Comparative Genomic Studies Research Articles

Transposable element accumulation drives genome size increase in Hylesia metabus (Lepidoptera: Saturniidae), an urticating moth species from South America

Abstract We present the first nuclear genome assembly and a complete mitogenome for Hylesia metabus (Arthropoda; Insecta; Lepidoptera; Saturniidae). The assembled nuclear genome sequence is 1,271 Mb long, which is among the 10 largest lepidopteran genome assemblies published to date. It is scaffolded in 31 pseudo chromosomes, has a BUSCO score of 99.5%, and has a highly conserved synteny compared to phylogenetically close species. Repetitive elements make up 67% of the nuclear genome and are mainly located in intergenic regions, among which LINEs were predominant, with CR1-Zenon being the most abundant. Phylogenetic and comparative analyses of H. metabus assembly and 17 additional Saturniidae and Sphingidae assemblies suggested that an accumulation of repetitive elements likely led to the increased size of H. metabus’ genome. Gene annotation using Helixer identified 26,122 transcripts. The Z scaffold was identified using both a synteny analysis and variations of coverage for two resequenced male and female H. metabus. The H. metabus nuclear genome and mitogenome assemblies can be found and browsed on the BIPAA website and constitute useful resources for future population and comparative genomics studies.

Repeatome Analysis and Satellite DNA Chromosome Patterns in Hedysarum Species

The cosmopolitan genus Hedysarum L. (Fabaceae) is divided into sections Hedysarum, Stracheya, and Multicaulia. This genus includes many valuable medicinal, melliferous, and forage species. The species taxonomy and genome relationships within the sections are still unclear. We examined intra- and interspecific diversity in the section (sect.) Hedysarum based on repeatome analyses using NGS data, bioinformatic technologies, and chromosome FISH mapping of 35S rDNA, 5S rDNA, and the identified satellite DNA families (satDNAs). A comparison of repeatomes of H. alpinum, H. theinum, and H. flavescens revealed differences in their composition. However, similarity in sequences of most satDNAs indicated a close relationship between genomes within sect. Hedysarum. New effective satDNA chromosomal markers were detected, which is important for karyotype analyses within Hedysarum. Intra- and interspecific variability in the chromosomal distribution patterns of the studied markers were revealed, and species karyograms were constructed. These results provided new insight into the karyotype structures and genomic diversity within sect. Hedysarum, clarified the systematic position of H. sachalinense and H. arcticum, and confirmed the distant genomic relationships between species from sections Hedysarum and Multicaulia. Our findings are important for further comparative genome studies within the genus Hedysarum.

Putative evolution of Myxococcus fulvus 124B02 plasmid pMF1 from a chromosomal segment in another Myxococcus species.

Myxobacteria or order Myxococcales (old nomenclature) or phylum Myxococcota (new terminology) are fascinating organisms well known for their diverse peculiar physiological, taxonomic, and genomic properties. Researchers have long sought to identify plasmids within these organisms, yet thus far, only two organisms from different families have been found to harbor a plasmid. This study delves into the putative evolution of one of these plasmids, i.e., pMF1 present in Myxococcus fulvus 124B02 in the suborder Cystobacterineae and family Myxococcaceae. Here, we first reannotated the pMF1 plasmid genome sequence and identified two additional open reading frames or putative genes which were not annotated until now. We further reported that all pMF1 plasmid genes depict homology with Myxococcus stipitatus CYD1 draft genome (contig 28) and a chromosomal segment of M. stipitatus DSM14675 in a syntenic manner, implying the presence of plasmid-like structure in M. stipitatus CYD1, integrated into its chromosome. To comprehend the relationship among these three species, we conducted phylogenetic analyses using 16S and concatenated housekeeping genes and genome-to-genome distance calculator (GGDC) analysis, which confirmed that M. stipitatus CYD1 is a distinct and novel species within the genus Myxococcus. Overall, this comparative genomic study sheds light on the putative emergence of the pMF1 plasmid from a common ancestor of closely related yet distinct species, M. stipitatus CYD1, possibly through the partition from its chromosome as a segment.IMPORTANCEMyxobacteria are not well known to have plasmids. Until now, only two organisms have been shown to have plasmids, raising a pertinent question about how these plasmids evolved randomly within the phylum Myxococcota. The study presented in this manuscript delves into the emergence of the pMF1 plasmid found in Myxococcus fulvus 124B02, a member of the suborder Cystobacterineae and family Myxococcaceae. Our research addresses this intriguing topic of plasmid identification and evolution within myxobacteria, which are a group of fascinating organisms that have garnered significant interest due to their diverse physiological, taxonomic, and genomic properties.

