LettuceGDB: The community database for lettuce genetics and omics

Guo, Zhonglong; Li, Bo; Du, Jianjun; Shen, Fei; Zhang, Yongxin; Deng, Yang; Kuang, Zhizhou; Tao, Yihan; Wan, Miaomiao; Lu, Xianju; Wang, Dong; Wang, Ying; Han, Yingyan; Wei, Jianhua; Li, Lei; Guo, Xinyu; Zhao, Chunjiang; Yang, Xiaozeng

doi:10.1016/j.xplc.2022.100425

Cited by 20 publications

(12 citation statements)

References 58 publications

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“…Furthermore, it will be relevant to sequence and produce high-quality assemblies of other wild relatives of lettuce, such as L. georgica , L. serriola , and L. aculeata, to obtain an overview of the entire Lactuca gene space ( Wei et al 2021 ; Guo et al 2023 ). Using high-quality genetic resources will enable the construction of a comprehensive pangenome that covers the variation in the genus Lactuca .…”

Section: Resultsmentioning

confidence: 99%

Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding

Xiong,

van Workum,

Berke

et al. 2023

G3: Genes, Genomes, Genetics

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Lettuce (Lactuca sativa L.) is a leafy vegetable crop with ongoing breeding efforts related to quality, resilience, and innovative production systems. To breed resilient and resistant lettuce in the future, valuable genetic variation found in close relatives could be further exploited. Lactuca virosa (2x=2n=18), a wild relative assigned to the tertiary lettuce gene pool, has a much larger genome (3.7 Gbp) than Lactuca sativa (2.5 Gbp). It has been used in interspecific crosses and is a donor to modern crisphead lettuce cultivars. Here, we present a de novo reference assembly of L. virosa with high continuity and complete gene space. This assembly facilitated comparisons to the genome of L. sativa and to that of the wild species L. saligna, a representative of the secondary lettuce gene pool. To assess the diversity in gene content, we classified the genes of the three Lactuca species as core, accessory and unique. In addition, we identified three interspecific chromosomal inversions compared to L. sativa, which each may cause recombination suppression and thus hamper future introgression breeding. Using three-way comparisons in both reference-based and reference-free manners, we show that the proliferation of long-terminal repeat elements has driven the genome expansion of L. virosa. Further, we performed a genome-wide comparison of immune genes, nucleotide-binding leucine-rich repeat, and receptor-like kinases among Lactuca spp. and indicate the evolutionary patterns and mechanisms behind their expansions. These genome analyses greatly facilitate the understanding of genetic variation in L. virosa, which is beneficial for the breeding of improved lettuce varieties.

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Section: Resultsmentioning

confidence: 99%

Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding

Xiong,

van Workum,

Berke

et al. 2023

G3: Genes, Genomes, Genetics

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“…Despite the richness of data type in LettuceDB, concerted efforts are still needed to enhance data sharing and integration. For instance, multi-omics data from 1333 germplasm have been integrated into the Lettuce Genome Database (LettuceGDB) ( https://lettucegdb.com/ ), representing additional data resource ( 22 ). However, because different collections of germplasm were used, it is difficult to directly compare the results between databases.…”

Section: Discussionmentioning

confidence: 99%

“…Leveraging artificial intelligence–based approaches for deep mining of these datasets holds a great promise in providing valuable insights. For instance, more than two thousand papers collected by LettuceGDB provide a valuable literature source ( 22 ), on which using the latest generative language model would potentially provide unprecedented knowledge for the research society.…”

Section: Discussionmentioning

confidence: 99%

LettuceDB: an integrated multi-omics database for cultivated lettuce

Zhou,

Yang,

Zeng

et al. 2024

Database

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Crop genomics has advanced rapidly during the past decade, which generated a great abundance of omics data from multi-omics studies. How to utilize the accumulating data becomes a critical and urgent demand in crop science. As an attempt to integrate multi-omics data, we developed a database, LettuceDB (https://db.cngb.org/lettuce/), aiming to assemble multidimensional data for cultivated and wild lettuce germplasm. The database includes genome, variome, phenome, microbiome and spatial transcriptome. By integrating user-friendly bioinformatics tools, LettuceDB will serve as a one-stop platform for lettuce research and breeding in the future. Database URL: https://db.cngb.org/lettuce/

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“…It is an excellent source of carbohydrates, fiber, essential amino acids, vitamins and other nutrients [10]. As a globally popular leaf vegetable and representative plant of the Asteraceae family, lettuce has great economic importance [11]. Recently, lettuce has attracted more attention and has become one of the main ingredients in the ready-to-eat fresh cut vegetable salad because of its convenience of use, freshness, its healthiness and high nutritional value [12].…”

Section: Introductionmentioning

confidence: 99%

Impact assessment of treated wastewater reuse for irrigation: growth potential and development of lettuce in Al Hoceima province, Morocco

Haj

Zhir²,

Aboulhassan

et al. 2023

E3S Web Conf.

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The reuse of treated wastewater for agricultural practices is becoming increasingly important due to the growing demand for the transition to a circular economy. It has the major advantage of providing an alternative resource to the conventional water used for agricultural irrigation. The main objective of this work is to study, through tests on experimental installations, the effect of the type of irrigation water on the growth and development of lettuce. The types of irrigation water were prepared from purified wastewater, treated wastewater plus fertilizer, conventional water, and conventional water plus fertilizer. The physicochemical analyzes of wastewater from the Imzouren-Bni Bouayach WWTP resulted in different values of the parameters measured (pH, temperature, electrical conductivity, oxygen below, suspended matter, BOD5, COD, nitrate, nitrite and phosphorus) which fall within the limited range of direct discharges and comply with Moroccan standards for the quality of water intended for irrigation. The results of the characterization of the soil showed that it is a basic soil (pH= 8.5), unsalted (electrical conductivity = 2.43 ms/cm) and poor in organic and nutrient elements (Carbon 0.8%, organic matter 1.46%, nitrogen 0.06 mg/l, phosphorus 10.5 mg/l, potassium 56.4 mg/l.) The main results of the plant analysis show that the production level of this study crop irrigated with conventional water is similar to that of this study crop irrigated with treated wastewater. In other words, irrigation with treated wastewater allows lettuce to guarantee irrigated production at least at the level of conventional water. Another motivated addition of nitrogen, phosphate and potash mineral supplement in the treated wastewater improves the production potential of lettuce.

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LettuceGDB: The community database for lettuce genetics and omics

Cited by 20 publications

References 58 publications

Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding

Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding

LettuceDB: an integrated multi-omics database for cultivated lettuce

Impact assessment of treated wastewater reuse for irrigation: growth potential and development of lettuce in Al Hoceima province, Morocco

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