Transcriptome analyses of leaf architecture in Sansevieria support a common genetic toolkit in the parallel evolution of unifacial leaves in monocots.

Planar structures dramatically increase the surface-area-to-volume ratio, which is critically important for multicellular organisms. In this study, we utilize naturally occurring phenotypic variation among three Sansivieria species (Asperagaceae) to investigate leaf margin expression patterns that are associated with mediolateral and adaxial/abaxial development. We identified differentially expressed genes (DEGs) between center and margin leaf tissues in two planar-leaf species Sansevieria subspicata and Sansevieria trifasciata and compared these with expression patterns within the cylindrically leaved Sansevieria cylindrica. Two YABBY family genes, homologs of FILAMENTOUS FLOWER and DROOPING LEAF, are overexpressed in the center leaf tissue in the planar-leaf species and in the tissue of the cylindrical leaves. As mesophyll structure does not indicate adaxial versus abaxial differentiation, increased leaf thickness results in more water-storage tissue and enhances resistance to aridity. This suggests that the cylindrical-leaf in S. cylindrica is analogous to the central leaf tissue in the planar-leaf species. Furthermore, the congruence of the expression patterns of these YABBY genes in Sansevieria with expression patterns found in other unifacial monocot species suggests that patterns of parallel evolution may be the result of similar solutions derived from a limited developmental toolbox.

Cloud and snow detection of remote sensing images based on improved Unet3.

Cloud detection is an important step in remote sensing image processing and a prerequisite for subsequent analysis and interpretation of remote sensing images. Traditional cloud detection methods are difficult to accurately detect clouds and snow with very similar features such as color and texture. In this paper, the features of cloud and snow in remote sensing images are deeply extracted, and an accurate cloud and snow detection method is proposed based on the advantages of Unet3+ network in feature fusion. Firstly, color space conversion is performed on remote sensing images, RGB images and HIS images are used as input of Unet3+ network. Resnet 50 is used to replace the Unet3+ feature extraction network to extract remote sensing image features at a deeper level, and add the Convolutional Block Attention Module in Resnet50 to improve the network's attention to cloud and snow. Finally, the weighted cross entropy loss is constructed to solve the problem of unbalanced sample number caused by high proportion of background area in the image. The results show that the proposed method has strong adaptability and moderate computation. The mPA value, mIoU value and mPrecision value can reach 92.76%, 81.74% and 86.49%, respectively. Compared with other algorithms, the proposed method can better eliminate all kinds of interference information in remote sensing images of different landforms and accurately detect cloud and snow in images.

Reconstruction of gene innovation associated with major evolutionary transitions in the kingdom Fungi.

BACKGROUND: Fungi exhibit astonishing diversity with multiple major phenotypic transitions over the kingdom's evolutionary history. As part of this process, fungi developed hyphae, adapted to land environments (terrestrialization), and innovated their sexual structures. These changes also helped fungi establish ecological relationships with other organisms (animals and plants), but the genomic basis of these changes remains largely unknown. RESULTS: By systematically analyzing 304 genomes from all major fungal groups, together with a broad range of eukaryotic outgroups, we have identified 188 novel orthogroups associated with major changes during the evolution of fungi. Functional annotations suggest that many of these orthogroups were involved in the formation of key trait innovations in extant fungi and are functionally connected. These innovations include components for cell wall formation, functioning of the spindle pole body, polarisome formation, hyphal growth, and mating group signaling. Innovation of mitochondria-localized proteins occurred widely during fungal transitions, indicating their previously unrecognized importance. We also find that prokaryote-derived horizontal gene transfer provided a small source of evolutionary novelty with such genes involved in key metabolic pathways. CONCLUSIONS: The overall picture is one of a relatively small number of novel genes appearing at major evolutionary transitions in the phylogeny of fungi, with most arising de novo and horizontal gene transfer providing only a small additional source of evolutionary novelty. Our findings contribute to an increasingly detailed portrait of the gene families that define fungal phyla and underpin core features of extant fungi.

