Mitogenome evolution in Trichoderma afroharzianum strains: for a better understanding of distinguishing genus

Trichoderma afroharzianum (Hypocreales) is known as an important mycoparasite and biocontrol fungus and feeds on fungal material by parasitizing other fungi. Recent studies indicate that this species is also an ear rot pathogen in Europe. Here, the complete mitochondrial genome of three T. afroharzianum strains was sequenced using next-generation sequencing and comparatively characterized by the reported Trichoderma mitogenomes. T. afroharzianum mitogenomes were varying between 29 511 bp and 29 517 bp in length, with an average A + T content of 72.32%. These mitogenomes contain 14 core protein coding genes (PCGs), 22 tRNAs, two rRNAs, one gene encoding the ribosomal protein S3, and three or four genes including conserved domains for the homing endonucleases (HEGs; GIY-YIG type and LAGLIDADG type). All PCGs are initiated by ATG codons, except for atp8, and all are terminated with TAA. A significant correlation was observed between nucleotide composition and codon preference. Four introns belonging to the group I intron class were predicted, accounting for about 14.54% of the size of the mitogenomes. Phylogenetic analyses confirmed the positions of T. afroharzianum strains within the genus of Trichoderma and supported a sister group relationship between T. afroharzianum and T. simmonsii. The recovered trees also supported the monophyly of all included families and of the genus of Acremonium. The characterization of mitochondrial genome of T. afroharzianum contributes to the understanding of phylogeny and evolution of Hypocreales.

Haplotype-resolved genome assembly of Phanera championii reveals molecular mechanisms of flavonoid synthesis and adaptive evolution

Phanera championii is a medicinal liana plant that has successfully adapted to hostile karst habitats. Despite extensive research on its medicinal components and pharmacological effects, the molecular mechanisms underlying the biosynthesis of critical flavonoids and its adaptation to karst habitats remain elusive. In this study, we performed high-coverage PacBio and Hi-C sequencing of P. championii, which revealed its high heterozygosity and phased the genome into two haplotypes: Hap1 (384.60 Mb) and Hap2 (383.70 Mb), encompassing a total of 58 612 annotated genes. Comparative genomes analysis revealed that P. championii experienced two whole-genome duplications (WGDs), with approximately 59.59% of genes originating from WGD events, thereby providing a valuable genetic resource for P. championii. Moreover, we identified a total of 112 genes that were strongly positively selected. Additionally, about 81.60 Mb of structural variations between the two haplotypes. The allele-specific expression patterns suggested that the dominant effect of P. championii was the elimination of deleterious mutations and the promotion of beneficial mutations to enhance fitness. Moreover, our transcriptome and metabolome analysis revealed alleles in different tissues or different haplotypes collectively regulate the synthesis of flavonoid metabolites. In summary, our comprehensive study highlights the significance of genomic and morphological adaptation in the successful adaptation of P. championii to karst habitats. The high-quality phased genomes obtained in this study serve as invaluable genomic resources for various applications, including germplasm conservation, breeding, evolutionary studies, and elucidation of pathways governing key biological traits of P. championii.

Impact of Homologous Recombination on Core Genome Evolution and Host Adaptation of Pectobacterium parmentieri

Homologous recombination is a major force mechanism driving bacterial evolution, host adaptability, and acquisition of novel virulence traits. Pectobacterium parmentieri is a plant bacterial pathogen distributed worldwide, primarily affecting potatoes, by causing soft rot and blackleg diseases. The goal of this investigation was to understand the impact of homologous recombination on the genomic evolution of P. parmentieri. Analysis of P. parmentieri genomes using Roary revealed a dynamic pan-genome with 3,742 core genes and over 55% accessory genome variability. Bayesian population structure analysis identified 7 lineages, indicating species heterogeneity. ClonalFrameML analysis displayed 5,125 recombination events, with the lineage 4 exhibiting the highest events. fastGEAR analysis identified 486 ancestral and 941 recent recombination events ranging from 43 bp to 119 kb and 36 bp to 13.96 kb, respectively, suggesting ongoing adaptation. Notably, 11% (412 genes) of the core genome underwent recent recombination, with lineage 1 as the main donor. The prevalence of recent recombination (double compared to ancient) events implies continuous adaptation, possibly driven by global potato trade. Recombination events were found in genes involved in vital cellular processes (DNA replication, DNA repair, RNA processing, homeostasis, and metabolism), pathogenicity determinants (type secretion systems, cell-wall degrading enzymes, iron scavengers, lipopolysaccharides (LPS), flagellum, etc.), antimicrobial compounds (phenazine and colicin) and even CRISPR-Cas genes. Overall, these results emphasize the potential role of homologous recombination in P. parmentieri's evolutionary dynamics, influencing host colonization, pathogenicity, adaptive immunity, and ecological fitness.

