Genome-wide identification and expression profiling of the carotenoid cleavage dioxygenase (CCD) gene family in Brassica napus L

Zhou, Xin-Tong; Jia, Longfei; Duan, Mouzheng; Chen, Xue; Qiao, Cailin; Ma, Jinqi; Zhang, Chao; Jing, Fuyu; Zhang, Shengsen; Yang, Bo; Zhang, Liyuan; Li, Jiana

doi:10.1371/journal.pone.0238179

Cited by 15 publications

(12 citation statements)

References 72 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Among the identified CBP, XBP, and ABP genes, none of these genes have a transmembrane region. Similar results were obtained in higher plants, such as Musa acuminata [ 64 ], Brassica napus [ 65 ], N. officinale (unpublished data), Triticum aestivum [ 24 ], and green algae Tetraselmis suecica [ 21 ], which do not possess any transmembrane regions in their CBP genes.…”

Section: Resultssupporting

confidence: 73%

Molecular Characterization, Expression Analysis of Carotenoid, Xanthophyll, Apocarotenoid Pathway Genes, and Carotenoid and Xanthophyll Accumulation in Chelidonium majus L.

Sathasivam

Yeo

Park

et al. 2021

Plants

View full text Add to dashboard Cite

Chelidonium majus L. is a perennial herbaceous plant that has various medicinal properties. However, the genomic information about its carotenoid biosynthesis pathway (CBP), xanthophyll biosynthesis pathway (XBP), and apocarotenoid biosynthesis pathway (ABP) genes were limited. Thus, the CBP, XBP, and ABP genes of C. majus were identified and analyzed. Among the 15 carotenoid pathway genes identified, 11 full and 4 partial open reading frames were determined. Phylogenetic analysis of these gene sequences showed higher similarity with higher plants. Through 3D structural analysis and multiple alignments, several distinct conserved motifs were identified, including dinucleotide binding motif, carotene binding motif, and aspartate or glutamate residues. Quantitative RT-PCR showed that CBP, XBP, and ABP genes were expressed in a tissue-specific manner; the highest expression levels were achieved in flowers, followed by those in leaves, roots, and stems. The HPLC analysis of the different organs showed the presence of eight different carotenoids. The highest total carotenoid content was found in leaves, followed by that in flowers, stems, and roots. This study provides information on the molecular mechanisms involved in CBP, XBP, and ABP genes, which might help optimize the carotenoid production in C. majus. The results could also be a basis of further studies on the molecular genetics and functional analysis of CBP, XBP, and ABP genes.

show abstract

Section: Resultssupporting

confidence: 73%

Molecular Characterization, Expression Analysis of Carotenoid, Xanthophyll, Apocarotenoid Pathway Genes, and Carotenoid and Xanthophyll Accumulation in Chelidonium majus L.

Sathasivam

Yeo

Park

et al. 2021

Plants

View full text Add to dashboard Cite

show abstract

“…majus . Similarly, some CBP genes in the higher plants such as Banana ( MaPSY1 and MaPSY3 ), wheat ( TaPSY3 ), and Brassica napus ( BnCCD ) also do not possess any transmembrane region. − Homology analysis using CDD showed that the CBP amino acid sequences had high similarity with other higher plant species, including the sequences of amino acids 66–407 for NoPSY , 4–564 for NoPDS , 1–137 for NoCrtISO , 56–501 for NoLCYB , 1–526 for NoLCYE , 1–303 for NoCHXB , 1–249 for NoZEP , 1–170 for NoCCD , 5–527 for NoNCED , 34–225 for NoCHXE-p , and 11–318 for NoZDS-p . In green algae, Dunaliella salina homology analysis of CBP genes by CCD showed high homology with other microalgae and higher plants. ,, From these results, it can be inferred that N.…”

Section: Results and Discussionmentioning

confidence: 99%

Identification, Characterization, and Expression Analysis of Carotenoid Biosynthesis Genes and Carotenoid Accumulation in Watercress (Nasturtium officinale R. Br.)

