CottonFGD: an integrated functional genomics database for cotton

Zhu, Τao; Liang, Chengzhen; Meng, Zhen; Sun, Guixin; Meng, Zhaoghong; Guo, Sandui; Zhang, Rui

doi:10.1186/s12870-017-1039-x

Cited by 304 publications

(289 citation statements)

References 44 publications

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“…The RNA-seq data was downloaded from the NCBI Sequence Read Archive (SRA: PRJNA248163, http:// www.ncbi.nlm.nih.gov/sra/?term=PRJNA248163) and CottonFGD website (Yuan et al 2015;Zhu et al 2017). The fragments per kilobase million (FPKM) values denoting the expression levels of SWEET genes were isolated from a comprehensive profile of the TM-1 transcriptome data (Trapnell et al 2012).…”

Section: Transcriptome Data Analysis Of Sweet Gene Expression From Hementioning

confidence: 99%

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A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

et al. 2018

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Background: The SWEET (Sugars will eventually be exported transporters) gene family plays multiple roles in plant physiological activities and development process. It participates in reproductive development and in the process of sugar transport and absorption, plant senescence and stress responses and plant-pathogen interaction. However, thecomprehensive analysis of SWEET genes has not been reported in cotton.

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Section: Transcriptome Data Analysis Of Sweet Gene Expression From Hementioning

confidence: 99%

“…XinHai-21 (NAU, version 2.1) were retrieved from the CottonGen website (Yu et al 2014) and the CottonFGD website (Zhu et al 2017).…”

Section: Gene Retrieval and Genome-wide Identification Analysismentioning

confidence: 99%

A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

et al. 2018

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“…The creation of a Pedimap file is simple, and a novice to informatics can curate and use Pedimap with a little training. Pedimap allows breeders to store data, fetch and visualize genomic information at any time with less effort and complete accuracy [47]. The straightforward accessibility, direct data interpretation, ability to customize the views in multiple fashions, and editable output file formats are the significant features of Pedimap.…”

Section: Resultsmentioning

confidence: 99%

Application of Pedimap — a pedigree visualization tool — to facilitate the decisioning of rice breeding in Sri Lanka

Rathnayake

Sahibdeen

Udawela³

et al. 2020

Preprint

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17The development of rice cultivars with desirable traits is essential. The decision-making is a 18 crucial step in rice breeding programs. The breeders can make efficient and pragmatic decisions 19 if an organized pedigree visualization platform is available for the material of the rice breeding 20 germplasm. The staple food in Sri Lanka is rice, and there is a great demand for improved 21 varieties with high yield and other promising traits. In the present study, the available data of 22 all the rice varieties released by Rice Research and Development Institute, Sri Lanka, and the 23 related landraces and genotypes were arranged in Pedimap, a pedigree visualization tool. 24 Pedimap can showcase pedigree relationships, phenotypic, and molecular data. The Identity by 25 Descent (IBD) probabilities were calculated using FlexQTL software and included in the 26 Pedimap database. The parentage selection based on the variations of phenotypic traits, 27 selection of marker alleles for molecular breeding, and detection of the founders of genetic 28 effects can be swiftly conducted using Pedimap. However, the power of harnessing the value 29of Pedimap for making breeding decisions relies on the availability of data for the traits, 30 markers, and genomic sequences. Thus, it is imperative to characterize the breeding 31 germplasms using standard phenomic and genomic characterization procedures before 32 organized into Pedimap. Thereby, the worldwide breeding programs can benefit from each 33 other to produce improved varieties to meet global challenges. 34 35

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“…4f). This tool used a stable version of NCBI BLAST-2.7.1 + as a back-end BLAST executable to embed in the back end of the database, while using the SequenceServer app as the front-end input (Zhu et al 2017;Camacho et al 2009). This website provides a more intuitive graphical interface for this function, making it easy and fast for users to use BLAST search.…”

Section: Blastmentioning

confidence: 99%

CSTDB: A Crop Stress-tolerance Gene and Protein Database Integrated by Convolutional Neural Networks

Zhang

Yue

Zhao

et al. 2018

Preprint

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Numerous studies have shown that many genes and proteins in plants are involved in the regulation of plant resistance to abiotic and biotic stresses. The researches on the stress tolerance of crops are also the focus of many researchers. To provides a reliable platform for collecting and retrieving genetic and protein information related to stress tolerance found in crops, we constructed CSTDB(Crops Stress-tolerance Database), an integrated database that includes stress-tolerance genes and proteins for many crop species. The database was developed based on convolutional neural network technology. It is a web-accessible database that contains detailed information on the stress-tolerance genes and proteins of major crop species. Currently, the database records four major crops containing 1,371 abiotic stress-tolerance genes or proteins, and 207 genes or proteins associated with biotic stress. Each gene and protein has detailed functional information and sequence information, such as stress types, Genbank ID, Pubmed ID，Protein ID，3D model picture and FASTA files. As a user-friendly browsing tool, this database provides search functions, BALST functions and file download functions. CSTDB can be a valuable resource，which is designed to meet the broad needs of researchers working on crops stress-tolerance experiments. Database URL: http://pcsb.ahau.edu.cn:8080/CSTDB

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CottonFGD: an integrated functional genomics database for cotton

Cited by 304 publications

References 44 publications

A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

Application of Pedimap — a pedigree visualization tool — to facilitate the decisioning of rice breeding in Sri Lanka

CSTDB: A Crop Stress-tolerance Gene and Protein Database Integrated by Convolutional Neural Networks

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