Genomic evolutional analysis of surgical resected specimen to assess osimertinib as a first-line therapy in two patients with lung cancer harboring EGFR mutation: Case series

Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) is crucial for patients with lung cancer harboring EGFR mutations. However, almost all patients experience disease progression, regardless of their response to the targeted therapy, necessitating the development of additional treatment options. Two patients with lung cancer harboring EGFR-L858R mutations in exon 21 were treated by surgical resection during successful osimertinib treatment. Because the pathological diagnosis was suspected to be pleural metastasis, osimertinib treatment was continued until disease progression. We analyzed the evolution of genomic alterations and the levels of AXL using tumor specimens obtained by repeated biopsies during the course of treatment: initial diagnosis, operation, and disease progression. Genetic alterations detected at the three time points were dramatically changed and showed reductions in numbers, while EGFR-L858R mutations were detected in all samples tested in both patients. Immunohistochemical expression of AXL remained positive from the beginning of analysis to disease progression. Clonal evolution under oncogenesis is related to gradual accumulation of genomic alterations during tumor growth. However, our case series revealed that volume reduction procedures may cause this phenomenon. Therefore, identification of intrinsic drug-resistant cells in tumors may be as important as detection of acquired genetic alterations.

Continuing genomic evolution of the Neisseria meningitidis cc11.2 urethritis clade, NmUC: a narrative review

Neisseria meningitidis (Nm) is a bacterial pathogen responsible for invasive meningococcal disease. Though typically colonizing the nasopharynx, multiple outbreaks of meningococcal urethritis were first reported in 2015-2016; outbreaks originally presumed to be caused by Neisseria gonorrhoeae (Ng). Genomic analysis revealed that the Nm isolates causing these outbreaks were a distinct clade, and had integrated gonococcal DNA at multiple genomic sites, including the gonococcal denitrification apparatus aniA-norB, a partial gonococcal operon of five genes containing ispD, and the acetylglutamate kinase gene argB with the adjacent gonococcal locus NGO0843. The urethritis isolates had also deleted the group C capsule biosynthesis genes cssA/B/C and csc, resulting in loss of capsule. Collectively, these isolates form the N. meningitidis urethritis clade (NmUC). Genomic analysis of recent (2016-2022) NmUC isolates revealed that the genomic features have been maintained in the clade, implying that they are important for NmUC's status as a urogenital pathogen. Furthermore, the analysis revealed the emergence of a sub-clade, designated NmUC-B, phylogenetically separated from the earlier NmUC-A. This sub-clade has integrated additional gonococcal alleles into the genome, including alleles associated with antimicrobial resistance. NmUC continues to adapt to a urethral niche and evolve as a urogenital pathogen.

Expression of EGFR-mutant proteins and genomic evolution in EGFR-mutant transformed small cell lung cancer

Background

The transformation of epidermal growth factor receptor (EGFR)-mutant lung adenocarcinoma (LUAD) into small cell lung cancer (SCLC) accounts for 3-14% of the resistance mechanism to EGFR tyrosine kinase inhibitors (TKIs). At present, there is no relevant research to explore the dynamic expression of EGFR-mutant proteins and genomic evolution in EGFR-mutant transformed SCLC/neuroendocrine carcinoma (NEC).

Methods

Genetic analysis and protein level analysis by next-generation sequencing (NGS), Whole-exome sequencing (WES) and immunohistochemistry were performed to explore expression of EGFR-mutant proteins and genomic evolution in EGFR-mutant transformed SCLC. The research used three patient-derived organoids (PDOs) to explore the efficacy of combo [chemotherapy (chemo) plus TKI or bevacizumab] treatment. According to the subsequent treatment regimens after SCLC/NEC transformation, 35 patients were divided into chemo (n=21) and combo (n=14) groups.

