Molecular evidence for segmental duplication across chromosomes of soybean using transcription factor gene family

Duplication of genome is an important genetic innovation. Large genome size (1.1 Gb) along with ancient and recent duplication events make the soybean genome more complex. Analyzing the distribution and duplication event in soybean transcription family genes, the segmental duplication within chromosomes was revealed. Our study provides a strong evidence that the large segmental duplication event in genome architecture and evolution of soybean genome using simple method of sequence and order analysis of TF genes. Finally, a scheme for interrelationship of different chromosomes has been proposed.

Evolution of 14-3-3 Proteins in Angiosperm Plants: Recurring Gene Duplication and Loss

14-3-3 proteins are key regulatory factors in plants and are involved in a broad range of physiological processes. We addressed the evolutionary history of 14-3-3s from 46 angiosperm species, including basal angiosperm Amborella and major lineage of monocotyledons and eudicotyledons. Orthologs of Arabidopsis isoforms were detected. There were several rounds of duplication events in the evolutionary history of the 14-3-3 protein family in plants. At least four subfamilies (iota, epsilon, kappa, and psi) formed as a result of ancient duplication in a common ancestor of angiosperm plants. Recent duplication events followed by gene loss in plant lineage, among others Brassicaceae, Fabaceae, and Poaceae, further shaped the high diversity of 14-3-3 isoforms in plants. Coexpression data showed that 14-3-3 proteins formed different functional groups in different species. In some species, evolutionarily related groups of 14-3-3 proteins had coexpressed together under certain physiological conditions, whereas in other species, closely related isoforms expressed in the opposite manner. A possible explanation is that gene duplication and loss is accompanied by functional plasticity of 14-3-3 proteins.

Extensive duplication and convergent sequence evolution of an antimicrobial peptide gene

Antimicrobial peptides (AMPs) are host-encoded antibiotics that combat invading pathogens. AMPs are encoded by short genes that tend to evolve rapidly, likely responding to host-pathogen arms races. However recent studies have highlighted roles for AMPs in neurological contexts suggesting functions for these defence molecules beyond infection. Here we characterize the evolution of the Drosophila Baramicin (Bara) AMP gene family. We describe a recent duplication of the immune-induced BaraA locus, and trans-species polymorphisms in BaraA peptides that suggest dynamic selective pressures. We further recover multiple Baramicin paralogs in Drosophila melanogaster and other species, united by their N-terminal IM24 domain. Strikingly, some paralogs are no longer immune-induced. A careful dissection of the Baramicin family’s evolutionary history indicates that these non-immune paralogs result from repeated events of duplication and subsequent truncation of the coding sequence, leaving only the IM24 domain as the prominent gene product. Using mutation and targeted gene silencing, we demonstrate that two such genes are adapted for function in neural contexts in D. melanogaster. Using the Baramicin evolutionary history, we reveal unique properties of the different Baramicin domains. In doing so, we provide a case study for how an AMP-encoding gene might play dual roles in both immune and non-immune processes.

Immunoglobulin T genes in Neopterygii

In teleost fishes there are three immunoglobulin isotypes named immunoglobulin M (IgM), D (IgD) and T (IgT). IgT has been the last to be described and is considered a teleosts-fish specific isotype. From the recent availability of genome sequences of fishes, an in-depth analysis of Actinopterygii immunoglobulin heavy chain genes was undertaken. With the aid of a bioinformatics pipeline, a machine learning software, CHfinder, was developed that identifies the coding exons of the CH domains of fish immunoglobulins. Using this pipeline, a high number of such sequences were obtained from teleosts and holostean fishes. IgT was found in teleost and holostean fishes that had not been previously described. A phylogenetic analysis reveals that IgT CH1 exons are similar to the IgM CH1. This analysis also demonstrates that the other three domains (CH2, CH3 and CH4) were not generated by recent duplication processes of IgM in Actinopterygii, indicating it is an immunoglobulin with an earlier origin.

Evolution of the extracytoplasmic function σ factor protein family

Understanding transcription has been a central goal of the scientific community for decades. However, much is still unknown, especially concerning how it is regulated. In bacteria, a single DNA-directed RNA-polymerase performs the whole of transcription. It contains multiple subunits, among which the σ factor that confers promoter specificity. Besides the housekeeping σ factor, bacteria encode several alternative σ factors. The most abundant and diverse family of alternative σ factors, the extracytoplasmic function (ECF) family, regulates transcription of genes associated with stressful scenarios, making them key elements of adaptation to specific environmental changes. Despite this, the evolutionary history of ECF σ factors has never been investigated. Here, we report on our analysis of thousands of members of this family. We show that single events are in the origin of alternative modes of regulation of ECF σ factor activity that require partner proteins, but that multiple events resulted in acquisition of regulatory extensions. Moreover, in Bacteroidetes there is a recent duplication of an ecologically relevant gene cluster that includes an ECF σ factor, whereas in Planctomycetes duplication generates distinct C-terminal extensions after fortuitous insertion of the duplicated σ factor. At last, we also demonstrate horizontal transfer of ECF σ factors between soil bacteria.

Evolution of developmental plasticity by opposing dosage of signalling-modifying enzymes

Polyphenism, the extreme form of developmental plasticity, is the ability of a genotype to produce discrete morphologies matched to alternative environments. Because polyphenism is likely to be under switch-like molecular control, a comparative genetic approach could reveal the molecular targets of plasticity evolution. In the nematode Pristionchus pacificus, which form two alternative feeding-morphs, the polyphenism threshold is set by relative dosage of two lineage-specific enzymes that respond to morph-inducing cues. One enzyme, the sulfotransferase SEUD-1, integrates an intercellular signalling mechanism at its ultimate target, the cells producing dimorphic mouthparts. Additionally, multiple alterations of seud-1 support it as a potential target for plasticity evolution. First, a recent duplication of seud-1 in a sister species reveals a direct correlation between genomic dosage and the polyphenism threshold. Second, laboratory selection on the polyphenism threshold resulted in changes in relative transcriptional dosage. Our study thus offers a genetic explanation for how plastic responses evolve.

Birth of a new gene on the Y chromosome of Drosophila melanogaster

Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes.