IGDD: a database of intronless genes in dicots

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Abstract

Background

Intronless genes are a significant characteristic of prokaryotes. Systematic identification and annotation are primary and crucial steps for determining the functions of intronless genes and understanding their occurrence in eukaryotes.

Description

In this paper, we describe the construction of the Intronless Genes Database in Dicots (IGDD; available at http://bio.njfu.edu.cn/igdd/), which contains data for five well-annotated plants including Arabidopsis thaliana, Carica papaya, Populus trichocarpa, Salix suchowensis and Vitis vinifera. Using highly visual settings, IGDD displays the structural and functional annotations, the homolog groups, the syntenic relationships, the expression patterns, and the statistical characteristics of intronless genes. In addition, useful tools such as an advanced search and local BLAST are available through a user-friendly and intuitive web interface.

Conclusion

In conclusion, the IGDD provides a comprehensive and up-to-date platform for researchers to assist the exploration of intronless genes in dicot plants.

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Most cited references 11

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The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

Alberto Casagrande (2007)

The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.

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KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

Dapeng Wang, Yubin Zhang, Zhang-Yun Zhang … (2010)

We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we added our modified versions of several widely used methods as the gamma series including γ-NG, γ-LWL, γ-MLWL, γ-LPB, γ-MLPB, γ-YN and γ-MYN, which have been demonstrated to perform better under certain conditions than their original forms and are not implemented in the previous version. The package is readily used for the identification of positively selected sites based on a sliding window across the sequences of interests in 5’ to 3’ direction of protein-coding sequences, and have improved the overall performance on sequence analysis for evolution studies. A toolbox, including C++ and Java source code and executable files on both Windows and Linux platforms together with a user instruction, is downloadable from the website for academic purpose at https://sourceforge.net/projects/kakscalculator2/.

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Evolution by gene duplication: an update

Jianzhi Zhang (2003)

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Author and article information

Contributors

Hanwei Yan: hwyanahau@163.com

Xiaogang Dai: xgdai@njfu.com.cn

Kai Feng: fk1qaz@163.com

Qiuyue Ma: yue.870808@163.com

Tongming Yin: tmyin@njfu.com.cn

Journal

Journal ID (nlm-ta): BMC Bioinformatics

Journal ID (iso-abbrev): BMC Bioinformatics

Title: BMC Bioinformatics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2105

Publication date (Electronic): 27 July 2016

Publication date PMC-release: 27 July 2016

Publication date Collection: 2016

Volume: 17

Electronic Location Identifier: 289

Affiliations

[1 ]Key Laboratory of Forest Genetics & Biotechnology, Nanjing Forestry University, Nanjing, China

[2 ]Laboratory of Modern Biotechnology, Anhui Agricultural University, Hefei, China

Article

Publisher ID: 1148

DOI: 10.1186/s12859-016-1148-9

PMC ID: 4964316

PubMed ID: 27465544

SO-VID: 52e5d199-2a91-4e84-9e94-44292d54212f

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 28 November 2015

Date accepted : 13 July 2016

Funding

Funded by: the National Basic Research Project

Award ID: 2012CB114505

Award Recipient : Tongming Yin

Funded by: the Natural Science Foundation of China

Award ID: 31570662

Award Recipient : Tongming Yin

Funded by: the Innovative Research Team of the Educational Department of China

Funded by: the PAPD (Priority Academic Program Development) program at Nanjing Forestry University

Funded by: Anhui provincial Natural Science Foundation

Award ID: 1608085QC65

Award Recipient : Hanwei Yan

Funded by: FundRef http://dx.doi.org/10.13039/501100002858, China postdoctoral science foundation;

Award ID: 2015M581806

Award Recipient : Hanwei Yan

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ScienceOpen disciplines: Bioinformatics & Computational biology

Keywords: intronless genes,database,dicots

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ScienceOpen disciplines: Bioinformatics & Computational biology

Keywords: intronless genes, database, dicots

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IGDD: a database of intronless genes in dicots

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Abstract

Background

Description

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Most cited references 11

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

Evolution by gene duplication: an update

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Cited by 8

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