Results

EGFR L858R and EGFR E746-750 del protein expression by immunohistochemistry was 80.0% (4/5) and 100% (6/6), respectively (P=0.455) in initially-transformed tissues. Meanwhile, EGFR-mutant proteins were expressed in 85.7% (6/7) of dynamic rebiopsy tissues or effusion samples after the first transformation. Then, by the pathway enrichment analysis of tissue and plasma NGS, the EGFR-related pathways were still activated after SCLC/NEC transformation. Moreover, WES analysis revealed that transformed SCLC shared a common clonal origin from the baseline LUAD. The drug sensitivity of three PDOs demonstrated potent anti-cancer activity of EGFR-TKIs plus chemo, compared with chemo or TKI alone. There were significant differences in objective response rate (ORR) between the combo and chemo groups [42.9 % vs. 4.8%, P=0.010, 95% confidence interval (CI): 1.5-145.2]. Furthermore, the median post-transformation progression-free survival (pPFS) was significantly prolonged in the combo group, with 5.4 (95% CI: 3.4-7.4) versus 3.5 (95% CI: 2.7-4.3, P=0.012) months.

Conclusions

EGFR 19del or L858R-mutant proteins could be constantly expressed, and EGFR pathway still existed in EGFR-mutant transformed SCLC/NEC with a common clonal origin from the baseline LUAD. Taking together, these molecular characteristics potentially favored clinical efficacy in transformed SCLC/NEC treated with the combo regimen.

Modular and Flexible Molecular Device for Simultaneous Cytosine and Adenine Base Editing at Random Genomic Loci in Filamentous Fungi

Random base editing is regarded as a fundamental method for accelerating the genomic evolution in both scientific research and industrial applications. In this study, we designed a modular interaction-based dual base editor (MIDBE) that assembled a DNA helicase and various base editors through dockerin/cohesin-mediated protein-protein interactions, resulting in a self-assembled MIDBE complex capable of editing bases at any locus in the genome. The base editing type of MIDBE can be readily controlled by the induction of cytidine or/and adenine deaminase gene expression. MIDBE exhibited the highest editing efficiency 2.3 × 10³ times greater than the native genomic mutation rate. To evaluate the potential of MIDBE in genomic evolution, we developed a removable plasmid-based MIDBE tool, which led to a remarkable 977.1% increase of lovastatin production in Monascus purpureus HJ11. MIDBE represents the first biological tool for generating and accumulating base mutations in Monascus chromosome and also offers a bottom-up strategy for designing the base editor.

Genetic characteristics of classical astroviruses in Shenzhen, China, 2016-2019

Human astrovirus (HAstV) is a single-stranded, positive-sense RNA virus and is the leading cause of viral gastroenteritis. However, despite its prevalence, astroviruses still remain one of the least studied enteroviruses. In this study, we sequenced 11 classical astrovirus strains from clinical samples collected in Shenzhen, China from 2016 to 2019, analyzed their genetic characteristics, and deposited them into GenBank. We conducted phylogenetic analysis using IQ-TREE software, with references to astrovirus sequences worldwide. The phylogeographic analysis was performed using the Bayesian Evolutionary Analysis Sampling Trees program, through Bayesian Markov Chain Monte Carlo sampling. We also conducted recombination analysis with the Recombination Detection Program. The newly sequenced strains were categorized as HAstV genotype 1, which is the predominant genotype in Shenzhen. Phylogeographic reconstruction indicated that HAstV-1 may have migrated from the United States to China, followed by frequent transmission between China and Japan. The recombination analysis revealed recombination events within and across genotypes, and identified a recombination-prone region that produced relatively uniform recombination breakpoints and fragment lengths. The genetic analysis of HAstV strains in Shenzhen addresses the current lack of astrovirus data in the region of Shenzhen and provides key insights to the evolution and transmission of astroviruses worldwide. These findings highlight the importance of improving surveillance of astroviruses.

Phenotypic and genomic analysis of the hypervirulent ST22 methicillin-resistant Staphylococcus aureus in China

ST22 MRSA (methicillin-resistant Staphylococcus aureus) strains are only sporadically reported in China. Through the phylogenetic reconstruction of 30 ST22 strains from China and 480 ST22 strains from global sources, we found that the global ST22 strains can be divided into three clades (I, II, and III). The China ST22 strains were found primarily in clade II (IIb and IIc) and also in clade III, indicating that the China ST22-MRSA clones have different origins. The China subclade IIb strains (SCCmec Vb-t309) may evolve from the native ST22 MSSA clone, while the China IIc strains may have spread from other countries. Subclade IIc (SCCmecIVa-t309) strains exhibited particularly strong lethality and invasiveness in Galleria mellonella infection and mouse skin abscess models in comparison to USA300 and other dominant China HA-MRSA (ST5 and ST239) or CA-MRSA (ST59) strains. This study described the emergence of a highly virulent ST22 MRSA subclade and improved our insight into the molecular epidemiology of ST22 strains in China.

