Construction and characterization of a bacterial artificial chromosome library for Gossypium mustelinum

Liu, Yuling; Zhang, Baohong; Wen, Xinpeng; Zhang, Shulin; Wei, Yangyang; Lú, Quánwěi; Liu, Zhen; Wang, Kunbo; Liu, Fang; Peng, Renhai

doi:10.1371/journal.pone.0196847

Cited by 3 publications

(2 citation statements)

References 29 publications

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“…After fragmentation and purification, the desired size of fragmented DNAs can be separated by multi-rounds PFGE. The size-selected fragments were end-repaired and ligated to the digested and dephosphorylated vector, such as cosmid, fosmid, BAC, or PAC ( Table 1) (Liu et al, 2018;Tu et al, 2018;Clos and Zander-Dinse, 2019). Total ligation products can be transformed into E. coli or packaged into a phage for infecting bacteria.…”

Section: Cloning Strategiesmentioning

confidence: 99%

Bioprospecting Through Cloning of Whole Natural Product Biosynthetic Gene Clusters

Lin

Nielsen

Liu

2020

Front. Bioeng. Biotechnol.

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Since the discovery of penicillin, natural products and their derivatives have been a valuable resource for drug discovery. With recent development of genome mining approaches in the post-genome era, a great number of natural product biosynthetic gene clusters (BGCs) have been identified and these can potentially be exploited for the discovery of novel natural products that can find application as pharmaceuticals. Since many BGCs are silent or do not express in native hosts under laboratory conditions, heterologous expression of BGCs in genetically tractable hosts becomes an attractive route to activate these BGCs to discover the corresponding products. Here, we highlight recent achievements in cloning and discovery of natural product biosynthetic pathways via intact BGC capturing, and discuss the prospects of high-throughput and multiplexed cloning of rational-designed gene clusters in the future.

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Section: Cloning Strategiesmentioning

confidence: 99%

Bioprospecting Through Cloning of Whole Natural Product Biosynthetic Gene Clusters

Lin

Nielsen

Liu

2020

Front. Bioeng. Biotechnol.

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“…Duplicated homologs are often observed in different subgenomes, which leads to difficulties in the isolation of subgenome-specific sequences or gene variations related to phenotypic trait variations. In particular, when certain genomic information is missing in a reference genome, bacterial artificial chromosome (BAC) libraries carrying large insert genomic DNA can be an effective tool for map-based gene cloning and characterization of target genomic regions in polyploids ( Klymiuk et al, 2018 ; Liu et al, 2018 ). Because of the complexity of the octoploid strawberry genome, the recent construction of high-quality subgenome-specific reference sequences significantly facilitates identification of quantitative trait loci (QTL) and development of DNA markers tightly linked to agronomical important traits.…”

Section: Introductionmentioning

confidence: 99%

Genomic Characterization of the Fruity Aroma Gene, FaFAD1, Reveals a Gene Dosage Effect on γ-Decalactone Production in Strawberry (Fragaria × ananassa)

Barbey

Chandra

et al. 2021

Front. Plant Sci.

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Strawberries produce numerous volatile compounds that contribute to the unique flavors of fruits. Among the many volatiles, γ-decalactone (γ-D) has the greatest contribution to the characteristic fruity aroma in strawberry fruit. The presence or absence of γ-D is controlled by a single locus, FaFAD1. However, this locus has not yet been systematically characterized in the octoploid strawberry genome. It has also been reported that the volatile content greatly varies among the strawberry varieties possessing FaFAD1, suggesting that another genetic factor could be responsible for the different levels of γ-D in fruit. In this study, we explored the genomic structure of FaFAD1 and determined the allele dosage of FaFAD1 that regulates variations of γ-D production in cultivated octoploid strawberry. The genome-wide association studies confirmed the major locus FaFAD1 that regulates the γ-D production in cultivated strawberry. With the hybrid capture-based next-generation sequencing analysis, a major presence–absence variation of FaFAD1 was discovered among γ-D producers and non-producers. To explore the genomic structure of FaFAD1 in the octoploid strawberry, three bacterial artificial chromosome (BAC) libraries were developed. A deletion of 8,262 bp was consistently found in the FaFAD1 region of γ-D non-producing varieties. With the newly developed InDel-based codominant marker genotyping, along with γ-D metabolite profiling data, we revealed the impact of gene dosage effect for the production of γ-D in the octoploid strawberry varieties. Altogether, this study provides systematic information of the prominent role of FaFAD1 presence and absence polymorphism in producing γ-D and proposes that both alleles of FaFAD1 are required to produce the highest content of fruity aroma in strawberry fruit.

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L-Glutamate Regulates Npy via the mGluR4-Ca2+-ERK1/2 Signaling Pathway in Mandarin Fish (Siniperca chuatsi)

Duan,

Wang,

et al. 2024

IJMS

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Metabotropic glutamate receptor 4 (mGluR4) is widely regarded as an umami receptor activated by L-glutamate to exert essential functions. Numerous studies have shown that umami receptors participate in food intake regulation. However, little is known about mGluR4’s role in mediating food ingestion and its possible molecular mechanism. Mandarin fish, a typical carnivorous fish, is sensitive to umami substances and is a promising vertebrate model organism for studying the umami receptor. In this study, we identified the mGluR4 gene and conducted evolutionary analyses from diverse fish species with different feeding habits. mGluR4 of mandarin fish was cloned and functionally expressed to investigate the effects of L-glutamate on mGluR4. We further explored whether the signal pathway mGluR4-Ca2+-ERK1/2 participates in the process in mandarin fish brain cells. The results suggest that L-glutamate could regulate Neuropeptide Y (Npy) via the mGluR4-Ca2+-ERK1/2 signaling pathway in mandarin fish. Our findings unveil the role of mGluR4 in feeding decisions and its possible molecular mechanisms in carnivorous fishes.

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Construction and characterization of a bacterial artificial chromosome library for Gossypium mustelinum

Cited by 3 publications

References 29 publications

Bioprospecting Through Cloning of Whole Natural Product Biosynthetic Gene Clusters

Bioprospecting Through Cloning of Whole Natural Product Biosynthetic Gene Clusters

Genomic Characterization of the Fruity Aroma Gene, FaFAD1, Reveals a Gene Dosage Effect on γ-Decalactone Production in Strawberry (Fragaria × ananassa)

L-Glutamate Regulates Npy via the mGluR4-Ca2+-ERK1/2 Signaling Pathway in Mandarin Fish (Siniperca chuatsi)

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