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   Location:Home > Research > Research Progress
Regulation function of leucine rich repeat dominates in transpiration of Ficus
Author: Lang Tiange
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Update time: 2014-10-17
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Massive genomic sequence data could be produced with Next Generation Sequencing method, but there are many problems for de novo assembly, especially when the structure of the genome is complex which is often the case in plant species. In such cases, DNA reads could only be assembled to scaffold or contig level. Thus, methods based on the analysis of fragments are necessary. Some of the problems associated with full-length assembly without a reference genome can be avoided by protein domain analysis.

One of the strategies used by plants to respond to drought stress events is plant transpiration efficiency. In the model plant Arabidopsis, plant transpiration efficiency is a quantitative trait. In contrast to model species, the molecular mechanism of plant transpiration efficiency still remains unclear in many plant and tree species, especially those without reference genomes. Improving functional annotation of assembled data obtained from next-generation sequencing (NGS) technology may provide new insights into genes potentially involved in this important trait.

In a study conducted by researchers from Xishuangbanna Tropical Botanical Garden (XTBG) of Chinese Academy of Sciences and Beijing Forestry University, it’s demonstrated that the regulation function of leucine rich repeat (LRR) dominated in transpiration of Ficus by taking use of the sequence of protein domains.

The objective of the research was to develop a method for obtaining high quality contigs from low coverage NGS data, to predict protein domains from contigs obtained through above method; and to discuss the relationship between LRR domain numbers and plant transpiration efficiency.

The programming functionality in the study was proved to be a useful tool in biological studies by showing that the LRRNT_2 and LRR_8 domains were potentially related to plant transpiration efficiency, as we can see from the stomata index in F. altissima, F. tinctoria, F. langkokensis, and F. fistulosa. The main benefit of the functionality is that it overcomes many of the complex problems associated with de novo assembly.

  The result has been published in PLOS ONE with title “Protein Domain Analysis of Genomic Sequence Data Reveals Regulation of LRR Related Domains in Plant Transpiration in Ficus”.

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Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences. Menglun, Mengla, Yunnan 666303, China
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