
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影响因子：
6.9
作者：
Agustí J;Merelo P;Cercós M;Tadeo FR;Talón M
通讯作者：
Talón M
影响因子：
4
作者：
Hieke, S;Menzel, CM;Lüdders, P
通讯作者：
Lüdders, P
DOI：
10.21273/jashs.137.5.275
发表时间：
2012-09-01
影响因子：
1.9
作者：
Dash, Madhumita;Johnson, Lisa K.;Malladi, Anish
通讯作者：
Malladi, Anish
影响因子：
4.4
作者：
Feng C;Chen M;Xu CJ;Bai L;Yin XR;Li X;Allan AC;Ferguson IB;Chen KS
通讯作者：
Chen KS
影响因子：
7.4
作者：
DELCAMPILLO, E;LEWIS, LN
通讯作者：
LEWIS, LN