et al. 2021

View full text Add to dashboard Cite

Watercress ( Nasturtium officinale R. Br.) is an important aquatic herb species belonging to the Brassicaceae family. It has various medicinal properties and has been utilized for the treatment of cancer and other diseases; however, currently available genomic information regarding this species is limited. Here, we performed the first comprehensive analysis of the carotenoid biosynthesis pathway (CBP) genes of N. officinale , which were identified from next-generation sequencing data. We identified and characterized 11 putative carotenoid pathway genes; among these, nine full and two partial open reading frames were determined. These genes were closely related to CBP genes of the other higher plants in the phylogenetic tree. Three-dimensional structure analysis and multiple alignments revealed several distinct conserved motifs, including aspartate or glutamate residues, carotene-binding motifs, and dinucleotide-binding motifs. Quantitative reverse transcription-polymerase chain reaction results showed that the CBP was expressed in a tissue-specific manner: expression levels of NoPSY , NoPDS , NoZDS-p , NoCrtISO , NoLCYE , NoCHXE-p , and NoCCD were highest in the flower, whereas NoLCYB , NoCHXB , NoZEP , and NoNCED were highest in the leaves. Stems, roots, and seeds did not show a significant change in the expression compared to the leaves and flowers. High-performance liquid chromatography analysis of the same organs showed the presence of seven distinct carotenoid compounds. The total carotenoid content was highest in the leaves followed by flowers, seeds, stems, and roots. Among the seven individual carotenoids, the levels of six carotenoids (i.e., 13-Z-β-carotene, 9-Z-β-carotene, E-β-carotene, lutein, violaxanthin, and β-cryptoxanthin) were highest in the leaves. The highest content was observed for lutein, followed by E-β-carotene, and 9-Z-β-carotene; these carotenoids were much higher in the leaves compared to the other organs. The results will be useful references for further molecular genetics and functional studies involving this species and other closely related species.

show abstract

“…In the present study, 10, 9, 9, 13, 8, and 8 CCDs protein sequences were identified in watermelon, melon, cucumber, pumpkin, bottle gourd, and wax gourd, respectively ( Table 1 ). A total of 30, 19, 7, and 11 CCDs protein sequences were identified in oilseed rape [ 34 ], tobacco [ 1 ], tomato [ 11 ], and pepper [ 12 ], respectively. Molecular characteristics of all CCDs protein members of Cucurbitaceae are different, and proteins in the same clade showed different molecular weights and isoelectric points.…”

Section: Discussionmentioning

confidence: 99%

“…The CCD gene family is an ancient gene family in plants that plays a vital role in plant growth and stress response [ 34 ]. CCDs proteins are implicated in the production of various hormones and aromatic substances in plants [ 37 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification of CCD Gene Family in Six Cucurbitaceae Species and Its Expression Profiles in Melon

Cheng

Wang

et al. 2022

Genes

View full text Add to dashboard Cite

The carotenoid cleavage dioxygenase (CCD) gene family in plants comprises two subfamilies: CCD and 9-cis-epoxycarotenoid dioxygenase (NCED). Genes in the NCED subfamily are mainly involved in plant responses to abiotic stresses such as salt, low temperature, and drought. Members of the NCED subfamily are the most important rate-limiting enzymes in the biosynthesis of abscisic acid (ABA). In the present study, genome-wide analysis was performed to identify CCD gene members in six Cucurbitaceae species, including watermelon (Citrullus lanatus), melon (Cucumis melo), cucumber (C.sativus), pumpkin (Cucurbita moschata), bottle gourd (Lagenaria siceraria), and wax gourd (Benincasa hispida). A total of 10, 9, 9, 13, 8, 8 CCD genes were identified in the six species, respectively, and these genes were unevenly distributed in different chromosomes. Phylogenetic analysis showed that CCD genes of the six species clustered into two subfamilies: CCD and NCED, with five and three independent clades, respectively. The number of exons ranged from 1 to 15, and the number of motifs were set to 15 at most. The cis-acting elements analysis showed that a lot of the cis-acting elements were implicated in stress and hormone response. Melon seedlings were treated with salt, low temperature, drought, and ABA, and then tissue-specific analysis of CCDs expression were performed on the root, stem, upper leaf, middle leaf, female flower, male flower, and tendril of melon. The results showed that genes in CCD family exhibited various expression patterns. Different CCD genes of melon showed different degrees of response to abiotic stress. This study presents a comprehensive analysis of CCD gene family in six species of Cucurbitaceae, providing a strong foundation for future studies on specific genes in this family.

show abstract

Genome-wide identification and expression profiling of the carotenoid cleavage dioxygenase (CCD) gene family in Brassica napus L

Cited by 15 publications

References 72 publications

Molecular Characterization, Expression Analysis of Carotenoid, Xanthophyll, Apocarotenoid Pathway Genes, and Carotenoid and Xanthophyll Accumulation in Chelidonium majus L.

Molecular Characterization, Expression Analysis of Carotenoid, Xanthophyll, Apocarotenoid Pathway Genes, and Carotenoid and Xanthophyll Accumulation in Chelidonium majus L.

Identification, Characterization, and Expression Analysis of Carotenoid Biosynthesis Genes and Carotenoid Accumulation in Watercress (Nasturtium officinale R. Br.)

Genome-Wide Identification of CCD Gene Family in Six Cucurbitaceae Species and Its Expression Profiles in Melon

Contact Info

Product

Resources

About