Comparative genomics of obligate predatory bacteria belonging to phylum Bdellovibrionota highlights distribution and predicted functions of lineage-specific protein families.

Comparative genomics of predatory bacteria is important to understand their ecology and evolution and explore their potential to treat drug-resistant infections. We compared chromosomes of 18 obligate predators from phylum Bdellovibrionota (16 intraperiplasmic, two epibiotic) and 15 non-predatory bacteria. Phylogenetics of conserved single-copy genes and analysis of genome-wide average amino acid identity provide evidence for at least five Bdellovibrio species and support recent reclassifications of predatory taxa. To define shared and differential genome content, we grouped predicted protein sequences into gene clusters based on sequence similarity. Few gene clusters are shared by all 33 bacteria or all 18 predatory bacteria; however, we identified gene clusters conserved within lineages, such as intraperiplasmic Bdellovibrio, and not found in other bacteria. Many of these are predicted to function in cell envelope biogenesis, signal transduction, and other roles important for predatory lifestyles. Among intraperiplasmic Bdellovibrio, we detected high abundance of gene clusters predicted to encode transglycosylases, endopeptidases, and lysozymes, and we identified six gene clusters (amidase, L,D-transpeptidase, four transglycosylases) with evidence of recent gene duplication and gene family expansion. Focusing on peptidoglycan metabolism, we defined a suite of gene clusters that include peptidoglycan-degrading and -modifying enzymes and occur only in predatory bacteria, suggesting these proteins may have evolved activities specific to predation. Our analyses highlight key genome content differences between obligate predatory bacteria and non-predatory relatives and identify gene clusters that may encode enzymes adapted to predatory lifestyles. These lineage-specific proteins are strong candidates for functional characterization to clarify their role in predation.IMPORTANCEEvolution of predation as a bacterial lifestyle involves selective pressure on and adaptation of enzymes that contribute to killing and digestion of prey bacteria, in some cases from within the prey itself. Such enzymes are a hallmark of obligate predatory bacteria belonging to phylum Bdellovibrionota, which includes the well-studied predator Bdellovibrio. By comparing protein sequences of obligate predatory bacteria and their non-predatory relatives, we define key genome content differences that distinguish bacterial predators and identify lineage-specific enzymes that may have evolved unique activities due to selective pressures related to a predatory lifestyle. In addition to providing insights into the ecology and evolution of predatory bacteria, comparative genomics studies, like this, can inform efforts to develop predatory bacteria and/or their enzymes as potential biocontrol agents to combat drug-resistant bacterial infections.

Plastid genomics of wild grapevines (<i>Vitis vinifera</i> subsp. <i>sylvestris</i>) of Georgia the cradle of viticulture

The species Vitis vinifera (common grape) is dividing into two sub-species: Vitis vinifera subsp. vinifera (cultivated grapevines) and Vitis vinifera subsp. sylvestris (wild grapevines). Vitis vinifera subsp. vinifera is widely utilised for table fruits and serves as the primary source for the production of grape-related beverages, including wine and vinegar. Wild grapevines (Vitis vinifera subsp. sylvestris) are of great interest as they are considered the progenitors of cultivated varieties and are key to understanding the grapevine domestication process in general. To unlock the molecular mechanisms of grapevine domestication, genome-based studies are widely carried out. In this study, the complete chloroplast genome of two Georgian wild grapevine samples is subject to Illumina sequencing and in silico genome assembly, followed by gene annotation. According to the results, each analysed chloroplast genome is 160.928 bp in length, comprises a total of 128 genes (83 protein coding, 37 tRNA, 8 rRNA) and belongs to the genetically unique ‘Rkatsiteli’ haplotype (AAA). A comparative genomic study reveals the presence of certain InDels and SNPs in the chloroplast genomes.

