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Intron losses and gains in the nematodes
Ming-Yue Ma1, Ji Xia1, Kun-Xian Shu2
1Chongqing Key Laboratory of Big Data for Bio Intelligence, School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.
Biology Direct
|June 6, 2022
Summary
Nematode intron evolution is typical, not eccentric. Analysis of 104 genomes reveals varied intron density and rates of loss/gain, with losses dominating, aligning nematodes with other eukaryotes.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Biology
Background:
- Spliceosomal intron evolution is well-studied in eukaryotes, with near consensus on loss/gain patterns.
- Previous research suggested nematodes might be an outlier in intron evolution based on limited data.
Purpose of the Study:
- To extensively analyze intron losses and gains in nematodes.
- To determine if nematodes are typical or eccentric in their intron evolution patterns.
Main Methods:
- Analysis of 104 nematode genomes from all five clades.
- Examination of intron density, loss, and gain rates across lineages and evolutionary stages.
- Investigation of evidence supporting cDNA-mediated intron loss in Caenorhabditis species.
Main Results:
- Nematodes exhibit a wide range of intron densities (0.1 to >9 per kbp).
- Intron loss and gain rates are highly heterogeneous across nematode lineages and evolutionary stages.
- Intron losses significantly outnumbered intron gains, with strong evidence for cDNA-mediated loss in Caenorhabditis.
Conclusions:
- Nematodes are a typical eukaryotic group regarding intron evolution.
- The study refutes the notion of nematodes being an outlier in intron dynamics.
