The Class III Peroxidase (POD) Gene Family in Cassava: Identification, Phylogeny, Duplication, and Expression

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Abstract

The class III peroxidase (POD) enzymes participate in plant development, hormone signaling, and stress responses. However, little is known about the POD family in cassava. Here, we identified 91 cassava POD genes ( MePODs) and classified them into six subgroups using phylogenetic analysis. Conserved motif analysis demonstrated that all MePOD proteins have typical peroxidase domains, and gene structure analysis showed that MePOD genes have between one and nine exons. Duplication pattern analysis suggests that tandem duplication has played a role in MePOD gene expansion. Comprehensive transcriptomic analysis revealed that MePOD genes in cassava are involved in the drought response and postharvest physiological deterioration. Several MePODs underwent transcriptional changes after various stresses and related signaling treatments were applied. In sum, we characterized the POD family in cassava and uncovered the transcriptional control of POD genes in response to various stresses and postharvest physiological deterioration conditions. These results can be used to identify potential target genes for improving the stress tolerance of cassava crops.

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Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition.

Michael Freeling (2009)

Each mode of gene duplication (tandem, tetraploid, segmental, transpositional) retains genes in a biased manner. A reciprocal relationship exists between plant genes retained postpaleotetraploidy versus genes retained after an ancient tandem duplication. Among the models (C, neofunctionalization, balanced gene drive) and ideas that might explain this relationship, only balanced gene drive predicts reciprocity. The gene balance hypothesis explains that more "connected" genes--by protein-protein interactions in a heteromer, for example--are less likely to be retained as a tandem or transposed duplicate and are more likely to be retained postpaleotetraploidy; otherwise, selectively negative dosage effects are created. Biased duplicate retention is an instant and neutral by-product, a spandrel, of purifying selection. Balanced gene drive expanded plant gene families, including those encoding proteasomal proteins, protein kinases, motors, and transcription factors, with each paleotetraploidy, which could explain trends involving complexity. Balanced gene drive is a saltation mechanism in the mutationist tradition.

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CDD: specific functional annotation with the Conserved Domain Database

Aron Marchler-Bauer, John B. Anderson, Farideh Chitsaz … (2009)

NCBI's Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. The collection can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml, and is also part of NCBI's Entrez query and retrieval system, cross-linked to numerous other resources. CDD provides annotation of domain footprints and conserved functional sites on protein sequences. Precalculated domain annotation can be retrieved for protein sequences tracked in NCBI's Entrez system, and CDD's collection of models can be queried with novel protein sequences via the CD-Search service at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. Starting with the latest version of CDD, v2.14, information from redundant and homologous domain models is summarized at a superfamily level, and domain annotation on proteins is flagged as either ‘specific’ (identifying molecular function with high confidence) or as ‘non-specific’ (identifying superfamily membership only).

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SMART 4.0: towards genomic data integration.

Ivica Letunic, Richard Copley, Steffen Schmidt … (2004)

SMART (Simple Modular Architecture Research Tool) is a web tool (http://smart.embl.de/) for the identification and annotation of protein domains, and provides a platform for the comparative study of complex domain architectures in genes and proteins. The January 2004 release of SMART contains 685 protein domains. New developments in SMART are centred on the integration of data from completed metazoan genomes. SMART now uses predicted proteins from complete genomes in its source sequence databases, and integrates these with predictions of orthology. New visualization tools have been developed to allow analysis of gene intron-exon structure within the context of protein domain structure, and to align these displays to provide schematic comparisons of orthologous genes, or multiple transcripts from the same gene. Other improvements include the ability to query SMART by Gene Ontology terms, improved structure database searching and batch retrieval of multiple entries.

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Author and article information

Journal

Journal ID (nlm-ta): Int J Mol Sci

Journal ID (iso-abbrev): Int J Mol Sci

Journal ID (publisher-id): ijms

Title: International Journal of Molecular Sciences

Publisher: MDPI

ISSN (Electronic): 1422-0067

Publication date (Electronic): 03 June 2019

Publication date Collection: June 2019

Volume: 20

Issue: 11

Electronic Location Identifier: 2730

Affiliations

[1 ]Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; wuchunlai19900109@ 123456126.com (C.W.); dingxupo@ 123456itbb.org.cn (X.D.); dingzehong@ 123456itbb.org.cn (Z.D.); tieweiwei@ 123456itbb.org.cn (W.T.); yanyan@ 123456itbb.org.cn (Y.Y.)

[2 ]The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China

[3 ]Beijing Commerce and Trade School, Beijing 100162, China; wangyu7071@ 123456126.com

[4 ]National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China

Author notes

[* ]Correspondence: YangHai@ 123456hust.edu.cn (H.Y.); huwei2013@ 123456itbb.org.cn (W.H.)

[†]

These authors contributed equally to this work.

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Xupo Ding https://orcid.org/0000-0001-9195-7112

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Publisher ID: ijms-20-02730

DOI: 10.3390/ijms20112730

PMC ID: 6600411

PubMed ID: 31163686

SO-VID: 689b3590-28b8-4aef-8810-7ad30a931025

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Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

The Class III Peroxidase (POD) Gene Family in Cassava: Identification, Phylogeny, Duplication, and Expression

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Stress signalling in stem cells

Most cited references 59

Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition.

CDD: specific functional annotation with the Conserved Domain Database

SMART 4.0: towards genomic data integration.

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