The Clausena lansium (Wampee) genome reveal new insights into the carbazole alkaloids biosynthesis pathway

Fan, Yannan; Sahu, Sunil Kumar; Yang, Ting; Mu, Weixue; Wei, Jinpu; Cheng, Lei; Yang, Jing; Liu, Jie; Zhao, Yihe; Lisby, Michael; Liu, Huan

doi:10.1016/j.ygeno.2021.09.007

Cited by 18 publications

(10 citation statements)

References 66 publications

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“…The ultimate genome assembly of ’JinFeng’ was 297.07 Mb in size, with 93.83% of the assembled sequences mapped onto nine pseudochromosomes ( Figure 1B ) with contig and scaffold N50 of 10.2 Mb and 29.2 Mb, separately ( Table 1 ). This demonstrates a notable advancement beyond the previously announced assembly with a contig N50 of 0.039 Mb 11 . The genome integrity was evaluated applying the Benchmarking Universal Single Copy Orthologs (BUSCO) database v5.3.2, revealing a 98.0% completeness for ’JinFeng’ ( Table 1, Table S2 ).…”

Section: Resultsmentioning

confidence: 81%

“…In this research, we provide a high-quality chromosome-scale genome assembly of a wampee, which is the most advanced assembly reported to date. Compared to a previous assembly based on 10× genomics technology 11 , our wampee genome assembly showed substantial improvements, with a longer contig N50 of 10.2 Mb and scaffold N50 of 29.2 Mb. This indicated that long read sequencing (LRS) effectively resolved the highly fragmented contigs and scaffolds present in the previous assembly.…”

Section: Discussionmentioning

confidence: 78%

Section: Discussionmentioning

confidence: 83%

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Wampee chromosome-level reference genome elucidates fruit sugar-acid metabolism

Chen,

Wang,

Wang

et al. 2024

Preprint

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Wampee (Clausena lansium) is an economically significant subtropical fruit tree widely cultivated in Southern China. High-quality genomic resources are unavailable, but they are essential for functional genomics and germplasm enhancement of wampee. Here, we provide a chromosome-level genome sequence for the wampee cultivar JinFeng and a population genomic analysis of 266 accessions. The 297.1 Mb wampee genome, containing nine chromosomes with a scaffold N50 of 29.2 Mb and encoding 23,468 protein-coding genes, showed a significant improvement over the previous version. We dissected the wampee population structure and genetic differentiation in China using population genomic analysis, which detected 110 and 671 genes under a selective sweep associated with sour and sweet wampee evolution in domesticated clones, respectively. Homozygous non-synonymous single nucleotide polymorphisms are likely associated with fruit flavor differentiation. A genome-wide association study identified 220 remarkable marker-trait associations for total acid content, harboring 289 genes encoding transcription factors, transporters, and enzymes involved in sugar and acid metabolism, which are potentially useful for sour and sweet taste development in wampee fruit. Furthermore, the ethylene response factor family gene ClERF061 and the SWEET family gene ClSWEET7 were identified. Linkage assessment between the relative expression levels of ClERF061 or ClSWEET7 and the total acid/total sugar contents implied their potential involvement in sugar-acid metabolism in wampee fruits. High-quality genome resources are valuable for expediting wampee research and genome-assisted breeding.

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Section: Resultsmentioning

confidence: 81%

Section: Discussionmentioning

confidence: 78%

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Wampee chromosome-level reference genome elucidates fruit sugar-acid metabolism

Chen,

Wang,

Wang

et al. 2024

Preprint

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“…Genomics is based on information acquired from the Human Genome Project and other genomes, which resulted in a wealth of information on genes and their role in determining our health. The knowledge gained from these genomes has considerably improved our understanding of nutrition, diversity, and evolution of organisms [ 13 , 14 , 15 , 16 , 17 , 18 ]. The nutrition sciences are developing a relationship with the “omics,” disciplines bolstered by the Genome Project’s recent revelations, and new technical developments are coming at a breakneck pace.…”

