A Complete Sequence and Transcriptomic Analyses of Date Palm (Phoenix dactylifera L.) Mitochondrial Genome

Fang, Yuxiao; Wu, Hao; Zhang, Tongwu; Yang, Meng; Yin, Yuxin; Pan, Li-Long; Yu, Xiongbin; Zhang, Xiaowei; Hu, Songnian; Al-Mssallem, Ibrahim S.; Yu, Jun

doi:10.1371/journal.pone.0037164

Cited by 112 publications

(94 citation statements)

References 69 publications

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“…It is only recently that the genome of date palm has been sequenced [33–35] alongside the mitochondrial [36] and chloroplastic [37] genomes, with the latter two revealing intra- and inter-varietal variations in the genome sequences. These variations could be useful in understanding cultivar differences in stress tolerance.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide expression profiling in leaves and roots of date palm (Phoenix dactylifera L.) exposed to salinity

et al. 2017

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BackgroundDate palm, as one of the most important fruit crops in North African and West Asian countries including Oman, is facing serious growth problems due to salinity, arising from persistent use of saline water for irrigation. Although date palm is a relatively salt-tolerant plant species, its adaptive mechanisms to salt stress are largely unknown.ResultsIn order to get an insight into molecular mechanisms of salt tolerance, RNA was profiled in leaves and roots of date palm seedlings subjected to NaCl for 10 days. Under salt stress, photosynthetic parameters were differentially affected; all gas exchange parameters were decreased but the quantum yield of PSII was unaffected while non-photochemical quenching was increased. Analyses of gene expression profiles revealed 2630 and 4687 genes were differentially expressed in leaves and roots, respectively, under salt stress. Of these, 194 genes were identified as commonly responding in both the tissue sources. Gene ontology (GO) analysis in leaves revealed enrichment of transcripts involved in metabolic pathways including photosynthesis, sucrose and starch metabolism, and oxidative phosphorylation, while in roots genes involved in membrane transport, phenylpropanoid biosynthesis, purine, thiamine, and tryptophan metabolism, and casparian strip development were enriched. Differentially expressed genes (DEGs) common to both tissues included the auxin responsive gene, GH3, a putative potassium transporter 8 and vacuolar membrane proton pump.ConclusionsLeaf and root tissues respond differentially to salinity stress and this study has revealed genes and pathways that are associated with responses to elevated NaCl levels and thus may play important roles in salt tolerance providing a foundation for functional characterization of salt stress-responsive genes in the date palm.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3633-6) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Genome-wide expression profiling in leaves and roots of date palm (Phoenix dactylifera L.) exposed to salinity

et al. 2017

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“…Another is a comparative transcriptomic study on mesocarps of both oil and date palms based on pyrosequencing data from the Roche GS FLX Titanium platform7. Our effort on P. dactylifera genomics was launched in August 2008 and has delivered full-genome assemblies of its two organelles (158,462 and 715,001 bp for plastid8 and mitochondrion9, respectively). We also constructed transcriptomic profiles for fruit development based on pyrosequencing data10.…”

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confidence: 99%

Genome sequence of the date palm Phoenix dactylifera L

et al. 2013

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Date palm (Phoenix dactylifera L.) is a cultivated woody plant species with agricultural and economic importance. Here we report a genome assembly for an elite variety (Khalas), which is 605.4 Mb in size and covers >90% of the genome (~671 Mb) and >96% of its genes (~41,660 genes). Genomic sequence analysis demonstrates that P. dactylifera experienced a clear genome-wide duplication after either ancient whole genome duplications or massive segmental duplications. Genetic diversity analysis indicates that its stress resistance and sugar metabolism-related genes tend to be enriched in the chromosomal regions where the density of single-nucleotide polymorphisms is relatively low. Using transcriptomic data, we also illustrate the date palm’s unique sugar metabolism that underlies fruit development and ripening. Our large-scale genomic and transcriptomic data pave the way for further genomic studies not only on P. dactylifera but also other Arecaceae plants.

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“…Notably, some evidence suggests that at least in some cases, natural selection may have played a key role in shaping the evolution of syntenic gene clusters. Specifically, some syntenic clusters are co-transcribed, such as rrn5-rrn18, rps3-rpl16 and nad3-rps12 in rice and palm, among others (Nakazono et al, 1995;Fang et al, 2012). While the origin of these syntenic co-transcribed gene clusters is unclear, they appear to be distributed consistently throughout plant taxonomic groups .…”

Section: Gene Loss and Collinearitymentioning

confidence: 99%