ArticleBMC genomics2015
Identification, characterization and expression analysis of lineage-specific genes within sweet orange (Citrus sinensis).
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 38 citations in OpenAlex.
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- A deep learning approach for orphan gene identification in moso bamboo (Phyllostachys edulis) based on the CNN + Transformer model.BMC bioinformatics · 2022Article
- Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes.Frontiers in plant science · 2022Article
- Research Advances and Prospects of Orphan Genes in Plants.Frontiers in plant science · 2022Review
- Taxonomically Restricted Genes Are Associated With Responses to Biotic and Abiotic Stresses in Sugarcane (Frontiers in plant science · 2022Article
- Identification, characterization and expression analysis of lineage-specific genes within mangrove species Aegiceras corniculatum.Molecular genetics and genomics : MGG · 2021Article
- Genome-Wide Identification, Characterization and Function Analysis of Lineage-Specific Genes in the Tea PlantFrontiers in genetics · 2021Article
- Brassica rapa orphan genes largely affect soluble sugar metabolism.Horticulture research · 2020Article
- The high-quality genome of diploid strawberry (Fragaria nilgerrensis) provides new insights into anthocyanin accumulation.Plant biotechnology journal · 2020Article
- Identification of Orphan Genes in Unbalanced Datasets Based on Ensemble Learning.Frontiers in genetics · 2020Article
- Mining ofInternational journal of molecular sciences · 2018Article
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- Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs?BMC bioinformatics · 2016Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWith the availability of rapidly increasing number of genome and transcriptome sequences, lineage-specific genes (LSGs) can be identified and characterized. Like other conserved functional genes, LSGs play important roles in biological evolution and functions.
resultsTwo set of citrus LSGs, 296 citrus-specific genes (CSGs) and 1039 orphan genes specific to sweet orange, were identified by comparative analysis between the sweet orange genome sequences and 41 genomes and 273 transcriptomes. With the two sets of genes, gene structure and gene expression pattern were investigated. On average, both the CSGs and orphan genes have fewer exons, shorter gene length and higher GC content when compared with those evolutionarily conserved genes (ECs). Expression profiling indicated that most of the LSGs expressed in various tissues of sweet orange and some of them exhibited distinct temporal and spatial expression patterns. Particularly, the orphan genes were preferentially expressed in callus, which is an important pluripotent tissue of citrus. Besides, part of the CSGs and orphan genes expressed responsive to abiotic stress, indicating their potential functions during interaction with environment.
conclusionThis study identified and characterized two sets of LSGs in citrus, dissected their sequence features and expression patterns, and provided valuable clues for future functional analysis of the LSGs in sweet orange.
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