Transcriptome resources and genome-wide marker development for Japanese larch (Larix kaempferi)
Transcriptome resources and genome-wide marker development for Japanese larch (Larix kaempferi)
复制标题
日本落叶松 (Larix kaempferi) 的转录组资源和全基因组标记开发
DOI：
10.15302/j-fase-2014010
复制
发表时间：
2014-02-01
影响因子：
3.7
通讯作者：
Zhang, Shougong
中科院分区：
文献类型：
--
作者：
Li, Wanfeng;Han, Suying;Zhang, Shougong
虽然随着年龄的增长，树木对气候和环境条件变化的不同反应已经得到证明，但树木生长和发育的基本机制和年龄控制是复杂的，特别是在分子水平上了解甚少。日本落叶松是一种广泛分布于北方的具有重要生态和经济价值的落叶针叶树。使用高通量RNA测序，我们从1年、2年、5年、10年、25年和50年生的L.山柰树将这些与已发表的Roche 454测序读数和表达的序列标签（两者主要来自落叶松胚胎发生细胞培养物）相结合，我们将26670549个读数组装成146786个转录本，其中我们注释了79182个转录本，以支持树木老化和适应、体细胞胚胎发生和木材形成的分子基础的研究。利用这些序列，我们还确定了许多单核苷酸多态性，简单重复序列，插入和缺失标记，以协助育种和遗传多样性的落叶松研究。
While the differential responses of trees to changes in climatic and environmental conditions have been demonstrated as they age, the underlying mechanisms and age control of tree growth and development are complex and poorly understood particularly at a molecular level. In this paper, we present a transcriptome analysis of Larix kaempferi, a deciduous conifer that is widely-grown in the northern hemisphere and of significant ecological and economic value. Using high-throughput RNA sequencing, we obtained about 26 million reads from the stems of 1-, 2-, 5-, 10-, 25-and 50-year-old L. kaempferi trees. Combining these with the published Roche 454 sequencing reads and the expressed sequence tags (both mainly from Larix embryogenic cell cultures), we assembled 26670549 reads into 146786 transcripts, of which we annotated 79182 to support investigations of the molecular basis of tree aging and adaption, somatic embryogenesis and wood formation. Using these sequences we also identified many single-nucleotide polymorphisms, simple sequence repeats, and insertion and deletion markers to assist breeding and genetic diversity studies of Larix.