Codon usage in histone gene families of higher eukaryotes reflects functional rather than phylogenetic relationships

BackgroundWhole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups. In the case of decapod crustaceans, several infraorders, including Axiidea (ghost shrimps, sponge shrimps, and mud lobsters) and Caridea (true shrimps) are still under-represented, limiting comprehensive phylogenetic studies that utilize mitogenomic information.MethodsSequence reads from partial genome scans were generated using the Illumina MiSeq platform and mitogenome sequences were assembled from these low coverage reads. In addition to examining phylogenetic relationships within the three infraorders, Axiidea, Gebiidea, and Caridea, we also investigated the diversity and frequency of codon usage bias and mitogenome gene order rearrangements.ResultsWe present new mitogenome sequences for five shrimp species from Australia that includes two ghost shrimps,Callianassa ceramicaandTrypaea australiensis, along with three caridean shrimps,Macrobrachium bullatum,Alpheus lobidens, andCaridinacf.nilotica. Strong differences in codon usage were discovered among the three infraorders and significant gene order rearrangements were observed. While the gene order rearrangements are congruent with the inferred phylogenetic relationships and consistent with taxonomic classification, they are unevenly distributed within and among the three infraorders.DiscussionOur findings suggest potential for mitogenome rearrangements to be useful phylogenetic markers for decapod crustaceans and at the same time raise important questions concerning the drivers of mitogenome evolution in different decapod crustacean lineages.

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Two Human Gene Families Display Preferences for Different Nucleotides and Have Distinct Codon Usage Patterns

Experimental and Clinical Immunogenetics ◽

10.1159/000019122 ◽

2000 ◽

Vol 17 (1) ◽

pp. 29-41

Author(s):

Christine Skerka ◽

Wolfgang O. Abel ◽

Peter F. Zipfel

Keyword(s):

Codon Usage ◽

Human Gene ◽

Gene Families ◽

Usage Patterns

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Comparative Analysis of Eight Mitogenomes of Bark Beetles and Their Phylogenetic Implications

Insects ◽

10.3390/insects12100949 ◽

2021 ◽

Vol 12 (10) ◽

pp. 949

Author(s):

Huicong Du ◽

Jiaxing Fang ◽

Xia Shi ◽

Sufang Zhang ◽

Fu Liu ◽

...

Keyword(s):

Codon Usage ◽

Bark Beetle ◽

Phylogenetic Relationships ◽

Bark Beetles ◽

Sequence Data ◽

Stop Codon ◽

Structural Characteristics ◽

Gene Arrangement ◽

Beetle Species ◽

Phylogenetic Implications

Many bark beetles of the subfamily Scolytinae are the most economically important insect pests of coniferous forests worldwide. In this study, we sequenced the mitochondrial genomes of eight bark beetle species, including Dendroctonus micans, Orthotomicus erosus, Polygraphus poligraphus, Dryocoetes hectographus, Ips nitidus, Ips typographus, Ips subelongatus, and Ips hauseri, to examine their structural characteristics and determine their phylogenetic relationships. We also used previously published mitochondrial genome sequence data from other Scolytinae species to identify and localize the eight species studied within the bark beetle phylogeny. Their gene arrangement matched the presumed ancestral pattern of these bark beetles. Start and stop codon usage, amino acid abundance, and the relative codon usage frequencies were conserved among bark beetles. Genetic distances between species ranged from 0.037 to 0.418, and evolutionary rates of protein-coding genes ranged from 0.07 for COI to 0.69 for ND2. Our results shed light on the phylogenetic relationships and taxonomic status of several bark beetles in the subfamily Scolytinae and highlight the need for further sequencing analyses and taxonomic revisions in additional bark beetle species.

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Eukaryote-Conserved Methylarginine Is Absent in Diplomonads and Functionally Compensated in Giardia

Molecular Biology and Evolution ◽

10.1093/molbev/msaa186 ◽

2020 ◽

Vol 37 (12) ◽

pp. 3525-3549 ◽

Cited By ~ 3

Author(s):

Samantha J Emery-Corbin ◽

Joshua J Hamey ◽

Brendan R E Ansell ◽

Balu Balan ◽

Swapnil Tichkule ◽

...

Keyword(s):

