Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies.
Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies.
复制标题
DOI：
10.3389/fpls.2018.01625
复制
发表时间：
2018
影响因子：
5.6
通讯作者：
Sundström JF
中科院分区：
文献类型：
--
作者：
Akhter S;Kretzschmar WW;Nordal V;Delhomme N;Street NR;Nilsson O;Emanuelsson O;Sundström JF
最近对几种裸子植物的基因组和转录组进行测序的结果表明，与被子植物相比，裸子植物中某些基因家族的复杂性增加了。这方面的一个例子是裸子植物的姐妹进化枝到被子植物TM 3样MADS盒基因，至少在针叶树谱系中基因的数量已经扩大。我们以前已经确定了这个分支的一个成员，针叶树基因DEFICIENS AGAMOUS LIKE 19（DAL 19），作为在锥设置拍摄具体上调。在这里，我们显示通过桑格测序的mRNA衍生的cDNA和映射到组装的针叶树基因组序列，DAL 19产生6个成熟的mRNA剪接变异体云杉。这些剪接变体使用交替的第一个和最后一个外显子，而它们的四个中心外显子构成了所有六个转录本中存在的核心区域。因此，它们可能是转录物同种型。定量实时PCR显示，两个相互排斥的第一DAL 19外显子的差异表达的分生组织，将形成男性或女性锥，或营养芽。此外，mRNA原位杂交显示，两个相互排斥的最后DAL 19外显子在芽分生组织内以细胞特异性模式表达。基于DAL 19中的这些发现，我们开发了一种灵敏的方法，从mRNA的短读测序中进行转录异构体组装。我们将这种方法应用于42个假定的MADS盒核心区域，从这些区域中我们组装了1084个假定的转录本。我们手动策划这些转录本，以达到38个假定的MADS盒基因的933个组装的转录本异构体。152这些异构体，我们分配到28个假定的MADS盒基因，在8个女性，男性和营养芽的差异表达。我们进一步提供了证据的表达的16个38个推定的MADS盒基因的映射PacBio Iso-Seq环状共识读取来自汇集的样品测序组装转录。总之，我们的分析揭示了MADS-box基因异构体的互斥外显子在P. abies早期芽发育过程中的使用，并且我们发现，P. abies中大量鉴定的MADS-box转录本不仅来自于通过基因复制事件的基因家族的扩展，而且来自于许多剪接变体的产生。
Recent efforts to sequence the genomes and transcriptomes of several gymnosperm species have revealed an increased complexity in certain gene families in gymnosperms as compared to angiosperms. One example of this is the gymnosperm sister clade to angiosperm TM3-like MADS-box genes, which at least in the conifer lineage has expanded in number of genes. We have previously identified a member of this sub-clade, the conifer gene DEFICIENS AGAMOUS LIKE 19 (DAL19), as being specifically upregulated in cone-setting shoots. Here, we show through Sanger sequencing of mRNA-derived cDNA and mapping to assembled conifer genomic sequences that DAL19 produces six mature mRNA splice variants in Picea abies. These splice variants use alternate first and last exons, while their four central exons constitute a core region present in all six transcripts. Thus, they are likely to be transcript isoforms. Quantitative Real-Time PCR revealed that two mutually exclusive first DAL19 exons are differentially expressed across meristems that will form either male or female cones, or vegetative shoots. Furthermore, mRNA in situ hybridization revealed that two mutually exclusive last DAL19 exons were expressed in a cell-specific pattern within bud meristems. Based on these findings in DAL19, we developed a sensitive approach to transcript isoform assembly from short-read sequencing of mRNA. We applied this method to 42 putative MADS-box core regions in P. abies, from which we assembled 1084 putative transcripts. We manually curated these transcripts to arrive at 933 assembled transcript isoforms of 38 putative MADS-box genes. 152 of these isoforms, which we assign to 28 putative MADS-box genes, were differentially expressed across eight female, male, and vegetative buds. We further provide evidence of the expression of 16 out of the 38 putative MADS-box genes by mapping PacBio Iso-Seq circular consensus reads derived from pooled sample sequencing to assembled transcripts. In summary, our analyses reveal the use of mutually exclusive exons of MADS-box gene isoforms during early bud development in P. abies, and we find that the large number of identified MADS-box transcripts in P. abies results not only from expansion of the gene family through gene duplication events but also from the generation of numerous splice variants.
登录
查看更多内容
影响因子：
16.6
作者：
Abdel-Ghany SE;Hamilton M;Jacobi JL;Ngam P;Devitt N;Schilkey F;Ben-Hur A;Reddy AS
通讯作者：
Reddy AS
裸子植物和被子植物 MIKCc 型 MADS-Box 基因的进化分析
影响因子：
5.6
作者：
Chen F;Zhang X;Liu X;Zhang L
通讯作者：
Zhang L
影响因子：
3.7
作者：
Gordon SP;Tseng E;Salamov A;Zhang J;Meng X;Zhao Z;Kang D;Underwood J;Grigoriev IV;Figueroa M;Schilling JS;Chen F;Wang Z
通讯作者：
Wang Z
影响因子：
6.9
作者：
Capovilla G;Symeonidi E;Wu R;Schmid M
通讯作者：
Schmid M
影响因子：
4.4
作者：
Hoang NV;Furtado A;Mason PJ;Marquardt A;Kasirajan L;Thirugnanasambandam PP;Botha FC;Henry RJ
通讯作者：
Henry RJ