Antimicrobial resistance, virulence factors and phylogenetic profiles of Vibrio parahaemolyticus in the eastern coast of Shenzhen

Vibrio parahaemolyticus (V. parahaemolyticus) is a major food-borne pathogen which causes human gastroenteritis. Since the characteristics of V. parahaemolyticus remain unknown, 220 isolates selected from clinical and environmental samples in Dapeng of Shenzhen were tested for the presence of two hemolysin-expressing genes tdh and trh. Among 27 clinical isolates, 26 carrired the tdh gene, and the other one carried both tdh and trh genes, however neither genes were detected in environmental isolates. Meanwhile, antimicrobial susceptibility profiles revealed the isolates with high frequency of resistance to ampicillin (77.73%) and colistin (71.82%) and medium to streptomycin (57.27%). Genetically, by whole genome sequencing (WGS), comparative genomics studies was performed on isolates from various districts and GenBank. Data analysis showed that antimicrobial resistance genes (ARGs) blaCARB, tet(34) and tet(35) were harbored in all genomes and other ARGs was absent in the genomes of 27 clinical isolates. Besides, little regional difference was observed. As for virulence factors, MAM7, T3SS1, T3SS1 secret effector, T3SS2, T3SS2 secret effector, and VpadF were carried by most isolates. Two isolates from other districts were tdh gene positive which clustered with clinical isolates from Dapeng in the same clade, indicating close genetic distance. This study revealed the widely distribution of V. parahaemolyticus in Shenzhen and the diverse ARGs and virulence genes it carried. Furthermore, pathways that pathogen disseminated through were discussed.

SoIR: a comprehensive Solanaceae information resource for comparative and functional genomic study.

The Solanaceae family, which includes economically important crops such as tomatoes, potatoes and peppers, has experienced a rapid expansion in genomic data due to advancements in sequencing technologies. However, existing databases are limited by incomplete species representation, a lack of comprehensive comparative genomic tools and the absence of systematic pan-genomic analyses. To address these gaps, we developed the Solanaceae Information Resource (SoIR, https://soir.bio2db.com), a comprehensive genomics database for the Solanaceae family. SoIR integrates genomic data from 81 species and transcriptomic data from 41 species, encompassing a total of 3908408 gene annotations derived from Gene Ontology, nonredundant protein, Pfam, Swiss-Prot and TrEMBL databases. The resource also includes 3437115 CRISPR guide sequences, 212395 transcription factorsand 19086 genes associated with methylation modification. In addition to species-specific analyses, SoIR provides extensive bioinformatics tools for investigating gene family evolution, phylogenetic relationships and karyotype reconstruction across 25 fully sequenced genomes. With advanced tools such as Blast, Synteny and Sequence Alignment, the platform provides users with interactive and intuitive visualizations for conducting cross-species comparative genomics. As the first comprehensive pan-genomic resource for the entire Solanaceae family, SoIR facilitates in-depth cross-species analysis, supporting global research initiatives in plant evolution, functional genomics and crop improvement.

Characterization, Genome Sequencing, and Development of a Rapid PCR Identification Primer for Fusarium oxysporum f. sp. crocus, a New forma specialis Causing Saffron Corm Rot

