Comparative Analysis of the Exon-Intron Structure in Eukaryotic Genomes

Li, Yongfa; Xu, Yanhua; Ma, Zhaowu

doi:10.4236/ym.2017.11006

Cited by 11 publications

(7 citation statements)

References 41 publications

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“…Different from the above four gene families, ADH genes were expanded in two branches of the gene tree, one of which probably originated by duplication from B. xylophilus' own gene Bxy-ADH3, and the other potentially resulting from HGTs from fungi (Figure 3; Figure S18). The intron number of these potential HGT genes was an average of 2.3 per gene, while for the remainder it was 5 per gene (Table S12), consistent with previous studies that fungi usually have about 0.05-3.43 introns and invertebrates usually have 2.92-7.42 introns (Li, Xu, & Ma, 2017). Interestingly, these candidate HGT genes grouped most closely with fungal species in the genera Sporothrix ( Figure S18), which are abundant in pine niches (Chu, Wang, Wang, Chen, & Tang, 2016;Lou et al, 2014;Péter, Dlauchy, Tornai-Lehoczki, Gouliamova, & Kurtzman, 2011;Zhao et al, 2013).…”

Section: Discussionsupporting

confidence: 89%

Gene family expansion of pinewood nematode to detoxify its host defence chemicals

Zhang

et al. 2020

Molecular Ecology

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Gene gain/loss in the context of gene family dynamics plays an important role in evolutionary processes as organisms, particularly invasive species, adapt to new environments or niches. One notable example of this is the duplication of digestive proteases in some parasitic insects and helminths to meet nutritional requirements during animal parasitism. However, whether gene family expansion participates in the adaptation of a plant parasite nematode to its host remains unknown. Here, we compared the newly sequenced genomes of the pinewood nematode, Bursaphelenchus xylophilus, with the genomes of free‐living, animal‐parasitic and plant‐parasitic nematodes. The results showed gene expansions occurring in 51 gene families in B. xylophilus, especially in xenobiotic detoxification pathways, including flavin monooxygenase (FMO), cytochrome P450 (CYP450), short chain dehydrogenase (SDR), alcohol dehydrogenase (ADH), aldehyde dehydrogenase (ALDH), UDP‐glucuronosyltransferase (UGT) and glutathione S‐transferase (GST). Although a majority of these expansions probably resulted from gene duplications, nine ADH genes were potentially acquired by horizontal gene transfer (HGT) from fungi. From the transcriptomes of B. xylophilus treated with pine saplings and terpenes, candidate xenobiotic detoxification genes were identified. We propose that host defence chemicals led to gene family expansions of xenobiotic detoxification pathways in B. xylophilus facilitating its survival in pine resin ducts. This study contributes to a better understanding of how a parasitic nematode adapts to its host.

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Section: Discussionsupporting

confidence: 89%

Gene family expansion of pinewood nematode to detoxify its host defence chemicals

Zhang

et al. 2020

Molecular Ecology

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“…Our analyses show that the mean and median exon sizes are smaller compared to intron sizes, suggesting a more compact distribution, as observed in other Pleuronectiformes species (Robledo et al, 2017). As observed in previous studies, no differences in exon sizes were detected between species (Li et al, 2017). Knowledge of exon loci is important for phylogenomic analyses (Hughes et al, 2021).…”

Section: Discussionsupporting

confidence: 87%

De novoassembly of the black flounder genome. Why do pleuronectiformes have such a small genome size?

Villarreal

Burguener

Sosa

et al. 2023

Preprint

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Black flounder (Paralichthys orbignyanus) is an economically important marine fish with aquaculture potential in Argentina due to its market value. In this study, we sequenced the whole genome using an Illumina sequencing technology. We started with two independent libraries (from one female and one pool of females; each with 150 bp paired-end reads, a mean insert length of 350 bp, and >35 X-fold coverage). Each library was assembled separately using SOAPdenovo2 and the resulting contigs were scaffolded with SSPACE3 before gaps were filled with GapCloser. In vertebrates, including teleosts, the number of transposable elements (TEs) is related to genome size, but it remains unclear whether the size of introns and exons also plays a role. Therefore, the main objective of the present study was to test whether the small genome size of Pleuronectiformes is related to the size of their introns and exons. The assemblies resulted in a genome size of ~538 Mbp (41.35% GC content, 0.11% undetermined bases). Analysis of the assemblies at the core genes level (subset of the 458 universally expressed KOG families) revealed that more than 98% of core genes are present, with more than 78% of them having more than 50% coverage. This indicates a fairly complete and accurate genome at the coding sequence level. Prediction of genes based on statistical predictors (geneid) and sequence-based predictors (Exonerate, using a closely related species, Paralichthys olivaceus, as a reference) was performed. This revealed 25,231 protein-coding genes, 445 tRNAs, 3 rRNAs, and more than 1,500 non-coding RNAs of other types (including a complete set of spliceosomes and several types of snoRNA and miRNA). As a result, this study concluded that the reduced genome size of flounders is related to a reduction in transcript size, mainly through a reduction in exon number, but also through a reduction in large introns. Thus, both components seem to be involved in the strategy of genome reduction in Pleuronectiformes.

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“…However, the low content of small and very long introns in P. orbignyanus could explain the gene size reduction observed in this species. Regarding exon size, as reported in previous studies, no remarkable differences in exon size distribution were detected between species (Li et al, 2017). Considering these results, we concluded that intron size may have an impact in gene size and consequently genome shrinkage in Black ounder, particularly associated to lower contents of very large and small introns.…”

Section: Discussionsupporting

confidence: 80%

Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure

Villarreal,

Burguener,

Sosa

et al. 2023

Preprint

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Black flounder (Paralichthys orbignyanus, Pleuronectiformes) is an economically important marine fish with aquaculture potential in Argentina. In this study, we sequenced the whole genome of this species using an Illumina sequencing technology. We started with two independent libraries (from one female and one male; each with 150 bp paired-end reads, a mean insert length of 350 bp, and > 35 X-fold coverage). The assemblies yielded a genome size of ~ 538 Mbp. Analysis of the assemblies at the core gene level revealed that more than 98% of the core genes were present, with more than 78% of them having more than 50% coverage. This indicates a somehow complete and accurate genome at the coding sequence level. This genome contains 25,231 protein-coding genes, 445 tRNAs, 3 rRNAs, and more than 1,500 non-coding RNAs of other types. On the other hand, in vertebrates the number of transposable elements (TEs) is related to genome size, but it remains unclear whether the size of introns and exons also plays a role. Therefore, the main objective of the present study was to determine whether the small genome size of Black flounder and other Pleuronectiformes is related to the size of their introns and exons. Indeed, Black flounder, along with pufferfishes, seahorses, pipefishes and anabantid fish appear to have smaller genomes than most other teleost groups. We performed a comparative genomic analysis between Black flounder and other teleost order, in order to determine if the small genomic size could be explained by gene features, including the whole genome genes and introns sizes. We show that the smaller genome size of flounders can be attributed to several factors, including changes in the number of repetitive elements, and decreased gene size, particularly due to lower amount of very large and small introns. Thus, these components appear to be involved in the genome reduction in Black flounder.

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Comparative Analysis of the Exon-Intron Structure in Eukaryotic Genomes

Cited by 11 publications

References 41 publications

Gene family expansion of pinewood nematode to detoxify its host defence chemicals

Gene family expansion of pinewood nematode to detoxify its host defence chemicals

De novoassembly of the black flounder genome. Why do pleuronectiformes have such a small genome size?

Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure

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