Genomic footprints of Kam Sweet Rice domestication indicate possible migration routes of the Dong people in China and provide resources for future rice breeding

The Dong people are one of China's 55 recognized ethnic minorities, but there has been a long-standing debate about their origins. In this study, we performed whole-genome resequencing of Kam Sweet Rice (KSR), a valuable, rare, and ancient rice landrace unique to the Dong people. Through comparative genomic analyses of KSR and other rice landraces from south of the Yangtze River Basin in China, we provide evidence that the ancestors of the Dong people likely originated from the southeast coast of China at least 1000 years ago. Alien introgression and admixture in KSR demonstrated multiple migration events in the history of the Dong people. Genomic footprints of domestication demonstrated characteristics of KSR that arose from artificial selection and geographical adaptation by the Dong people. The key genes GS3, Hd1, and DPS1 (related to agronomic traits) and LTG1 and MYBS3 (related to cold tolerance) were identified as domestication targets, reflecting crop improvement and changes in the geographical environment of the Dong people during migration. A genome-wide association study revealed a candidate yield-associated gene, Os01g0923300, a specific haplotype in KSR that is important for regulating grain number per panicle. RNA-sequencing and quantitative reverse transcription-PCR results showed that this gene was more highly expressed in KSR than in ancestral populations, indicating that it may have great value in increasing yield potential in other rice accessions. In summary, our work develops a novel approach for studying human civilization and migration patterns and provides valuable genomic datasets and resources for future breeding of high-yield and climate-resilient rice varieties.

Clinical and Molecular Characterizations of Carbapenem-Resistant Klebsiella pneumoniae Causing Bloodstream Infection in a Chinese Hospital

Bloodstream infection (BSI) caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious and urgent threat for hospitalized patients. This study aims to describe the clinical and molecular characteristics of CRKP causing BSI in a tertiary-care hospital in Beijing, China. A total of 146 CRKP strains and 39 carbapenem-susceptible K. pneumoniae (CSKP) strains collected in the hospital from 2017 to 2020 were sent for whole-genome sequencing. Univariate and multivariate analyses were used to evaluate risk factors for in-hospital mortality of CRKP-BSI cases. Thirty (20.5%) of 146 CRKP-BSI patients and three (7.7%) of 39 CSKP-BSI patients died at discharge (χ² = 3.471, P = 0.062). Multivariate logistic regression analysis indicated that age and use of urinary catheters were independent risk factors for the death of CRKP-BSI. The 146 CRKP isolates belonged to 9 sequence types (STs) and 11 serotypes, while the 39 CSKP isolates belonged to 23 STs and 27 serotypes. The mechanism of carbapenem resistance for all the CRKP strains was the acquisition of carbapenemase, mainly KPC-2 (n = 127). There were 2 predominant serotypes for ST11 CRKP, namely, KL47 (n = 82) and KL64 (n = 42). Some virulent genes, including rmpA2, iucABCD and iutA, and repB gene, which was involved in plasmid replication, were detected in all ST11-KL64 strains. Evolutionary transmission analysis suggested that ST11 CRKP strains might have evolved from KL47 into KL64 and were accompanied by multiple outbreak events. This study poses an urgent need for enhancing infection control measures in the hospital, especially in the intensive care unit where the patients are at high-risk for acquiring CRKP-BSI. IMPORTANCE CRKP-BSI is demonstrated to cause high mortality. In this study, we demonstrated that ST11 CRKP strains might carry many virulent genes. Meanwhile, outbreak events occurred several times in the strains collected. Carbapenemase acquisition (mainly KPC-2 carbapenemase) was responsible for carbapenem resistance of all the 146 CRKP strains. As 2 predominant strains, all ST11-KL64 strains, but not ST11-KL47 strains, carried rmpA2, iucABCD, iutA, as well as a plasmid replication initiator (repB). Our study suggested that the occurrence of region-specific recombination events manifested by the acquisition of some virulence genes might contribute to serotype switching from ST11-KL47 to ST11-KL64. The accumulation of virulent genes in epidemic resistant strains poses a great challenge for the prevention and treatment of BSI caused by K. pneumoniae in high-risk patients.

