Intron losses and gains in the nematodes
Abstract Background The evolution of spliceosomal introns has been widely studied among various eukaryotic groups. Researchers nearly reached the consensuses on the pattern and the mechanisms of intron losses and gains across eukaryotes. However, according to previous studies that analyzed a few gen...
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| Format: | Article |
| Language: | English |
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BMC
2022-06-01
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| Series: | Biology Direct |
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| Online Access: | https://doi.org/10.1186/s13062-022-00328-8 |
| _version_ | 1817975419181203456 |
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| author | Ming-Yue Ma Ji Xia Kun-Xian Shu Deng-Ke Niu |
| author_facet | Ming-Yue Ma Ji Xia Kun-Xian Shu Deng-Ke Niu |
| author_sort | Ming-Yue Ma |
| collection | DOAJ |
| description | Abstract Background The evolution of spliceosomal introns has been widely studied among various eukaryotic groups. Researchers nearly reached the consensuses on the pattern and the mechanisms of intron losses and gains across eukaryotes. However, according to previous studies that analyzed a few genes or genomes, Nematoda seems to be an eccentric group. Results Taking advantage of the recent accumulation of sequenced genomes, we extensively analyzed the intron losses and gains using 104 nematode genomes across all the five Clades of the phylum. Nematodes have a wide range of intron density, from less than one to more than nine per kbp coding sequence. The rates of intron losses and gains exhibit significant heterogeneity both across different nematode lineages and across different evolutionary stages of the same lineage. The frequency of intron losses far exceeds that of intron gains. Five pieces of evidence supporting the model of cDNA-mediated intron loss have been observed in ten Caenorhabditis species, the dominance of the precise intron losses, frequent loss of adjacent introns, high-level expression of the intron-lost genes, preferential losses of short introns, and the preferential losses of introns close to 3′-ends of genes. Like studies in most eukaryotic groups, we cannot find the source sequences for the limited number of intron gains detected in the Caenorhabditis genomes. Conclusions These results indicate that nematodes are a typical eukaryotic group rather than an outlier in intron evolution. |
| first_indexed | 2024-04-13T21:49:48Z |
| format | Article |
| id | doaj.art-2688a77d62cc424087b95c4afdaf9316 |
| institution | Directory Open Access Journal |
| issn | 1745-6150 |
| language | English |
| last_indexed | 2024-04-13T21:49:48Z |
| publishDate | 2022-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Biology Direct |
| spelling | doaj.art-2688a77d62cc424087b95c4afdaf93162022-12-22T02:28:27ZengBMCBiology Direct1745-61502022-06-0117111610.1186/s13062-022-00328-8Intron losses and gains in the nematodesMing-Yue Ma0Ji Xia1Kun-Xian Shu2Deng-Ke Niu3Chongqing Key Laboratory of Big Data for Bio Intelligence, School of Bioinformatics, Chongqing University of Posts and TelecommunicationsChongqing Key Laboratory of Big Data for Bio Intelligence, School of Bioinformatics, Chongqing University of Posts and TelecommunicationsChongqing Key Laboratory of Big Data for Bio Intelligence, School of Bioinformatics, Chongqing University of Posts and TelecommunicationsMOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal UniversityAbstract Background The evolution of spliceosomal introns has been widely studied among various eukaryotic groups. Researchers nearly reached the consensuses on the pattern and the mechanisms of intron losses and gains across eukaryotes. However, according to previous studies that analyzed a few genes or genomes, Nematoda seems to be an eccentric group. Results Taking advantage of the recent accumulation of sequenced genomes, we extensively analyzed the intron losses and gains using 104 nematode genomes across all the five Clades of the phylum. Nematodes have a wide range of intron density, from less than one to more than nine per kbp coding sequence. The rates of intron losses and gains exhibit significant heterogeneity both across different nematode lineages and across different evolutionary stages of the same lineage. The frequency of intron losses far exceeds that of intron gains. Five pieces of evidence supporting the model of cDNA-mediated intron loss have been observed in ten Caenorhabditis species, the dominance of the precise intron losses, frequent loss of adjacent introns, high-level expression of the intron-lost genes, preferential losses of short introns, and the preferential losses of introns close to 3′-ends of genes. Like studies in most eukaryotic groups, we cannot find the source sequences for the limited number of intron gains detected in the Caenorhabditis genomes. Conclusions These results indicate that nematodes are a typical eukaryotic group rather than an outlier in intron evolution.https://doi.org/10.1186/s13062-022-00328-8Intron gainIntron lossNematodaCaenorhabditis elegansPhylogenetic |
| spellingShingle | Ming-Yue Ma Ji Xia Kun-Xian Shu Deng-Ke Niu Intron losses and gains in the nematodes Biology Direct Intron gain Intron loss Nematoda Caenorhabditis elegans Phylogenetic |
| title | Intron losses and gains in the nematodes |
| title_full | Intron losses and gains in the nematodes |
| title_fullStr | Intron losses and gains in the nematodes |
| title_full_unstemmed | Intron losses and gains in the nematodes |
| title_short | Intron losses and gains in the nematodes |
| title_sort | intron losses and gains in the nematodes |
| topic | Intron gain Intron loss Nematoda Caenorhabditis elegans Phylogenetic |
| url | https://doi.org/10.1186/s13062-022-00328-8 |
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