Comparative transcriptome analysis of oil palm flowers reveals an EAR-motif-containing R2R3-MYB that modulates phenylpropene biosynthesis

Li, Ran; Reddy, Vaishnavi Amarr; Jin, Jingjing; Rajan, Chakaravarthy; Wang, Qian; Yue, Gen Hua; Lim, Chin Huat; Chua, Nam‐Hai; Ye, Jian; Sarojam, Rajani

doi:10.1186/s12870-017-1174-4

Cited by 11 publications

(6 citation statements)

References 73 publications

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“…Clustering analysis of the R2R3-MYB gene family in A. thaliana revealed that the R2R3-MYB genes could be divided into 25 subfamilies ( Matus, Aquea & Arce-Johnson, 2009 ; Stracke, Werber & Weisshaar, 2001 ). Of all these subfamilies, the S4 subfamily was involved in the synthesis of various alkenes in Oil palm ( Li et al, 2017a ; Li et al, 2017b ). The S6 subfamily was proved to be closely related to the synthesis of carotenoids and anthocyanins ( Li et al, 2017a ; Li et al, 2017b ).…”

Section: Introductionmentioning

confidence: 99%

“…Of all these subfamilies, the S4 subfamily was involved in the synthesis of various alkenes in Oil palm ( Li et al, 2017a ; Li et al, 2017b ). The S6 subfamily was proved to be closely related to the synthesis of carotenoids and anthocyanins ( Li et al, 2017a ; Li et al, 2017b ). The S7 subfamily was demonstrated to play a regulatory role in the terpenoid synthesis pathway in A. thaliana and M. spicata ( Reddy et al, 2017 ; Stracke et al, 2007 ).…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and expression analyses of R2R3-MYB transcription factor genes from two Orchid species

Fan

Cui

et al. 2020

PeerJ

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MYB transcription factors play important roles in different plant biological processes during plant growth, development and stress response. In this study, 101 (DoMYB1-101) and 99 (PaMYB1-99) R2R3-MYB genes were identified in the genomes of Dendrobium officinale and Phalaenopsis aphrodite, respectively. To classify the isolated candidate genes, the R2R3-MYB genes from A. thaliana were selected as references. As a result, all identified DoMYB and PaMYB genes were classified into 22 subfamilies. Phylogenetic analysis revealed that S21 had the largest number of members of all the subfamilies. The numbers of introns, exons and conserved sequences in all of the identified genes are different. In addition, 20 DoMYB genes from six subfamilies were selected for further analysis of tissue-specific expression and responses to various abiotic stresses treatments. The results showed that all of the DoMYB genes in S4 and S19 subfamilies exhibited the highest relative expression levels in flowers. And five DoMYB genes including DoMYB31, DoMYB40, DoMYB49, DoMYB52 and DoMYB54, responded to the stress response. These results may provide useful information for further studies of the R2R3-MYB gene family.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and expression analyses of R2R3-MYB transcription factor genes from two Orchid species

Fan

Cui

et al. 2020

PeerJ

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“…Lack of seeds due to the lack of endogenous hormones as a result of the expression change of the gene involved in the post-transcriptional products of the genes reduces the development of ovaries (Li et al, 2017) leads to small dates without seeds with low-quality features, also known as "Shees" (Khalil et al, 2021). Abd-Alaal et al…”

Section: Resultsmentioning

confidence: 99%

Effect of Pollen Treatments on Fruit Yield and Gene Expression in Offshoot and Tissue Culture Date Palms (Phoenix dactylifera L. cv. Barhi)