Coiled Coil ◽

Giardia Duodenalis ◽

Elongation Factor ◽

Gene Families ◽

Cyst Formation ◽

Arginine Methylation ◽

Specific Gene ◽

Parasitic Protist ◽

Higher Eukaryotes ◽

Species Specific

Abstract Methylation is a common posttranslational modification of arginine and lysine in eukaryotic proteins. Methylproteomes are best characterized for higher eukaryotes, where they are functionally expanded and evolved complex regulation. However, this is not the case for protist species evolved from the earliest eukaryotic lineages. Here, we integrated bioinformatic, proteomic, and drug-screening data sets to comprehensively explore the methylproteome of Giardia duodenalis—a deeply branching parasitic protist. We demonstrate that Giardia and related diplomonads lack arginine-methyltransferases and have remodeled conserved RGG/RG motifs targeted by these enzymes. We also provide experimental evidence for methylarginine absence in proteomes of Giardia but readily detect methyllysine. We bioinformatically infer 11 lysine-methyltransferases in Giardia, including highly diverged Su(var)3-9, Enhancer-of-zeste and Trithorax proteins with reduced domain architectures, and novel annotations demonstrating conserved methyllysine regulation of eukaryotic elongation factor 1 alpha. Using mass spectrometry, we identify more than 200 methyllysine sites in Giardia, including in species-specific gene families involved in cytoskeletal regulation, enriched in coiled-coil features. Finally, we use known methylation inhibitors to show that methylation plays key roles in replication and cyst formation in this parasite. This study highlights reduced methylation enzymes, sites, and functions early in eukaryote evolution, including absent methylarginine networks in the Diplomonadida. These results challenge the view that arginine methylation is eukaryote conserved and demonstrate that functional compensation of methylarginine was possible preceding expansion and diversification of these key networks in higher eukaryotes.

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Comparative Analysis of Genomic and Transcriptome Sequences Reveals Divergent Patterns of Codon Bias in Wheat and Its Ancestor Species

Frontiers in Genetics ◽

10.3389/fgene.2021.732432 ◽

2021 ◽

Vol 12 ◽

Author(s):

Chenkang Yang ◽

Qi Zhao ◽

Ying Wang ◽

Jiajia Zhao ◽

Ling Qiao ◽

...

Keyword(s):

Triticum Aestivum ◽

Codon Usage ◽

Hexaploid Wheat ◽

Triticum Turgidum ◽

Synonymous Codon ◽

Regression Line ◽

Aegilops Tauschii ◽

Gc Content ◽

Gene Families ◽

Synonymous Codon Usage

The synonymous codons usage shows a characteristic pattern of preference in each organism. This codon usage bias is thought to have evolved for efficient protein synthesis. Synonymous codon usage was studied in genes of the hexaploid wheat Triticum aestivum (AABBDD) and its progenitor species, Triticum urartu (AA), Aegilops tauschii (DD), and Triticum turgidum (AABB). Triticum aestivum exhibited stronger usage bias for G/C-ending codons than did the three progenitor species, and this bias was especially higher compared to T. turgidum and Ae. tauschii. High GC content is a primary factor influencing codon usage in T. aestivum. Neutrality analysis showed a significant positive correlation (p<0.001) between GC12 and GC3 in the four species with regression line slopes near zero (0.16–0.20), suggesting that the effect of mutation on codon usage was only 16–20%. The GC3s values of genes were associated with gene length and distribution density within chromosomes. tRNA abundance data indicated that codon preference corresponded to the relative abundance of isoaccepting tRNAs in the four species. Both mutation and selection have affected synonymous codon usage in hexaploid wheat and its progenitor species. GO enrichment showed that GC biased genes were commonly enriched in physiological processes such as photosynthesis and response to acid chemical. In some certain gene families with important functions, the codon usage of small parts of genes has changed during the evolution process of T. aestivum.

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Corrigendum to: Bioinformatic Analysis of Codon Usage and Phylogenetic Relationships in Different Genotypes of the Hepatitis C Virus

Hepatitis Monthly ◽

10.5812/hepatmon.99558 ◽

2019 ◽

Vol 19 (11) ◽

Author(s):

Seyed Moayed Alavian

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Codon Usage ◽

Phylogenetic Relationships ◽

Bioinformatic Analysis

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The human canonical core histone catalogue

10.1101/720235 ◽

2019 ◽

Author(s):

David Miguel Susano Pinto ◽

Andrew Flaus

Keyword(s):

Human Genome ◽

Large Family ◽

Gene Families ◽

Histone Gene ◽

Protein Isoforms ◽

Core Histone ◽

Reproducible Research ◽

Histone Genes ◽

Histone Proteins ◽

Protein Diversity

AbstractCore histone proteins H2A, H2B, H3, and H4 are encoded by a large family of genes distributed across the human genome. Canonical core histones contribute the majority of proteins to bulk chromatin packaging, and are encoded in 4 clusters by 65 coding genes comprising 17 for H2A, 18 for H2B, 15 for H3, and 15 for H4, along with at least 17 total pseudogenes. The canonical core histone genes display coding variation that gives rise to 11 H2A, 15 H2B, 4 H3, and 2 H4 unique protein isoforms. Although histone proteins are highly conserved overall, these isoforms represent a surprising and seldom recognised variation with amino acid identity as low as 77% between canonical histone proteins of the same type. The gene sequence and protein isoform diversity also exceeds commonly used subtype designations such as H2A.1 and H3.1, and exists in parallel with the well-known specialisation of variant histone proteins. RNA sequencing of histone transcripts shows evidence for differential expression of histone genes but the functional significance of this variation has not yet been investigated. To assist understanding of the implications of histone gene and protein diversity we have catalogued the entire human canonical core histone gene and protein complement. In order to organise this information in a robust, accessible, and accurate form, we applied software build automation tools to dynamically generate the canonical core histone repertoire based on current genome annotations and then to organise the information into a manuscript format. Automatically generated values are shown with a light grey background. Alongside recognition of the encoded protein diversity, this has led to multiple corrections to human histone annotations, reflecting the flux of the human genome as it is updated and enriched in reference databases. This dynamic manuscript approach is inspired by the aims of reproducible research and can be readily adapted to other gene families.

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