Chin Bull Bot ›› 2017, Vol. 52 ›› Issue (4): 530-538.doi: 10.11983/CBB16113

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The Sasussured involucrata Transcriptome Knowledge Base

Jin Li1, Panyao Yan2, Feijian Qian2, Baoyi Qiu2, Wenwen Xia1, Xiaowei Mou2, Lijuan Qiu3, Zhongping Lin4, Ming Chen5, Jianbo Zhu1*, Xianfeng Chen1,2*   

  1. 1College of Life Sciences, Shihezi University, Shihezi 832003, China
    2ShengTing Bioinformatics Institute, Taizhou 318020, China
    3Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    4College of Life Sciences, Perking University, Beijing 100871, China
    5College of Life Sciences, Zhejiang University, Hangzhou 310058, China
  • Received:2016-05-25 Accepted:2016-09-18 Online:2017-05-05 Published:2017-07-01
  • Contact: Zhu Jianbo,Chen Xianfeng E-mail:zjbshz@126.com;jeff_chen@shengtinggroup.com
  • About author:

    # Co-first authors

Abstract:

The Sasussured involucrata possesses high cold-tolerance capacity, which could be a good experimental model for investigating the cold tolerance mechanism. The S. involucrata Transcriptome Knowledge Base (SITKB) (http://www.shengtingsystemsbiology.com/SaussureaKBase/) is a web-based comprehensive database system implemented via html, Perl and Perl CGI/DBI/DBD, Java and JavaScript programming languages on the web front end and PostgrelSQL Relational Database Management System as the backend for data, annotation and knowledge management. SITKB systems was designated to facilitate cold-tolerance gene mining and knowledge discovery and hosts useful knowledge sets such as datasets of raw sequence data quality control, GC contents of raw and assembled DNA sequences, functional annotation of the assembled contigs, assignment of metabolic pathways to the contigs with coding potential, statistics on the rate of meaningful annotation, and blast comparison against other plant transcriptomes or genomes. The knowledge base system also contains a set of software packages for bioinformatics analysis against its stored datasets. This new knowledge base would provide a resource for data mining and knowledge discovery of the functional genes and pathways responsive to cold perturbation and also enhance the capability for elucidating the cold tolerance mechanism. It also offers genomic data resources and a theoretical foundation to facilitate the molecular breeding of cold tolerant crops.

Figure 1

The logical relationship model of the management system within the Sasussured involucrata transcriptome knowledge base"

Figure 2

The architecture of data functional model in the Sasussured involucrata transcriptome knowledge base"

Figure 3

An illustration of gene metabolic pathway search in the Sasussured involucrata transcriptome knowledge base"

Table 1

The statistic of the annotation by blast against special species of Sasussured involucrata transcriptome knowledge base"

物种 比对上的基因数量 注释率(%)
大豆(Glycine max) 164940 82.57
水稻(Oryza sativa) 18101 (pep) 29.92
甜菜(Beta vulgaris) 58361/50002 (pep) 29.216/82.648
拟南芥(Arabidopsis thaliana) 11344 (pep) 18.75
莱茵衣藻(Chlamydomonas reinhardtii) 31638 (pep) 52.293
卷栢(Selaginella moellendorffii) 40281 (pep) 66.58
小立碗藓(Physcomitrella patens) 43298/52976 (pep) 26.52/71.557
无油樟(Amborellaceae trichopoda) 58449/46912 (pep) 29.26/77.54
芜菁(Brassica rapa) 64103/49989 (pep) 32.104/82.625
蒺藜苜蓿(Medicago truncatula) 64103/49989 (pep) 32.104/82.625
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