From Genome Variation to Molecular Mechanisms: What we Have Learned From Yeast Mitochondrial Genomes?

Analysis of genome variation provides insights into mechanisms in genome evolution. This is increasingly appreciated with the rapid growth of genomic data. Mitochondrial genomes (mitogenomes) are well known to vary substantially in many genomic aspects, such as genome size, sequence context, nucleotide base composition and substitution rate. Such substantial variation makes mitogenomes an excellent model system to study the mechanisms dictating mitogenome variation. Recent sequencing efforts have not only covered a rich number of yeast species but also generated genomes from abundant strains within the same species. The rich yeast genomic data have enabled detailed investigation from genome variation into molecular mechanisms in genome evolution. This mini-review highlights some recent progresses in yeast mitogenome studies.

Variable Spontaneous Mutation and Loss of Heterozygosity among Heterozygous Genomes in Yeast.

Mutation and recombination are the primary sources of genetic variation. To better understand the evolution of genetic variation, it is crucial to comprehensively investigate the processes involving mutation accumulation and recombination. In this study, we performed mutation accumulation experiments on four heterozygous diploid yeast species in the Saccharomycodaceae family to determine spontaneous mutation rates, mutation spectra, and losses of heterozygosity (LOH). We observed substantial variation in mutation rates and mutation spectra. We also observed high LOH rates (1.65-11.07×10-6 events per heterozygous site per cell division). Biases in spontaneous mutation and LOH together with selection ultimately shape the variable genome-wide nucleotide landscape in yeast species.

Evolution of a Record-Setting AT-Rich Genome: Indel Mutation, Recombination, and Substitution Bias.

Genome-wide nucleotide composition varies widely among species. Despite extensive research, the source of genome-wide nucleotide composition diversity remains elusive. Yeast mitochondrial genomes (mitogenomes) are highly A + T rich, and they provide a unique opportunity to study the evolution of AT-biased landscape. In this study, we sequenced ten complete mitogenomes of the Saccharomycodes ludwigii yeast with 8% G + C content, the lowest genome-wide %(G + C) in all published genomes to date. The S. ludwigii mitogenomes have high densities of short tandem repeats but severely underrepresented mononucleotide repeats. Comparative population genomics of these record-setting A + T-rich genomes shows dynamic indel mutations and strong mutation bias toward A/T. Indel mutations play a greater role in genomic variation among very closely related strains than nucleotide substitutions. Indels have resulted in presence-absence polymorphism of tRNAArg (ACG) among S. ludwigii mitogenomes. Interestingly, these mitogenomes have undergone recombination, a genetic process that can increase G + C content by GC-biased gene conversion. Finally, the expected equilibrium G + C content under mutation pressure alone is higher than observed G + C content, suggesting existence of mechanisms other than AT-biased mutation operating to increase A/T. Together, our findings shed new lights on mechanisms driving extremely AT-rich genomes.

The Absence of Calponin 2 in Rabbits Suggests Caution in Choosing Animal Models.

While the rapid development of CRISPR/CAS9 technology has allowed for readily performing site-specific genomic editing in non-rodent species, an emerging challenge is to select the most suitable species to generate animal models for the study of human biology and diseases. Improving CRISPR/CAS9 methodology for more effective and precise editing in the rabbit genome to replicate human disease is an active area of biomedical research. Although rabbits are more closely related to humans than mice (based on DNA sequence analysis), our whole-genome protein database search revealed that rabbits have more missing human protein sequences than mice. Hence, precisely replicating human diseases in rabbits requires further consideration, especially in studies involving essential functions of the missing proteins. For example, rabbits lack calponin 2, an actin-associated cytoskeletal protein that is important in the pathogenesis of inflammatory arthritis, atherosclerosis, and calcific aortic valve disease. The justification of using rabbits as models for human biomedical research is based on their larger size and their closer phylogenetic distance to humans (based on sequence similarity of conserved genes), but this may be misleading. Our findings, which consider whole-genome protein profiling together with actual protein expressions, serve as a warning to the scientific community to consider overall conservation as well as the conservation of specific proteins when choosing an animal model to study a particular aspect of human biology prior to investing in genetic engineering.

