The chromosome-level rambutan genome reveals a significant role of segmental duplication in the expansion of resistance genes

Zheng, Jie; Meinhardt, Lyndel W.; Goenaga, Ricardo; Matsumoto, Tracie K.; Zhang, Dapeng; Yin, Yanbin

doi:10.1093/hr/uhac014

Cited by 3 publications

(6 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Dovetail Omni-C library was constructed as previously described [ 33 , 34 ]. The library was sequenced on an Illumina HiSeqX platform to produce an approximately 112.2× sequence coverage.…”

Section: Methodsmentioning

confidence: 99%

“…The protein-coding genes were predicted using the approach described in our previous studies [ 33 , 34 ]. The ab initio and homology-based approaches were combined in the MAKER pipeline [ 45 ].…”

Section: Methodsmentioning

confidence: 99%

“…All proteins of the 20 genomes were annotated by using emapper [ 58 ] searching eggNOG database with e-value < 10 −5 . The GO enrichment analysis was performed using the binomial test described in our previous analysis [ 33 , 34 ]. First, the foreground and background datasets were selected for different purposes (See Section 3 ).…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

The American Cherimoya Genome Reveals Insights into the Intra-Specific Divergence, the Evolution of Magnoliales, and a Putative Gene Cluster for Acetogenin Biosynthesis

Li,

Zheng,

Nousias

et al. 2024

Plants

Self Cite

View full text Add to dashboard Cite

Annona cherimola (cherimoya) is a species renowned for its delectable fruit and medicinal properties. In this study, we developed a chromosome-level genome assembly for the cherimoya ‘Booth’ cultivar from the United States. The genome assembly has a size of 794 Mb with a N50 = 97.59 Mb. The seven longest scaffolds account for 87.6% of the total genome length, which corresponds to the seven pseudo-chromosomes. A total of 45,272 protein-coding genes (≥30 aa) were predicted with 92.9% gene content completeness. No recent whole genome duplications were identified by an intra-genome collinearity analysis. Phylogenetic analysis supports that eudicots and magnoliids are more closely related to each other than to monocots. Moreover, the Magnoliales was found to be more closely related to the Laurales than the Piperales. Genome comparison revealed that the ‘Booth’ cultivar has 200 Mb less repeats than the Spanish cultivar ‘Fino de Jete’, despite their highly similar (>99%) genome sequence identity and collinearity. These two cultivars were diverged during the early Pleistocene (1.93 Mya), which suggests a different origin and domestication of the cherimoya. Terpene/terpenoid metabolism functions were found to be enriched in Magnoliales, while TNL (Toll/Interleukin-1-NBS-LRR) disease resistance gene has been lost in Magnoliales during evolution. We have also identified a gene cluster that is potentially responsible for the biosynthesis of acetogenins, a class of natural products found exclusively in Annonaceae. The cherimoya genome provides an invaluable resource for supporting characterization, conservation, and utilization of Annona genetic resources.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

The American Cherimoya Genome Reveals Insights into the Intra-Specific Divergence, the Evolution of Magnoliales, and a Putative Gene Cluster for Acetogenin Biosynthesis

Li,

Zheng,

Nousias

et al. 2024

Plants

Self Cite

View full text Add to dashboard Cite

show abstract

“…The genome sequences of litchi, longan [ 29 ], and rambutan [ 30 ] were accessed. The genome of the seedless litchi as a reference was obtained from a previous study of our group.…”

Section: Methodsmentioning

confidence: 99%

“…The genome of the seedless litchi as a reference was obtained from a previous study of our group. Since all three species of Sapindaceae were fruit-bearing, the genome sequence of grape ( Vitis vinifera ) as the ancient fruit species was employed as a reference [ 29 , 30 ]. As the SUT s of Arabidopsis thaliana were relatively comprehensive, they were selected as a reference to classify all the genes.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of the SUT Family from Three Species of Sapindaceae Revealed Their Role in the Accumulation of Sugars in Fruits

Jiang,

An,

Xia

et al. 2023

Plants

View full text Add to dashboard Cite

Sapindaceae is an economically important family of Sapindales and includes many fruit crops. The dominant transport and storage form of photoassimilates in higher plants is sucrose. Sucrose transporter proteins play an irreplaceable role in the loading, transportation, unloading, and distribution of sucrose. A few SUT (sugar transporter) family genes have been identified and characterized in various plant species. In this study, 15, 15, and 10 genes were identified in litchi, longan, and rambutan, respectively, via genome-wide screening. These genes were divided into four subgroups based on phylogenetics. Gene duplication analysis suggested these genes underwent potent purifying selection and tandem duplications during evolution. The expression levels of SlSut01 and SlSut08 were significantly increased in the fruits of Sapindaceae members. The homologs of these two genes in longan and rambutan were also highly expressed in the fruits. The expression pattern of SUTs in three organs of the two varieties was also explored. Subcellular colocalization experiments revealed that the proteins encoded by both genes were present in the plasma membrane. This report provides data for the functional study of SUTs in litchi and provides a basis for screening sugar accumulation-related genes in fruits of Sapindaceae.

show abstract

Diversification of FT-like genes in the PEBP family contributes to the variation of flowering traits in Sapindaceae species

Huang,

Liu,

et al. 2024

Mol Horticulture

View full text Add to dashboard Cite

Many species of Sapindaceae, such as lychee, longan, and rambutan, provide nutritious and delicious fruit. Understanding the molecular genetic mechanisms that underlie the regulation of flowering is essential for securing flower and fruit productivity. Most endogenous and exogenous flowering cues are integrated into the florigen encoded by FLOWERING LOCUS T. However, the regulatory mechanisms of flowering remain poorly understood in Sapindaceae. Here, we identified 60 phosphatidylethanolamine-binding protein-coding genes from six Sapindaceae plants. Gene duplication events led to the emergence of two or more paralogs of the FT gene that have evolved antagonistic functions in Sapindaceae. Among them, the FT1-like genes are functionally conserved and promote flowering, while the FT2-like genes likely serve as repressors that delay flowering. Importantly, we show here that the natural variation at nucleotide position − 1437 of the lychee FT1 promoter determined the binding affinity of the SVP protein (LcSVP9), which was a negative regulator of flowering, resulting in the differential expression of LcFT1, which in turn affected flowering time in lychee. This finding provides a potential molecular marker for breeding lychee. Taken together, our results reveal some crucial aspects of FT gene family genetics that underlie the regulation of flowering in Sapindaceae.

show abstract

The chromosome-level rambutan genome reveals a significant role of segmental duplication in the expansion of resistance genes

Cited by 3 publications

References 10 publications

The American Cherimoya Genome Reveals Insights into the Intra-Specific Divergence, the Evolution of Magnoliales, and a Putative Gene Cluster for Acetogenin Biosynthesis

The American Cherimoya Genome Reveals Insights into the Intra-Specific Divergence, the Evolution of Magnoliales, and a Putative Gene Cluster for Acetogenin Biosynthesis

Genome-Wide Identification and Expression Analysis of the SUT Family from Three Species of Sapindaceae Revealed Their Role in the Accumulation of Sugars in Fruits

Diversification of FT-like genes in the PEBP family contributes to the variation of flowering traits in Sapindaceae species

Contact Info

Product

Resources

About