PlantGF: an analysis and annotation platform for plant gene families

Li, Jiaxuan; Yang, Shuai; Yang, Xiaojie; Wu, Hui; Tang, Heng; Yang, Long

doi:10.1093/database/baab088

Cited by 5 publications

(6 citation statements)

References 42 publications

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“…A plant gene family refers to a group of genes with related functions that are generated by gene duplication from a single-copy gene source in an ancestor, and retain similar sequence and structure ( Li et al, 2022 ). Gene families can be associated with repeated events, such as tandem replication, fragment replication, WGD, or transposable replication, based on the scope of replication, size of the replicated region, and influence of transposons ( Airoldi and Davies, 2012 ; Su et al, 2021 ).…”

Section: Overview Of Plant Gene Familiesmentioning

confidence: 99%

“…Plant genomes include protein-coding and non-coding RNA (ncRNA) gene families ( Song et al, 2021 ; Li et al, 2022 ). Gene families encoding ncRNA can be further subdivided into those encoding lncRNA (long non-coding RNA), miRNA (micro RNA), rRNA (ribosomal RNA), tRNA (transfer RNA), and circRNA (circular RNA), and will not be further discussed here.…”

Section: Overview Of Plant Gene Familiesmentioning

confidence: 99%

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Plant protein-coding gene families: Their origin and evolution

et al. 2022

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Steady advances in genome sequencing methods have provided valuable insights into the evolutionary processes of several gene families in plants. At the core of plant biodiversity is an extensive genetic diversity with functional divergence and expansion of genes across gene families, representing unique phenomena. The evolution of gene families underpins the evolutionary history and development of plants and is the subject of this review. We discuss the implications of the molecular evolution of gene families in plants, as well as the potential contributions, challenges, and strategies associated with investigating phenotypic alterations to explain the origin of plants and their tolerance to environmental stresses.

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Section: Overview Of Plant Gene Familiesmentioning

confidence: 99%

Section: Overview Of Plant Gene Familiesmentioning

confidence: 99%

Plant protein-coding gene families: Their origin and evolution

et al. 2022

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“…A gene family is a group of genes with a common origin that encode proteins with similar structural characteristics and biochemical functions [ 17 ]. Nuclear factor YC (NF-YC) is a class of transcription factors involved in various developmental processes in higher eukaryotes such as nutrient accumulation, flowering regulation, and ABA signal response.…”

Section: Gene Family Studiesmentioning

confidence: 99%

Research on Plant Genomics and Breeding 2.0

Jin,

Li,

Zhang

2024

IJMS

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“…Thus, it is essential to identify the genes in maize that are resistant to stress and to create varieties that can withstand stress in order to enhance both quality and yield. An essential approach to understanding gene origin and predicting gene function is the analysis of gene families [ 48 , 49 , 50 ]. Various gene families, such as C2H2 [ 51 ], GS [ 52 ], LACS [ 53 ], FAR1/FHY3 [ 54 ], and SWEET [ 55 ], have been characterized in maize using high-quality genomic data.…”

Section: Introductionmentioning

confidence: 99%

The Analysis, Description, and Examination of the Maize LAC Gene Family’s Reaction to Abiotic and Biotic Stress

Wang,

Liu,

Zou

et al. 2024

Genes

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Laccase (LAC) is a diverse group of genes found throughout the plant genome essential for plant growth and the response to stress by converting monolignin into intricate lignin formations. However, a comprehensive investigation of maize laccase has not yet been documented. A bioinformatics approach was utilized in this research to conduct a thorough examination of maize (Zea mays L.), resulting in the identification and categorization of 22 laccase genes (ZmLAC) into six subfamilies. The gene structure and motifs of each subgroup were largely consistent. The distribution of the 22 LAC genes was uneven among the maize chromosomes, with the exception of chromosome 9. The differentiation of the genes was based on fragment replication, and the differentiation time was about 33.37 million years ago. ZmLAC proteins are primarily acidic proteins. There are 18 cis-acting elements in the promoter sequences of the maize LAC gene family associated with growth and development, stress, hormones, light response, and stress response. The analysis of tissue-specific expression revealed a high expression of the maize LAC gene family prior to the V9 stage, with minimal expression at post-V9. Upon reviewing the RNA-seq information from the publicly available transcriptome, it was discovered that ZmLAC5, ZmLAC10, and ZmLAC17 exhibited significant expression levels when exposed to various biotic and abiotic stress factors, suggesting their crucial involvement in stress responses and potential value for further research. This study offers an understanding of the functions of the LAC genes in maize’s response to biotic and abiotic stress, along with a theoretical basis for comprehending the molecular processes at play.

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PlantGF: an analysis and annotation platform for plant gene families

Cited by 5 publications

References 42 publications

Plant protein-coding gene families: Their origin and evolution

Plant protein-coding gene families: Their origin and evolution

Research on Plant Genomics and Breeding 2.0

The Analysis, Description, and Examination of the Maize LAC Gene Family’s Reaction to Abiotic and Biotic Stress

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