Estimating transcriptome complexities across eukaryotes
Abstract Background Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth of knowledge ripe for exploration. With...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-05-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-023-09326-0 |
| _version_ | 1797827658371825664 |
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| author | James E. Titus-McQuillan Adalena V. Nanni Lauren M. McIntyre Rebekah L. Rogers |
| author_facet | James E. Titus-McQuillan Adalena V. Nanni Lauren M. McIntyre Rebekah L. Rogers |
| author_sort | James E. Titus-McQuillan |
| collection | DOAJ |
| description | Abstract Background Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth of knowledge ripe for exploration. With the “remarkable lack of correspondence” between genome size and complexity, there needs to be a way to quantify complexity across organisms. In this study, we use a set of complexity metrics that allow for evaluating changes in complexity using TranD. Results We ascertain if complexity is increasing or decreasing across transcriptomes and at what structural level, as complexity varies. In this study, we define three metrics – TpG, EpT, and EpG- to quantify the transcriptome's complexity that encapsulates the dynamics of alternative splicing. Here we compare complexity metrics across 1) whole genome annotations, 2) a filtered subset of orthologs, and 3) novel genes to elucidate the impacts of orthologs and novel genes in transcript model analysis. Effective Exon Number (EEN) issued to compare the distribution of exon sizes within transcripts against random expectations of uniform exon placement. EEN accounts for differences in exon size, which is important because novel gene differences in complexity for orthologs and whole-transcriptome analyses are biased towards low-complexity genes with few exons and few alternative transcripts. Conclusions With our metric analyses, we are able to quantify changes in complexity across diverse lineages with greater precision and accuracy than previous cross-species comparisons under ortholog conditioning. These analyses represent a step toward whole-transcriptome analysis in the emerging field of non-model evolutionary genomics, with key insights for evolutionary inference of complexity changes on deep timescales across the tree of life. We suggest a means to quantify biases generated in ortholog calling and correct complexity analysis for lineage-specific effects. With these metrics, we directly assay the quantitative properties of newly formed lineage-specific genes as they lower complexity. |
| first_indexed | 2024-04-09T12:51:52Z |
| format | Article |
| id | doaj.art-9f571859f5c24c0e85b11355eb614495 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-09T12:51:52Z |
| publishDate | 2023-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-9f571859f5c24c0e85b11355eb6144952023-05-14T11:09:31ZengBMCBMC Genomics1471-21642023-05-0124112010.1186/s12864-023-09326-0Estimating transcriptome complexities across eukaryotesJames E. Titus-McQuillan0Adalena V. Nanni1Lauren M. McIntyre2Rebekah L. Rogers3Department of Bioinformatics and Genomics, University of North Carolina at CharlotteDepartment of Molecular Genetics and Microbiology, University of FloridaDepartment of Molecular Genetics and Microbiology, University of FloridaDepartment of Bioinformatics and Genomics, University of North Carolina at CharlotteAbstract Background Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth of knowledge ripe for exploration. With the “remarkable lack of correspondence” between genome size and complexity, there needs to be a way to quantify complexity across organisms. In this study, we use a set of complexity metrics that allow for evaluating changes in complexity using TranD. Results We ascertain if complexity is increasing or decreasing across transcriptomes and at what structural level, as complexity varies. In this study, we define three metrics – TpG, EpT, and EpG- to quantify the transcriptome's complexity that encapsulates the dynamics of alternative splicing. Here we compare complexity metrics across 1) whole genome annotations, 2) a filtered subset of orthologs, and 3) novel genes to elucidate the impacts of orthologs and novel genes in transcript model analysis. Effective Exon Number (EEN) issued to compare the distribution of exon sizes within transcripts against random expectations of uniform exon placement. EEN accounts for differences in exon size, which is important because novel gene differences in complexity for orthologs and whole-transcriptome analyses are biased towards low-complexity genes with few exons and few alternative transcripts. Conclusions With our metric analyses, we are able to quantify changes in complexity across diverse lineages with greater precision and accuracy than previous cross-species comparisons under ortholog conditioning. These analyses represent a step toward whole-transcriptome analysis in the emerging field of non-model evolutionary genomics, with key insights for evolutionary inference of complexity changes on deep timescales across the tree of life. We suggest a means to quantify biases generated in ortholog calling and correct complexity analysis for lineage-specific effects. With these metrics, we directly assay the quantitative properties of newly formed lineage-specific genes as they lower complexity.https://doi.org/10.1186/s12864-023-09326-0OrthoDBTranscriptome complexityEvolutionary ratesOrthologsNovel genesEffective exon number |
| spellingShingle | James E. Titus-McQuillan Adalena V. Nanni Lauren M. McIntyre Rebekah L. Rogers Estimating transcriptome complexities across eukaryotes BMC Genomics OrthoDB Transcriptome complexity Evolutionary rates Orthologs Novel genes Effective exon number |
| title | Estimating transcriptome complexities across eukaryotes |
| title_full | Estimating transcriptome complexities across eukaryotes |
| title_fullStr | Estimating transcriptome complexities across eukaryotes |
| title_full_unstemmed | Estimating transcriptome complexities across eukaryotes |
| title_short | Estimating transcriptome complexities across eukaryotes |
| title_sort | estimating transcriptome complexities across eukaryotes |
| topic | OrthoDB Transcriptome complexity Evolutionary rates Orthologs Novel genes Effective exon number |
| url | https://doi.org/10.1186/s12864-023-09326-0 |
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