Mitochondrial-encoded endonucleases drive recombination of protein-coding genes in yeast.

Mitochondrial recombination in yeast is well recognized, yet the underlying genetic mechanisms are not well understood. Recent progress has suggested that mobile introns in mitochondrial genomes (mitogenomes) can facilitate the recombination of their corresponding intron-containing genes through a mechanism known as intron homing. As many mitochondrial genes lack introns, there is a critical need to determine the extent of recombination and underlying mechanism of intron-lacking genes. This study leverages yeast mitogenomes to address these questions. In Saccharomyces cerevisiae, the 3'-end sequences of at least three intron-lacking mitochondrial genes exhibit elevated nucleotide diversity and recombination hotspots. Each of these 3'-end sequences is immediately adjacent to or even fused as overlapping genes with a stand-alone endonuclease. Our findings suggest that SAEs are responsible for recombination and elevated diversity of adjacent intron-lacking genes. SAEs were also evident to drive recombination of intron-lacking genes in Lachancea kluyveri, a yeast species that diverged from S. cerevisiae more than 100 million years ago. These results suggest SAEs as a common driver in recombination of intron-lacking genes during mitogenome evolution. We postulate that the linkage between intron-lacking gene and its adjacent endonuclease gene is the result of co-evolution.

Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora.

Plastid genomes (plastomes) vary enormously in size and gene content among the many lineages of nonphotosynthetic plants, but key lineages remain unexplored. We therefore investigated plastome sequence and expression in the holoparasitic and morphologically bizarre Balanophoraceae. The two Balanophora plastomes examined are remarkable, exhibiting features rarely if ever seen before in plastomes or in any other genomes. At 15.5 kb in size and with only 19 genes, they are among the most reduced plastomes known. They have no tRNA genes for protein synthesis, a trait found in only three other plastid lineages, and thus Balanophora plastids must import all tRNAs needed for translation. Balanophora plastomes are exceptionally compact, with numerous overlapping genes, highly reduced spacers, loss of all cis-spliced introns, and shrunken protein genes. With A+T contents of 87.8% and 88.4%, the Balanophora genomes are the most AT-rich genomes known save for a single mitochondrial genome that is merely bloated with AT-rich spacer DNA. Most plastid protein genes in Balanophora consist of ≥90% AT, with several between 95% and 98% AT, resulting in the most biased codon usage in any genome described to date. A potential consequence of its radical compositional evolution is the novel genetic code used by Balanophora plastids, in which TAG has been reassigned from stop to tryptophan. Despite its many exceptional properties, the Balanophora plastome must be functional because all examined genes are transcribed, its only intron is correctly trans-spliced, and its protein genes, although highly divergent, are evolving under various degrees of selective constraint.

Case study on the soil antibiotic resistome in an urban community garden.

Urban agricultural soils can be an important reservoir of antibiotic resistance, and have great food safety and public health indications. This study investigated antibiotic-resistant bacteria and antibiotic resistance genes in urban agricultural soils using phenotypic and metagenomic tools. In total, 207 soil bacteria were recovered from 41 soil samples collected from an urban agricultural garden in Detroit, MI, USA. The most prevalent antibiotic resistance phenotype demonstrated by Gram-negative bacteria was resistance to ampicillin (94.2%), followed by chloramphenicol (80.0%), cefoxitin (79.5%), gentamicin (78.4%) and ceftriaxone (71.1%). All Gram-positive bacteria were resistant to gentamicin, kanamycin and penicillin. Genes encoding resistance to quinolones, ß-lactams and tetracyclines were the most prevalent and abundant in the soil. qepA and tetA, both encoding efflux pumps, predominated in the quinolone and tetracycline resistance genes tested, respectively. Positive correlation (P<0.05) was identified among groups of antibiotic resistance genes, and between antibiotic resistance genes and metal resistance genes. The data demonstrated a diverse population of antibiotic resistance in urban agricultural soils. Phenotypic determination together with soil metagenomics proved to be a valuable tool to study the nature and extent of antibiotic resistance in the environment.