Saffron corm rot (SCR), the most serious disease affecting saffron, has been confirmed to be caused by Fusarium oxysporum in previous studies. Compared to other fungal species, F. oxysporum exhibits host specialization, a special phenomenon associated with the secreted in xylem (SIX) genes. This study examined the pathogenicity specialization of F. oxysporum isolated from saffron corms with SCR disease. The results showed that this F. oxysporum strain was strongly pathogenic to saffron corms, causing SCR; weakly pathogenic to the corms of freesia, which is in the Iridaceae family along with saffron; and not pathogenic to watermelon, melon, and tomato. Other formae speciales of F. oxysporum were not pathogenic to saffron corms. This suggests that F. oxysporum saffron strains exhibit obvious pathogenicity specialization for Iridaceae spp. Subsequently, the F. oxysporum saffron strain (XHH35) genome was sequenced, and a comparative genomics study of XHH35 and three other formae speciales was conducted using OrthoVenn3. XHH35 contained 90 specific genes absent in the other three formae speciales. These genes are involved in certain key biological processes and molecular functions. Based on BLAST homology searching, the F. oxysporum saffron strain (XHH35) genome was predicted to contain seven SIX genes (SIX 4, SIX 6, SIX 7, SIX 10, SIX 11, SIX 12, and SIX 14) highly homologous to F. oxysporum f. sp. lycopersici, which was verified using polymerase chain reaction (PCR) amplification. The corresponding individual phylogenetic tree indicated that the F. oxysporum saffron strain (XHH35) showed a separate branch with different formae speciales. This study is the first-ever report of F. oxysporum f. sp. crocus, a new forma specialis. Based on the specificity of its SIX genes, the SIX 10 gene was selected to further establish a rapid identification technique for F. oxysporum f. sp. crocus, which will be useful in future research.

Repeated Shifts in Sociality Are Associated With Fine-tuning of Highly Conserved and Lineage-Specific Enhancers in a Socially Flexible Bee.

Comparative genomic studies of social insects suggest that changes in gene regulation are associated with evolutionary transitions in social behavior, but the activity of predicted regulatory regions has not been tested empirically. We used self-transcribing active regulatory region sequencing, a high-throughput enhancer discovery tool, to identify and measure the activity of enhancers in the socially variable sweat bee, Lasioglossum albipes. We identified over 36,000 enhancers in the L. albipes genome from 3 social and 3 solitary populations. Many enhancers were identified in only a subset of L. albipes populations, revealing rapid divergence in regulatory regions within this species. Population-specific enhancers were often proximal to the same genes across populations, suggesting compensatory gains and losses of regulatory regions may preserve gene activity. We also identified 1,182 enhancers with significant differences in activity between social and solitary populations, some of which are conserved regulatory regions across species of bees. These results indicate that social trait variation in L. albipes is associated with the fine-tuning of ancient enhancers as well as lineage-specific regulatory changes. Combining enhancer activity with population genetic data revealed variants associated with differences in enhancer activity and identified a subset of differential enhancers with signatures of selection associated with social behavior. Together, these results provide the first empirical map of enhancers in a socially flexible bee and highlight links between cis-regulatory variation and the evolution of social behavior.

First Complete Genome Sequence of Nigrospora osmanthi: A Fundamental Resource for Studying the Plant Pathogenic Fungus

Nigrospora osmanthi strain Z1 is a potential bioherbicide for the biological control of water lettuce, one of the most common invasive weeds. Here, the first high-quality genome assembly of N. osmanthi was obtained by a combination of PacBio and Illumina sequencing technologies. Twelve contigs representing the nuclear genome and one mitochondrial DNA were generated, with a total length of 45.94 Mb, an N50 equal to 6.99 Mb, and a GC content of 57.91%; 9 of the 12 nuclear contigs represented chromosomes from telomere to telomere characterized by telomeric-like repeats. A total of 11,051 genes were predicted using a combination of gene prediction tools, including 336 noncoding RNAs, 1,298 genes encoding secretory proteins, 1,735 genes encoding carbohydrate-active enzymes, 1,955 fungal virulence factors, and 50 putative secondary metabolite gene clusters. This complete genome sequence can serve as a valuable resource for future comparative genomic studies of the fungus Nigrospora for effective application in the biocontrol of invasive species and the discovery of fungal secondary metabolites. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Comparative Genomic Study of Non-typeable Haemophilus influenzae in Children with Pneumonia and Healthy Controls

Comparative Genomic Study of Non-typeable Haemophilus influenzae in Children with Pneumonia and Healthy Controls

Full-length transcriptome assembly of black amur bream (Megalobrama terminalis) as a reference resource.

