Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems
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ABSTRACT:
SUBMITTER: Moore‐Pollard E
PROVIDER: S-EPMC10873820 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
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Project description:MotivationGene trees often differ from the species trees that contain them due to various factors, including incomplete lineage sorting (ILS) and gene duplication and loss (GDL). Several highly accurate species tree estimation methods have been introduced to explicitly address ILS, including ASTRAL, a widely used statistically consistent method, and wQFM, a quartet amalgamation approach experimentally shown to be more accurate than ASTRAL. Two recent advancements, ASTRAL-Pro and DISCO, have emerged in phylogenomics to consider GDL. ASTRAL-Pro introduces a refined quartet similarity measure, accounting for orthology and paralogy. On the other hand, DISCO offers a general strategy to decompose multi-copy gene trees into a collection of single-copy trees, allowing the utilization of methods previously designed for species tree inference in the context of single-copy gene trees.ResultsIn this study, we first introduce some variants of DISCO to examine its underlying hypotheses and present analytical results on the statistical guarantees of DISCO. In particular, we introduce DISCO-R, a variant of DISCO with a refined and improved pruning strategy that provides more accurate and robust results. We then demonstrate with extensive evaluation studies on a collection of simulated and real data sets that wQFM paired with DISCO variants consistently matches or outperforms ASTRAL-Pro and other competing methods.Availability and implementationDISCO-R and other variants are freely available at https://github.com/skhakim/DISCO-variants.
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Project description:In recent years, many publications have established histone lysine methylation as a central epigenetic modification in the regulation of chromatin and transcription. The histone lysine methyltransferases contain a conserved SET domain and are widely distributed in various organisms. However, a comprehensive study on the origin and diversification of the SET-domain-containing genes in fungi has not been conducted. In this study, a total of 3816 SET-domain-containing genes, which were identified and characterized using HmmSearch from 229 whole genomes sequenced fungal species, were used to ascertain their evolution and diversification in fungi. Using the CLANS program, all the SET-domain-containing genes were grouped into three main clusters, and each cluster contains several groups. Domain organization analysis showed that genes belonging to the same group have similar sequence structures. In contrast, different groups process domain organizations or locations differently, suggesting the SET-domain-containing genes belonging to different groups may have obtained distinctive regulatory mechanisms during their evolution. These genes that conduct the histone methylations (such as H3K4me, H3K9me, H3K27me, H4K20me, H3K36me) are mainly grouped into Cluster 1 while the other genes grouped into Clusters 2 and 3 are still functionally undetermined. Our results also showed that numerous gene duplication and loss events have happened during the evolution of those fungal SET-domain-containing proteins. Our results provide novel insights into the roles of SET-domain genes in fungal evolution and pave a fundamental path to further understanding the epigenetic basis of gene regulation in fungi.
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Project description:Gene duplication provides an important source of genetic raw material for phenotypic diversification, but few studies have detailed the mechanisms through which duplications produce evolutionary novelty within species. Here, we investigate how a set of recently duplicated homologs of the floral inducer FLOWERING LOCUS T (FT) has contributed to sunflower domestication. We find that changes in expression of these duplicates are associated with differences in flowering behavior between wild and domesticated sunflower. In addition, we present genetic and functional evidence demonstrating that a frameshift mutation in one paralog, Helianthus annuus FT 1 (HaFT1), underlies a major QTL for flowering time and experienced a selective sweep during early domestication. Notably, this dominant-negative allele delays flowering through interference with action of another paralog, HaFT4. Together, these data reveal that changes affecting the expression, sequence, and gene interactions of HaFT paralogs have played key roles during sunflower domestication. Our findings also illustrate the important role that evolving interactions between new gene family members may play in fostering phenotypic change.
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Project description:Aster flaccidus is a perennial medicinal plant belong the sunflower family Compositae, which is widely distributed in China and some other Asian countries. The complete chloroplast genome sequence of A. flaccidus was sequenced using the Illumina Hiseq 4000 platform. The size of the A. flaccidus chloroplast genome is 151,329 bp, with an average GC content of 37.5%. This circular molecule has a typical quadripartite structure containing a large single copy (LSC) region of 83,480 bp, a small single copy (SSC) region of 18,149 bp, and two inverted (IRs) repeat regions of 24,850 bp. A total of 132 genes were successfully annotated containing 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes. A maximum likelihood (ML) phylogenetic tree supported that the chloroplast genome of A. flaccidus is closely related to that of Aster indicus.
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Project description:BACKGROUND: In order to interpret the results obtained from a microarray experiment, researchers often shift focus from analysis of individual differentially expressed genes to analyses of sets of genes. These gene-set analysis (GSA) methods use previously accumulated biological knowledge to group genes into sets and then aim to rank these gene sets in a way that reflects their relative importance in the experimental situation in question. We suspect that the presence of paralogs affects the ability of GSA methods to accurately identify the most important sets of genes for subsequent research. RESULTS: We show that paralogs, which typically have high sequence identity and similar molecular functions, also exhibit high correlation in their expression patterns. We investigate this correlation as a potential confounding factor common to current GSA methods using Indygene http://www.cbio.uct.ac.za/indygene, a web tool that reduces a supplied list of genes so that it includes no pairwise paralogy relationships above a specified sequence similarity threshold. We use the tool to reanalyse previously published microarray datasets and determine the potential utility of accounting for the presence of paralogs. CONCLUSIONS: The Indygene tool efficiently removes paralogy relationships from a given dataset and we found that such a reduction, performed prior to GSA, has the ability to generate significantly different results that often represent novel and plausible biological hypotheses. This was demonstrated for three different GSA approaches when applied to the reanalysis of previously published microarray datasets and suggests that the redundancy and non-independence of paralogs is an important consideration when dealing with GSA methodologies.
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Project description:MotivationWith the rapid growth rate of newly sequenced genomes, species tree inference from multiple genes has become a basic bioinformatics task in comparative and evolutionary biology. However, accurate species tree estimation is difficult in the presence of gene tree discordance, which is often due to incomplete lineage sorting (ILS), modelled by the multi-species coalescent. Several highly accurate coalescent-based species tree estimation methods have been developed over the last decade, including MP-EST. However, the running time for MP-EST increases rapidly as the number of species grows.ResultsWe present divide-and-conquer techniques that improve the scalability of MP-EST so that it can run efficiently on large datasets. Surprisingly, this technique also improves the accuracy of species trees estimated by MP-EST, as our study shows on a collection of simulated and biological datasets.
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