Genetic Drift and Indel Mutation in the Evolution of Yeast Mitochondrial Genome Size.

Mitochondrial genomes (mitogenomes) are remarkably diverse in genome size and organization, but the origins of dynamic mitogenome architectures are still poorly understood. For instance, the mutational burden hypothesis postulates that the drastic difference between large plant mitogenomes and streamlined animal mitogenomes can be driven by their different mutation rates. However, inconsistent trends between mitogenome sizes and mutation rates have been documented in several lineages. These conflicting results highlight the need of systematic and sophisticated investigations on the evolution and diversity of mitogenome architecture. This study took advantage of the strikingly variable mitogenome size among different yeast species and also among intraspecific strains, examined sequence dynamics of introns, GC-clusters, tandem repeats, mononucleotide repeats (homopolymers) and evaluated their contributions to genome size variation. The contributions of these sequence features to mitogenomic variation are dependent on the timescale, over which extant genomes evolved from their last common ancestor, perhaps due to a combination of different turnover rates of mobile sequences, variable insertion spaces, and functional constraints. We observed a positive correlation between mitogenome size and the level of genetic drift, suggesting that mitogenome expansion in yeast is likely driven by multiple types of sequence insertions in a primarily nonadaptive manner. Although these cannot be explained directly by the mutational burden hypothesis, our results support an important role of genetic drift in the evolution of yeast mitogenomes.

Origin and Spread of Spliceosomal Introns: Insights from the Fungal Clade Zymoseptoria.

Spliceosomal introns are a key feature of eukaryote genome architecture and have been proposed to originate from selfish group II introns from an endosymbiotic bacterium, that is, the ancestor of mitochondria. However, the mechanisms underlying the wide spread of spliceosomal introns across eukaryotic genomes have been obscure. In this study, we characterize the dynamic evolution of spliceosomal introns in the fungal genus Zymoseptoria at different evolutionary scales, that is, within a genome, among conspecific strains within species, and between different species. Within the genome, spliceosomal introns can proliferate in unrelated genes and intergenic regions. Among conspecific strains, spliceosomal introns undergo rapid turnover (gains and losses) and frequent sequence exchange between geographically distinct strains. Furthermore, spliceosomal introns could undergo introgression between distinct species, which can further promote intron invasion and proliferation. The dynamic invasion and proliferation processes of spliceosomal introns resemble the life cycles of mobile selfish (group I/II) introns, and these intron movements, at least in part, account for the dramatic processes of intron gain and intron loss during eukaryotic evolution.

Rapidly Translated Polypeptides Are Preferred Substrates for Cotranslational Protein Degradation.

Nascent polypeptides are degraded by the proteasome concurrently with their synthesis on the ribosome. This process, called cotranslational protein degradation (CTPD), has been observed for years, but the underlying mechanisms remain poorly understood. Equally unclear are the identities of cellular proteins genuinely subjected to CTPD. Here we report the identification of CTPD substrates in the yeast Saccharomyces cerevisiae via a quantitative proteomic analysis. We compared the abundance of individual ribosome-bound nascent chains between a wild type strain and a mutant defective in CTPD. Of 1,422 proteins acquired from the proteomic analysis, 289 species are efficient CTPD substrates, with >30% of their nascent chains degraded cotranslationally. We found that proteins involved in translation, ribosome biogenesis, nuclear transport, and amino acid metabolism are more likely to be targeted for CTPD. There is a strong correlation between CTPD and the translation efficiency. CTPD occurs preferentially to rapidly translated polypeptides. CTPD is also influenced by the protein sequence length; longer polypeptides are more susceptible to CTPD. In addition, proteins with N-terminal disorder have a higher probability of being degraded cotranslationally. Interestingly, the CTPD efficiency is not related to the half-lives of mature proteins. These results for the first time indicate an inverse correlation between CTPD and cotranslational folding on a proteome scale. The implications of this study with respect to the physiological significance of CTPD are discussed.