The genus Megalobrama holds significant economic value in China, with M. terminalis (Black Amur bream) ranking second in production within this group. However, lacking comprehensive genomic and transcriptomic data has impeded research progress. This study aims to fill this gap through an extensive transcriptomic analysis of M. terminalis. We utilized PacBio Isoform Sequencing to generate 558,998 subreads, totaling 45.52 Gb, which yielded 22,141 transcripts after rigorous filtering and clustering. Complementary Illumina short-read sequencing corrected 967,114 errors across these transcripts. Our analysis identified 12,426 non-redundant isoforms, with 11,872 annotated in various databases. Functional annotation indicated 11,841 isoforms matched entries in the NCBI non-redundant protein sequences database. Gene Ontology analysis categorized 10,593 isoforms, revealing strong associations with cellular processes and binding functions. Additionally, 8203 isoforms were mapped to pathways in the Kyoto Encyclopedia of Genes and Genomes, highlighting significant involvement in immune system processes and complement cascades. We notably identified key immune molecules such as alpha-2-macroglobulin and complement component 3, each with multiple isoforms, underscoring their potential roles in the immune response. Our analysis also uncovered 853 alternative splicing events, predominantly involving retained introns, along with 672 transcription factors and 426 long non-coding RNAs. The high-quality reference transcriptome generated in this study provides a valuable resource for comparative genomic studies within the Megalobrama genus, supporting future research to enhance aquaculture stocks.

Visualizing genomic evolution in Caenorhabditis through WormSynteny

Understanding the syntenic relationships among genomes is crucial to elucidate the genomic mechanisms that drive the evolution of species. The nematode Caenorhabditis is a good model for studying genomic evolution due to the well-established biology of Caenorhabditis elegans and the availability of > 50 genomes in the genus. However, effective alignment of more than ten species in Caenorhabditis has not been conducted before, and there is currently no tool to visualize the synteny of more than two species. In this study, we used Progressive Cactus, a recently developed multigenome aligner, to align the genomes of eleven Caenorhabditis species. Through the progressive alignment, we reconstructed nine ancestral genomes, analyzed the mutational types that cause genomic rearrangement during speciation, and found that insertion and duplication are the major driving forces for genome expansion. Dioecious species appear to expand their genomes more than androdioecious species. We then built an online interactive app called WormSynteny to visualize the syntenic relationship among the eleven species. Users can search the alignment dataset using C. elegans query sequences, construct synteny plots at different genomic scales, and use a set of options to control alignment output and plot presentation. We showcased the use of WormSynteny to visualize the syntenic conservation of one-to-one orthologues among species, tandem and dispersed gene duplication in C. elegans, and the evolution of exon and intron structures. Importantly, the integration of orthogroup information with synteny linkage in WormSynteny allows the easy visualization of conserved genomic blocks and disruptive rearrangement. In conclusion, WormSynteny provides immediate access to the syntenic relationships among the most widely used Caenorhabditis species and can facilitate numerous comparative genomics studies. This pilot study with eleven species also serves as a proof-of-concept to a more comprehensive larger-scale analysis using hundreds of nematode genomes, which is expected to reveal mechanisms that drive genomic evolution in the Nematoda phylum. Finally, the WormSynteny software provides a generalizable solution for visualizing the output of Progressive Cactus with interactive graphics, which would be useful for a broad community of genome researchers.

Characterization of hAT DNA transposon superfamily in the genome of Neotropical fish Apareiodon sp.

DNA transposons are diverse in fish genomes and have been described to generate genomic evolutionary novelties. hAT transposable element data are scarce in Teleostei genomes, making it challenging to conduct comparative genomic studies to understand their neutrality or function. This study aimed to perform a genomic and molecular characterization of hAT copies to assess the diversity of these elements and associate changes in these sequences to genomic and karyotypic novelties in Apareiodon sp. The data revealed that hAT TEs are highly abundant in the Apareiodon sp. genome, with few possibly autonomous copies. Highly conserved sequences with likely functional transposases were observed in nine hAT elements. A great diversity of hAT subgroups was observed, especially from Ac, Charlie, Blackjack, Tip100, hAT6, and hAT5, and a similar wave of hAT genomic invasion was identified in the genome for these six groups of hAT sequences. The data also revealed a distinct number of microsatellites within degenerated hAT copies. hAT sites were demonstrated to be dispersed in the Apareiodon sp. chromosomes and not involved in W chromosome-specific region differentiation. In conclusion, the genomic analysis revealed a great diversity of hAT elements, possible autonomous copies, and differentiation of degenerated transposable elements into tandem sequences.

