Identification, characterization and expression analysis of lineage-specific genes within mangrove species Aegiceras corniculatum

Ma, Dongna; Ding, Qiansu; Guo, Zejun; Zhao, Zhonglong; Wei, Liufeng; Li, Yiying; Song, Shiwei; Hai-lei, Zheng

doi:10.1007/s00438-021-01810-0

Cited by 10 publications

(11 citation statements)

References 68 publications

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“…LSGs and LSEs were found to be less broadly expressed across development than shared genes, consistent with narrow expression of new genes observed in other taxa [15,17,49,55]. The high levels of expression specificity in these gene categories contributes to their enrichment among genes with biased expression, where they display predominant expression in a single developmental stage.…”

Section: Discussionsupporting

confidence: 78%

Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development

Luna

Chain

2021

Genes

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Gene duplications generate new genes that can contribute to expression changes and the evolution of new functions. Genomes often consist of gene families that undergo expansions, some of which occur in specific lineages that reflect recent adaptive diversification. In this study, lineage-specific genes and gene family expansions were studied across five dictyostelid species to determine when and how they are expressed during multicellular development. Lineage-specific genes were found to be enriched among genes with biased expression (predominant expression in one developmental stage) in each species and at most developmental time points, suggesting independent functional innovations of new genes throughout the phylogeny. Biased duplicate genes had greater expression divergence than their orthologs and paralogs, consistent with subfunctionalization or neofunctionalization. Lineage-specific expansions in particular had biased genes with both molecular signals of positive selection and high expression, suggesting adaptive genetic and transcriptional diversification following duplication. Our results present insights into the potential contributions of lineage-specific genes and families in generating species-specific phenotypes during multicellular development in dictyostelids.

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Section: Discussionsupporting

confidence: 78%

Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development

Luna

Chain

2021

Genes

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“…In Strobilanthes cusia , there was no difference in GC content ( Hu et al, 2021 ). In Aegiceras corniculatum and wheat, OGs were significantly less than that of NOGs ( Ma et al, 2021 ). Among Cucurbitaceae species, they also exhibited heterogeneously.…”

Section: Resultsmentioning

confidence: 91%

“…Using co-expressed genes to predict the function of OGs is an effective method ( Li G. et al, 2019 ; Zhang et al, 2019 ; Ma et al, 2021 ). To investigate the underlying functions of OGs in melon, we used WGCNA analysis to identify 12 co-expressed gene modules ( Figure 5A ).…”

Section: Resultsmentioning

confidence: 99%

Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes

Lai

Ding

et al. 2022

Front. Plant Sci.

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Orphan genes (OGs) that are missing identifiable homologs in other lineages may potentially make contributions to a variety of biological functions. The Cucurbitaceae family consists of a wide range of fruit crops of worldwide or local economic significance. To date, very few functional mechanisms of OGs in Cucurbitaceae are known. In this study, we systematically identified the OGs of eight Cucurbitaceae species using a comparative genomics approach. The content of OGs varied widely among the eight Cucurbitaceae species, ranging from 1.63% in chayote to 16.55% in wax gourd. Genetic structure analysis showed that OGs have significantly shorter protein lengths and fewer exons in Cucurbitaceae. The subcellular localizations of OGs were basically the same, with only subtle differences. Except for aggregation in some chromosomal regions, the distribution density of OGs was higher near the telomeres and relatively evenly distributed on the chromosomes. Gene expression analysis revealed that OGs had less abundantly and highly tissue-specific expression. Interestingly, the largest proportion of these OGs was significantly more tissue-specific expressed in the flower than in other tissues, and more detectable expression was found in the male flower. Functional prediction of OGs showed that (1) 18 OGs associated with male sterility in watermelon; (2) 182 OGs associated with flower development in cucumber; (3) 51 OGs associated with environmental adaptation in watermelon; (4) 520 OGs may help with the large fruit size in wax gourd. Our results provide the molecular basis and research direction for some important mechanisms in Cucurbitaceae species and domesticated crops.

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“…The rapid accumulation of genomic data on a large variety of plants will allow increasing integrity of identification of OGs. So far the presence of OGs has been reported in many plants or lineages [such as B. rapa (Jiang et al, 2018), A. thaliana (Yang et al, 2009;Lin et al, 2010;Donoghue et al, 2011;Cui et al, 2015), O. sativa (Guo et al, 2007;Yang et al, 2009;Cui et al, 2015;Jin et al, 2019), P. trichocarpa (Yang et al, 2009), V. unguiculata (Li G. et al, 2019), Poaceae (Campbell et al, 2007), Aegiceras corniculatum (Ma et al, 2021), C. sinensis (Xu et al, 2015), Amaranthus hypochondriacus (Cabrales-Orona and Délano-Frier, 2021), Camellia sinensis (Zhao and Ma, 2021), and eight Cucurbitaceae family members (Ma et al, 2022)]. Every sequenced genome contains OGs whose origins are obscure because of the absence of homologs (Blanco-Melo et al, 2016).…”

Section: Orphan Genes Identification and Its Fast Evolving Characteri...mentioning

confidence: 99%

“…Study showed that the elevated ratios of non-synonymous to synonymous SNPs (Single Nucleotide Polymorphisms) in the two sets of Arabidopsis OGs are mainly due to the elevated non-synonymous SNP density, indicating that a number of two sets of OGs evolve substantially faster than the ECGs at the protein sequence level (Lin et al, 2010). For example, due to their short evolutionary time, the genes generated in this time frame have shorter gene lengths (Ma et al, 2021). However, the GC content of CDS, genes, and introns are more variable in diverse species.…”

Section: Fast Evolving Characteristics Of Orphan Genesmentioning

confidence: 99%

Research Advances and Prospects of Orphan Genes in Plants

Jiang

Dong

et al. 2022

Front. Plant Sci.

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Orphan genes (OGs) are defined as genes having no sequence similarity with genes present in other lineages. OGs have been regarded to play a key role in the development of lineage-specific adaptations and can also serve as a constant source of evolutionary novelty. These genes have often been found related to various stress responses, species-specific traits, special expression regulation, and also participate in primary substance metabolism. The advancement in sequencing tools and genome analysis methods has made the identification and characterization of OGs comparatively easier. In the study of OG functions in plants, significant progress has been made. We review recent advances in the fast evolving characteristics, expression modulation, and functional analysis of OGs with a focus on their role in plant biology. We also emphasize current challenges, adoptable strategies and discuss possible future directions of functional study of OGs.

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Identification, characterization and expression analysis of lineage-specific genes within mangrove species Aegiceras corniculatum

Cited by 10 publications

References 68 publications

Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development

Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development

Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes

Research Advances and Prospects of Orphan Genes in Plants

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