Strand-biased cytosine deamination at the replication fork causes cytosine to thymine mutations in Escherichia coli.

The rate of cytosine deamination is much higher in single-stranded DNA (ssDNA) than in double-stranded DNA, and copying the resulting uracils causes C to T mutations. To study this phenomenon, the catalytic domain of APOBEC3G (A3G-CTD), an ssDNA-specific cytosine deaminase, was expressed in an Escherichia coli strain defective in uracil repair (ung mutant), and the mutations that accumulated over thousands of generations were determined by whole-genome sequencing. C:G to T:A transitions dominated, with significantly more cytosines mutated to thymine in the lagging-strand template (LGST) than in the leading-strand template (LDST). This strand bias was present in both repair-defective and repair-proficient cells and was strongest and highly significant in cells expressing A3G-CTD. These results show that the LGST is accessible to cellular cytosine deaminating agents, explains the well-known GC skew in microbial genomes, and suggests the APOBEC3 family of mutators may target the LGST in the human genome.

Extensive Horizontal Transfer and Homologous Recombination Generate Highly Chimeric Mitochondrial Genomes in Yeast.

The frequency of horizontal gene transfer (HGT) in mitochondrial DNA varies substantially. In plants, HGT is relatively common, whereas in animals it appears to be quite rare. It is of considerable importance to understand mitochondrial HGT across the major groups of eukaryotes at a genome-wide level, but so far this has been well studied only in plants. In this study, we generated ten new mitochondrial genome sequences and analyzed 40 mitochondrial genomes from the Saccharomycetaceae to assess the magnitude and nature of mitochondrial HGT in yeasts. We provide evidence for extensive, homologous-recombination-mediated, mitochondrial-to-mitochondrial HGT occurring throughout yeast mitochondrial genomes, leading to genomes that are highly chimeric evolutionarily. This HGT has led to substantial intraspecific polymorphism in both sequence content and sequence divergence, which to our knowledge has not been previously documented in any mitochondrial genome. The unexpectedly high frequency of mitochondrial HGT in yeast may be driven by frequent mitochondrial fusion, relatively low mitochondrial substitution rates and pseudohyphal fusion to produce heterokaryons. These findings suggest that mitochondrial HGT may play an important role in genome evolution of a much broader spectrum of eukaryotes than previously appreciated and that there is a critical need to systematically study the frequency, extent, and importance of mitochondrial HGT across eukaryotes.

A Dynamic Mobile DNA Family in the Yeast Mitochondrial Genome.

Transposable elements (TEs) are an important factor shaping eukaryotic genomes. Although a significant body of research has been conducted on the abundance of TEs in nuclear genomes, TEs in mitochondrial genomes remain elusive. In this study, we successfully assembled 28 complete yeast mitochondrial genomes and took advantage of the power of population genomics to determine mobile DNAs and their propensity. We have observed compelling evidence of GC clusters propagating within the mitochondrial genome and being horizontally transferred between species. These mitochondrial TEs experience rapid diversification by nucleotide substitution and, more importantly, undergo dynamic merger and shuffling to form new TEs. Given the hyper mobile and transformable nature of mitochondrial TEs, our findings open the door to a deeper understanding of eukaryotic mitochondrial genome evolution and the origin of nonautonomous TEs.

DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood.

BACKGROUND: The study of discrete characters is crucial for the understanding of evolutionary processes. Even though great advances have been made in the analysis of nucleotide sequences, computer programs for non-DNA discrete characters are often dedicated to specific analyses and lack flexibility. Discrete characters often have different transition rate matrices, variable rates among sites and sometimes contain unobservable states. To obtain the ability to accurately estimate a variety of discrete characters, programs with sophisticated methodologies and flexible settings are desired. RESULTS: DiscML performs maximum likelihood estimation for evolutionary rates of discrete characters on a provided phylogeny with the options that correct for unobservable data, rate variations, and unknown prior root probabilities from the empirical data. It gives users options to customize the instantaneous transition rate matrices, or to choose pre-determined matrices from models such as birth-and-death (BD), birth-death-and-innovation (BDI), equal rates (ER), symmetric (SYM), general time-reversible (GTR) and all rates different (ARD). Moreover, we show application examples of DiscML on gene family data and on intron presence/absence data. CONCLUSION: DiscML was developed as a unified R program for estimating evolutionary rates of discrete characters with no restriction on the number of character states, and with flexibility to use different transition models. DiscML is ideal for the analyses of binary (1s/0s) patterns, multi-gene families, and multistate discrete morphological characteristics.