Exploring pangenomic diversity and CRISPR-Cas evasion potential in jumbo phages: a comparative genomics study.

Jumbo phages are large bacterial viruses known for more than 50 years. However, only in recent years, a significant number of complete genome sequences of jumbo phages have become available. In this study, we employed comparative genomic approaches to investigate the genomic diversity and genome protection capabilities of the 331 jumbo phages. Our findings revealed that jumbo phages exhibit high genetic diversity, with only a few genes being relatively conserved across jumbo phages. Interestingly, our data suggest that jumbo phages employ yet-to-be-identified strategies to protect their DNA from the host immune system, such as CRISPR-Cas.

Reference-based genome assembly and comparative genomics of Calamus Brandisii Becc. for unveiling sex-specific genes for early gender detection.

Calamus brandisii Becc. is an endangered rattan species indigenous to the Western Ghats of India and used in the furniture and handicraft industries. However, its dioecious nature and longer flowering time pose challenges for conservation efforts. Developing markers for early gender detection in seedlings is crucial for maintaining viable populations for in-situ and ex-situ conservation. Currently, no sex chromosomes or gender-specific genes have been reported in the species. We report the first comprehensive comparative genomics study between the male and female genomes of C. brandisii to identify polymorphisms and potential genes for gender determination. Reference-based assembly was conducted and the male and female genomes were predicted to contain 43,810 and 50,493 protein-coding genes respectively. The haploid genome size was ∼691Mb and ∼884Mb for male and female genomes respectively. Comparative analysis revealed significant genetic variation between the two genomes including 619,776 SNPs, 73,659 InDels, 212,123 Structural variants (SVs) and 305 copy number variations (CNVs). A total of 5 male-specific and 11 female-specific genes linked to the sex determining region was predicted. The genomic variants identified between the two genomes could be used in development of markers for early gender identification in C. brandisii for restoration programs. The gender-specific genes identified in this study also provide new insights into the mechanisms of sex determination and differentiation in rattans.

A chromosome phased diploid genome assembly of African hunting dog (Lycaon pictus).

The African hunting dog (Lycaon pictus, 2n=78) once ranged over most sub-Saharan ecosystems except its deserts and rainforests. However as a result of (still ongoing) population declines, today they remain only as small fragmented populations. Furthermore, the future of the species remains unclear, due to both anthropogenic pressure as well as interactions with domestic dogs, thus their preservation is a conservation priority. On the tree of life, the hunting dog is basal to Canis and Cuon and forms a crown group with them, making it a useful species for comparative genomic studies. Here, we present a diploid chromosome level assembly of an African hunting dog. Assembled according to VGP guidelines from a combination of PacBio HiFi reads and HiC data, it is phased at the level of individual chromosomes. The maternal (pseudo)haplotype (mat) of our assembly has a length of 2.38 Gbp, and 99.36 % of the sequence is encompassed by 39 chromosomal scaffolds. The rest is included in only 36 unplaced short scaffolds. At the contig level, mat consists of only 166 contigs with an N50 of 39 Mbp. BUSCO analysis showed 95.4 % completeness based on Сarnivora conservative genes (carnivora_odb10). When compared to other available genomes from subtribe Canina, the quality of the assembly is excellent, typically between the 1st and 3rd depending on the parameter used, and a significant improvement on previously published genomes for the species. We hope this assembly will play an important role in future conservation efforts and comparative studies of canid genomes.