Section: Nutrigenomics and Public Healthmentioning

confidence: 99%

Nutrient-Mediated Perception and Signalling in Human Metabolism: A Perspective of Nutrigenomics

Lal

Sharma

Tiwari

et al. 2022

IJMS

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The interaction between selective nutrients and linked genes involving a specific organ reveals the genetic make-up of an individual in response to a particular nutrient. The interaction of genes with food opens opportunities for the addition of bioactive compounds for specific populations comprising identical genotypes. The slight difference in the genetic blueprints of humans is advantageous in determining the effect of nutrients and their metabolism in the body. The basic knowledge of emerging nutrigenomics and nutrigenetics can be applied to optimize health, prevention, and treatment of diseases. In addition, nutrient-mediated pathways detecting the cellular concentration of nutrients such as sugars, amino acids, lipids, and metabolites are integrated and coordinated at the organismal level via hormone signals. This review deals with the interaction of nutrients with various aspects of nutrigenetics and nutrigenomics along with pathways involved in nutrient sensing and regulation, which can provide a detailed understanding of this new leading edge in nutrition research and its potential application to dietetic practice.

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“…Clausena lansium (Lour.) Skeels (wampee) belongs to the genus Clausena in the family Rutaceae , originating from Southern China [ 1 ], and is mainly cultivated in tropical and subtropical regions of the world, such as Southern China, India, Vietnam, and Thailand [ 2 ]. Wampee fruit resembles grapes, with a brown or yellow peel that is usually eaten along with the pulp, and tastes sour and sweet, similar to the flavor of kumquat.…”

Section: Introductionmentioning

confidence: 99%

Free, Conjugated, and Bound Phenolics in Peel and Pulp from Four Wampee Varieties: Relationship between Phenolic Composition and Bio-Activities by Multivariate Analysis

et al. 2022

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Free, conjugated, and bound phenolic fractions of peel and pulp in four wampee varieties from South China were analyzed for their contents, composition, antioxidant capacities, and inhibitory activities against α-glucosidase. We found that there were significant differences in phenolic/flavonoid contents among diverse varieties and different parts (peel and pulp), and the contents were highest in the peel’s bound form. The results of UHPL-Q-Exactive HF-X and HPLC showed that chlorogenic acid, gentisic acid, and rutin were abundantly distributed over the three phenolic fractions in peel and pulp of all wampee samples, while isoquercitrin was the most abundant in the conjugated form of peel/pulp and myricetin had the richest content in the free form of peel/pulp. Wampee peel had stronger antioxidant capacities of ABTS+, DPPH, ·OH, and FRAP than the pulp, and the bound phenolic fraction of the peel/pulp had much higher antioxidant activities than FP and CP fractions. It is interesting that the same phenolic fraction of the wampee peel displayed roughly close IC50 values of α-glucosidase inhibition to those from the pulp samples. The relationship between individual phenolic and TPC/TFC/the bio-activities and the similarity among the free, conjugated, and bound phenolic fractions in peel and pulp samples were explored by using Pearson correlation analysis, principal component analysis, and hierarchical cluster analysis. This work provides a systematic and comprehensive comparison of the three phenolic fractions of diverse wampee varieties and different parts, and a rationale for applying phenolics from wampee fruits.

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The Clausena lansium (Wampee) genome reveal new insights into the carbazole alkaloids biosynthesis pathway

Cited by 18 publications

References 66 publications

Wampee chromosome-level reference genome elucidates fruit sugar-acid metabolism

Wampee chromosome-level reference genome elucidates fruit sugar-acid metabolism

Nutrient-Mediated Perception and Signalling in Human Metabolism: A Perspective of Nutrigenomics

Free, Conjugated, and Bound Phenolics in Peel and Pulp from Four Wampee Varieties: Relationship between Phenolic Composition and Bio-Activities by Multivariate Analysis

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