Horizontal transfer and gene conversion as an important driving force in shaping the landscape of mitochondrial introns.

Group I introns are highly dynamic and mobile, featuring extensive presence-absence variation and widespread horizontal transfer. Group I introns can invade intron-lacking alleles via intron homing powered by their own encoded homing endonuclease gene (HEG) after horizontal transfer or via reverse splicing through an RNA intermediate. After successful invasion, the intron and HEG are subject to degeneration and sequential loss. It remains unclear whether these mechanisms can fully address the high dynamics and mobility of group I introns. Here, we found that HEGs undergo a fast gain-and-loss turnover comparable with introns in the yeast mitochondrial 21S-rRNA gene, which is unexpected, as the intron and HEG are generally believed to move together as a unit. We further observed extensively mosaic sequences in both the introns and HEGs, and evidence of gene conversion between HEG-containing and HEG-lacking introns. Our findings suggest horizontal transfer and gene conversion can accelerate HEG/intron degeneration and loss, or rescue and propagate HEG/introns, and ultimately result in high HEG/intron turnover rate. Given that up to 25% of the yeast mitochondrial genome is composed of introns and most mitochondrial introns are group I introns, horizontal transfer and gene conversion could have served as an important mechanism in introducing mitochondrial intron diversity, promoting intron mobility and consequently shaping mitochondrial genome architecture.

Homologous recombination drives both sequence diversity and gene content variation in Neisseria meningitidis.

The study of genetic and phenotypic variation is fundamental for understanding the dynamics of bacterial genome evolution and untangling the evolution and epidemiology of bacterial pathogens. Neisseria meningitidis (Nm) is among the most intriguing bacterial pathogens in genomic studies due to its dynamic population structure and complex forms of pathogenicity. Extensive genomic variation within identical clonal complexes (CCs) in Nm has been recently reported and suggested to be the result of homologous recombination, but the extent to which recombination contributes to genomic variation within identical CCs has remained unclear. In this study, we sequenced two Nm strains of identical serogroup (C) and multi-locus sequence type (ST60), and conducted a systematic analysis with an additional 34 Nm genomes. Our results revealed that all gene content variation between the two ST60 genomes was introduced by homologous recombination at the conserved flanking genes, and 94.25% or more of sequence divergence was caused by homologous recombination. Recombination was found in genes associated with virulence factors, antigenic outer membrane proteins, and vaccine targets, suggesting an important role of homologous recombination in rapidly altering the pathogenicity and antigenicity of Nm. Recombination was also evident in genes of the restriction and modification systems, which may undermine barriers to DNA exchange. In conclusion, homologous recombination can drive both gene content variation and sequence divergence in Nm. These findings shed new light on the understanding of the rapid pathoadaptive evolution of Nm and other recombinogenic bacterial pathogens.

Extensive genomic variation within clonal bacterial groups resulted from homologous recombination.

Due to divergence, genetic variation is generally believed to be high among distantly related strains, low among closely related ones and little or none within the same classified clonal groups. Several recent genome-wide studies, however, revealed that significant genetic variation resides in a considerable number of genes among strains with identical MLST (Multilocus sequence typing) types and much of the variation was introduced by homologous recombination. Recognizing and understanding genomic variation within clonal bacterial groups could shed new light on the evolutionary path of infectious agents and the emergence of particularly pathogenic or virulent variants. This commentary presents our recent contributions to this line of work.