Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion
Abstract Background Papain-like cysteine proteases (PLCPs), a large group of cysteine proteases structurally related to papain, play important roles in plant development, senescence, and defense responses. Papain, the first cysteine protease whose structure was determined by X-ray crystallography, p...
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doaj-13a4cc525c594df2a50d0e8d628909952020-11-25T01:38:53ZengBMCBMC Genomics1471-21642018-01-0119111210.1186/s12864-017-4394-yPapain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansionJuan Liu0Anupma Sharma1Marie Jamille Niewiara2Ratnesh Singh3Ray Ming4Qingyi Yu5FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education; College of Life Science; Fujian Agriculture and Forestry UniversityTexas A&M AgriLife Research Center at Dallas, Texas A&M University SystemDepartment of Plant Biology, School of Integrative Biology, University of Illinois at Urbana-ChampaignTexas A&M AgriLife Research Center at Dallas, Texas A&M University SystemFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education; College of Life Science; Fujian Agriculture and Forestry UniversityFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education; College of Life Science; Fujian Agriculture and Forestry UniversityAbstract Background Papain-like cysteine proteases (PLCPs), a large group of cysteine proteases structurally related to papain, play important roles in plant development, senescence, and defense responses. Papain, the first cysteine protease whose structure was determined by X-ray crystallography, plays a crucial role in protecting papaya from herbivorous insects. Except the four major PLCPs purified and characterized in papaya latex, the rest of the PLCPs in papaya genome are largely unknown. Results We identified 33 PLCP genes in papaya genome. Phylogenetic analysis clearly separated plant PLCP genes into nine subfamilies. PLCP genes are not equally distributed among the nine subfamilies and the number of PLCPs in each subfamily does not increase or decrease proportionally among the seven selected plant species. Papaya showed clear lineage-specific gene expansion in the subfamily III. Interestingly, all four major PLCPs purified from papaya latex, including papain, chymopapain, glycyl endopeptidase and caricain, were grouped into the lineage-specific expansion branch in the subfamily III. Mapping PLCP genes on chromosomes of five plant species revealed that lineage-specific expansions of PLCP genes were mostly derived from tandem duplications. We estimated divergence time of papaya PLCP genes of subfamily III. The major duplication events leading to lineage-specific expansion of papaya PLCP genes in subfamily III were estimated at 48 MYA, 34 MYA, and 16 MYA. The gene expression patterns of the papaya PLCP genes in different tissues were assessed by transcriptome sequencing and qRT-PCR. Most of the papaya PLCP genes of subfamily III expressed at high levels in leaf and green fruit tissues. Conclusions Tandem duplications played the dominant role in affecting copy number of PLCPs in plants. Significant variations in size of the PLCP subfamilies among species may reflect genetic adaptation of plant species to different environments. The lineage-specific expansion of papaya PLCPs of subfamily III might have been promoted by the continuous reciprocal selective effects of herbivore attack and plant defense.http://link.springer.com/article/10.1186/s12864-017-4394-yCarica papayaPapain-like cysteine proteasesPapaya latexGene duplication |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Juan Liu Anupma Sharma Marie Jamille Niewiara Ratnesh Singh Ray Ming Qingyi Yu |
spellingShingle |
Juan Liu Anupma Sharma Marie Jamille Niewiara Ratnesh Singh Ray Ming Qingyi Yu Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion BMC Genomics Carica papaya Papain-like cysteine proteases Papaya latex Gene duplication |
author_facet |
Juan Liu Anupma Sharma Marie Jamille Niewiara Ratnesh Singh Ray Ming Qingyi Yu |
author_sort |
Juan Liu |
title |
Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion |
title_short |
Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion |
title_full |
Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion |
title_fullStr |
Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion |
title_full_unstemmed |
Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion |
title_sort |
papain-like cysteine proteases in carica papaya: lineage-specific gene duplication and expansion |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2018-01-01 |
description |
Abstract Background Papain-like cysteine proteases (PLCPs), a large group of cysteine proteases structurally related to papain, play important roles in plant development, senescence, and defense responses. Papain, the first cysteine protease whose structure was determined by X-ray crystallography, plays a crucial role in protecting papaya from herbivorous insects. Except the four major PLCPs purified and characterized in papaya latex, the rest of the PLCPs in papaya genome are largely unknown. Results We identified 33 PLCP genes in papaya genome. Phylogenetic analysis clearly separated plant PLCP genes into nine subfamilies. PLCP genes are not equally distributed among the nine subfamilies and the number of PLCPs in each subfamily does not increase or decrease proportionally among the seven selected plant species. Papaya showed clear lineage-specific gene expansion in the subfamily III. Interestingly, all four major PLCPs purified from papaya latex, including papain, chymopapain, glycyl endopeptidase and caricain, were grouped into the lineage-specific expansion branch in the subfamily III. Mapping PLCP genes on chromosomes of five plant species revealed that lineage-specific expansions of PLCP genes were mostly derived from tandem duplications. We estimated divergence time of papaya PLCP genes of subfamily III. The major duplication events leading to lineage-specific expansion of papaya PLCP genes in subfamily III were estimated at 48 MYA, 34 MYA, and 16 MYA. The gene expression patterns of the papaya PLCP genes in different tissues were assessed by transcriptome sequencing and qRT-PCR. Most of the papaya PLCP genes of subfamily III expressed at high levels in leaf and green fruit tissues. Conclusions Tandem duplications played the dominant role in affecting copy number of PLCPs in plants. Significant variations in size of the PLCP subfamilies among species may reflect genetic adaptation of plant species to different environments. The lineage-specific expansion of papaya PLCPs of subfamily III might have been promoted by the continuous reciprocal selective effects of herbivore attack and plant defense. |
topic |
Carica papaya Papain-like cysteine proteases Papaya latex Gene duplication |
url |
http://link.springer.com/article/10.1186/s12864-017-4394-y |
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