A comparative genomic and phenotypic study of Vibrio cholerae model strains using hybrid sequencing

Next-generation sequencing methods have become essential for studying bacterial biology and pathogenesis, often depending on high-quality, closed genomes. In this study, we utilized a hybrid sequencing approach to assemble the genome of C6706, a widely used Vibrio cholerae model strain. We present a manually curated annotation of the genome, enhancing user accessibility by linking each coding sequence to its counterpart in N16961, the first sequenced V. cholerae isolate and a commonly used reference genome. Comparative genomic analysis between V. cholerae C6706 and N16961 uncovered multiple genetic differences in genes associated with key biological functions. To determine whether these genetic variations result in phenotypic differences, we compared several phenotypes relevant to V. cholerae pathogenicity like genetic stability, acid sensitivity, biofilm formation and motility. Notably, V. cholerae N16961 exhibited greater motility and reduced biofilm formation compared to V. cholerae C6706. These phenotypic differences appear to be mediated by variations in quorum sensing and cyclic di-GMP signalling pathways between the strains. This study provides valuable insights into the regulation of biofilm formation and motility in V. cholerae.

A synthetic review: natural history of amniote reproductive modes in light of comparative evolutionary genomics

ABSTRACTThere is a current lack of consensus on whether the ancestral parity mode was oviparity (egg‐laying) or viviparity (live‐birth) in amniotes and particularly in squamates (snakes, lizards, and amphisbaenids). How transitions between parity modes occur at the genomic level has primary importance for how science conceptualises the origin of amniotes, and highly variable parity modes in Squamata. Synthesising literature from medicine, poultry science, reproductive biology, and evolutionary biology, I review the genomics and physiology of five broad processes (here termed the ‘Main Five’) expected to change during transitions between parity modes: eggshell formation, embryonic retention, placentation, calcium transport, and maternal–fetal immune dynamics. Throughout, I offer alternative perspectives and testable hypotheses regarding proximate causes of parity mode evolution in amniotes and squamates. If viviparity did evolve early in the history of lepidosaurs, I offer the nucleation site hypothesis as a proximate explanation. The framework of this hypothesis can be extended to amniotes to infer their ancestral state. I also provide a mechanism and hypothesis on how squamates may transition from viviparity to oviparity and make predictions about the directionality of transitions in three species. After considering evidence for differing perspectives on amniote origins, I offer a framework that unifies (i) the extended embryonic retention model and (ii) the traditional model which describes the amniote egg as an adaptation to the terrestrial environment. Additionally, this review contextualises the origin of amniotes and parity mode evolution within Medawar's paradigm. Medawar posited that pregnancy could be supported by immunosuppression, inertness, evasion, or immunological barriers. I demonstrate that this does not support gestation or gravidity across most amniotes but may be an adequate paradigm to explain how the first amniote tolerated internal fertilization and delayed egg deposition. In this context, the eggshell can be thought of as an immunological barrier. If serving as a barrier underpins the origin of the amniote eggshell, there should be evidence that oviparous gravidity can be met with a lack of immunological responses in utero. Rare examples of two species that differentially express very few genes during gravidity, suggestive of an absent immunological reaction to oviparous gravidity, are two skinks Lampropholis guichenoti and Lerista bougainvillii. These species may serve as good models for the original amniote egg. Overall, this review grounds itself in the historical literature while offering a modern perspective on the origin of amniotes. I encourage the scientific community to utilise this review as a resource in evolutionary and comparative genomics studies, embrace the complexity of the system, and thoughtfully consider the frameworks proposed.

Pathogenicity, phylogenomic, and comparative genomic study of Pseudomonas syringae sensu lato affecting sweet cherry in California.

Comprehensive identification of phytopathogens and an in-depth understanding of their genomic architecture, particularly virulence determinants and antibiotic-resistant genes, are critical for several practical reasons. These include disease diagnosis, improved knowledge of disease epidemiology, pathogen diversity, and determination of the best possible management strategies. In this study, we provide the first report of the presence and pathogenicity of genomospecies Pseudomonas cerasi and Pseudomonas viridiflava in California sweet cherry. More importantly, we report a relatively high level of resistance to copper among the population of Pseudomonas syringae pv. syringae (47.5%). This implies copper cannot be effectively used to control bacterial blast and bacterial canker of sweet cherries. On the other hand, no isolates were resistant to kasugamycin, an indication that kasugamycin could be effectively used for the control of bacterial blast and bacterial canker. Our findings are important to improve the management of bacterial blast and bacterial canker of sweet cherries in California.