Alavipour,

Moallemi,

Khaleghi

et al. 2023

Preprint

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The low performance of date palm cv. Barhi resulting from tissue culturing is one of the main challenges in the production of these plants. On the other hand, the final yield of the plant depends on various metabolic and biochemical factors which are caused by gene expression. The plant reacts to environmental factors to survive in different growth and environmental conditions through gene expression. This experiment was conducted to investigate the relationship between the expression of certain genes before and up to two weeks after pollination with the yield of off-shoot and tissue culture of Phoenix dactylifera L. cv. Barhi (10-year-old). Off-shoot and tissue-culture date palms were pollinated with Red Ghanami pollen, Green Ghanami pollen, and Green Ghanami + Red Ghanami pollen (50:50) based on a factorial design in randomized complete blocks with three replications. To this end, the relative expression levels of Histone acetyltransferase HAC1-like (LOC103717600) (HAC 1), Arginine N-methyltransferase 6.1 (LOC103716582) (ANM), TIME FOR COFFEE-like (LOC103716450) (TFC), Homeobox-leucine zipper protein HOX9-like (LOC103703962) (HOX 9), MADS-box transcription factor 2-like (LOC103702602) (GLO 1), and MADS-box transcription factor 16 (LOC103701267) (DEF 1) genes were examined using qRT-PCR method in 3 times: (1) Before pollination, (2) 1 week after pollination, and (3) 2 weeks after pollination. The fruit yield was measured at 180 days after pollination (the end of the experiment). The results showed that the tissue culture palms had lower yield but higher relative genes expression in all pollen treatments compared to off-shoot palms. Off-shoot date palm pollinated with Red Ghanami pollen (5.93 tons/ha) showed the highest yield while the lowest yield was recorded in tissue culture date palm pollinated with Green Ghanami pollen (2.09 tons/ha). The relative expression of the six studied genes significantly increased in all treatments two weeks after pollination. Two weeks after all investigated treatments, the GLO gene had the highest expression, while the HAC gene showed the lowest relative expression. The relationship between the yield and the genes expression in the three studied times showed that the HOX gene had no considerable effect on flowering and yield. The ANM and TFC genes expression before pollination exhibited a positive relationship, whereas the expression of HAC, DEF, and GLO genes had a negative relationship with 1 week after pollination. Two weeks after pollination, the expression of the ANM gene revealed a significant positive relationship with the final yield of the date palm. Moreover, the correlation results showed the prominent role of the genes in different stages of growth and yield of date palms by influencing the expression of each other. In general, it is possible to improve the yield of the tissue culture date palm by affecting the expression of the genes in specific stages based on their function.

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“…To compare the expression patterns of homologous genes, RNA sequencing reads of various organs from oil palm in our previous studies [31, 68, 69] and from date palm [70] were reanalyzed. Raw reads were cleaned with process_shortreads in Stacks package with default parameters, to remove adaptors and low-quality reads.…”

Section: Methodsmentioning

confidence: 99%

Chromosome-level Reference Genome Provides Insights into Divergence and Stress Adaptation of the African Oil Palm

Wang

Lee

Wan

et al. 2022

Preprint

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The palm family (Arecaceae), consisting of ∼ 2600 species, is the third most economically important family of plants. The African oil palm (Elaeis guineensis) is one of the most important palms. However, the genome sequences of palms available are still limited and fragmented. Here, we report a high-quality chromosome-level reference genome of an oil palm Dura. The genome of 1.7 Gb was assembled by integrating long reads with ∼ 150 × genome coverage. The assembled genome covered 94.5% of the estimated genome size, within which 91.6% were assigned into 16 pseudochromosomes and 73.7% were repetitive sequences. Relying on the conserved synteny with oil palm, the existing draft genome sequences of both date palm and coconut were further assembled into chromosomal level. Transposon burst, particularly long terminal repeat retrotransposons (LTRs) retrotransposons, following the last whole-genome duplication (WGD), likely explains genome size variation across palms. Convergent evolution of fruit colors tends to eliminate the roles of the virescens gene in controlling accumulation of anthocyanins in exocarp of ripe fruit of palms. Recent duplications of high tandemly repeated pathogenesis-related proteins (PRs) from the same tandem arrays played an important role in defense responses to Ganoderma. Whole genome re-sequencing of both ancestral African and introduced oil palms in Southeast Asia revealed that genes under putative selection were notably associated with stress responses, suggesting adaptation to stresses in the new habitat. The genomic resources and insights gained in this study could be exploited for accelerating genetic improvement and understanding the evolution of palms.

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Comparative transcriptome analysis of oil palm flowers reveals an EAR-motif-containing R2R3-MYB that modulates phenylpropene biosynthesis

Cited by 11 publications

References 73 publications

Genome-wide identification and expression analyses of R2R3-MYB transcription factor genes from two Orchid species

Genome-wide identification and expression analyses of R2R3-MYB transcription factor genes from two Orchid species

Effect of Pollen Treatments on Fruit Yield and Gene Expression in Offshoot and Tissue Culture Date Palms (Phoenix dactylifera L. cv. Barhi)

Chromosome-level Reference Genome Provides Insights into Divergence and Stress Adaptation of the African Oil Palm

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