Bioinformatic Analysis of a Set of 14 Temperate Bacteriophages Isolated from Staphylococcus aureus Strains Highlights Their Massive Genetic Diversity

Epidemiology and virulence studies of Staphylococcus aureus showed that temperate bacteriophages are one of the most powerful drivers for its evolution not only because of their abundance but also because of the richness of their genetic payload. Here, we report the isolation, genome sequencing, and bioinformatic analysis of 14 bacteriophages induced from lysogenic S. aureus strains from human or veterinary (cattle) origin. The bacteriophages belonged to the Siphoviridae family; were of similar genome size (40 to 45 kbp); and fell into clusters B2, B3, B5, and B7 according to a recent clustering proposal. One of the phages, namely, vB_SauS_308, was the most unusual one, belonging to the sparsely populated subcluster B7 but showing differences in protein family contents compared with the rest of the members. This phage contains a type I endolysin (one catalytic domain and noncanonical cell wall domain [CBD]) and a host recognition module lacking receptor binding protein, cell wall hydrolase, and tail fiber proteins. This phage also lacked virulence genes, which is opposite to what has been reported for subcluster B6 and B7 members. None of six phages, taken as representatives of each of the four subclusters, showed activity on coagulase-negative staphylococci (excepted for two Staphylococcus hominis strains in which propagation and a very slow adsorption rate were observed) nor transducing ability. Immunity tests on S. aureus RN4220 lysogens with each of these phages showed no cross immunity. IMPORTANCE To the best of our knowledge, this set of sequenced bacteriophages is the largest one in South America. Our report describes for the first time the utilization of MultiTwin software to analyze the relationship between phage protein families. Notwithstanding the fact that most of the genetic information obtained correlated with recently published information, due to their geographical origin, the reported analysis adds up to and confirms currently available knowledge of Staphylococcus aureus temperate bacteriophages in terms of phylogeny and role in host evolution.

Plant pan-genomics: recent advances, new challenges, and roads ahead

Pan-genomics can encompass most of the genetic diversity of a species or population and has proved to be a powerful tool for studying genomic evolution and the origin and domestication of species, and for providing information for plant improvement. Plant genomics has greatly progressed because of improvements in sequencing technologies and the rapid reduction of sequencing costs. Nevertheless, pan-genomics still presents many challenges, including computationally intensive assembly methods, high costs with large numbers of samples, ineffective integration of big data, and difficulty in applying it to downstream multi-omics analysis and breeding research. In this review, we summarize the definition and recent achievements of plant pan-genomics, computational technologies used for pan-genome construction, and the applications of pan-genomes in plant genomics and molecular breeding. We also discuss challenges and perspectives for future pan-genomics studies and provide a detailed pipeline for sample selection, genome assembly and annotation, structural variation identification, and construction and application of graph-based pan-genomes. The aim is to provide important guidance for plant pan-genome research and a better understanding of the genetic basis of genome evolution, crop domestication, and phenotypic diversity for future studies.

Deciphering the Biological Enigma-Genomic Evolution Underlying Anhydrobiosis in the Phylum Tardigrada and the Chironomid Polypedilum vanderplanki

Anhydrobiosis, an ametabolic dehydrated state triggered by water loss, is observed in several invertebrate lineages. Anhydrobiotes revive when rehydrated, and seem not to suffer the ultimately lethal cell damage that results from severe loss of water in other organisms. Here, we review the biochemical and genomic evidence that has revealed the protectant molecules, repair systems, and maintenance pathways associated with anhydrobiosis. We then introduce two lineages in which anhydrobiosis has evolved independently: Tardigrada, where anhydrobiosis characterizes many species within the phylum, and the genus Polypedilum, where anhydrobiosis occurs in only two species. Finally, we discuss the complexity of the evolution of anhydrobiosis within invertebrates based on current knowledge, and propose perspectives to enhance the understanding of anhydrobiosis.

Comparison of Genetic Features and Evolution of Global and Chinese Strains of Community-Associated Methicillin-Resistant Staphylococcus aureus ST22

Methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST) 22, especially the epidemic MRSA-15 (EMRSA-15), has been one of the most important disease-causing clones transmitting rapidly within and between hospitals globally. However, the genetic features and evolution of Chinese MRSA ST22 remain to be determined. Herein, we performed comparative genomics analysis of 12 ST22 community-associated (CA) MRSA isolates from China with 9 Chinese ST22 CA-MSSA isolates and 284 ST22 genomes from global sources, to clarify the genotypic features and potential transmission of MRSA ST22 strains isolated in China. Phylogenetic reconstruction and time estimation suggested that the Chinese subclade emerged around 2006, and the ST22-SCCmec V clone may have evolved from the native ST22-MSSA clone rather than spread from other regions, indicating that the Chinese ST22-MRSA-V clone is independent of the EMRSA-15 and Gaza clone, with differences in lukSF-PV and tsst-1 carriage. Virulence assays suggested that the ST22-MRSA clone was highly virulent, displaying higher or similar virulence potential as MSSA ST22 predecessors and the epidemic USA300 and ST22-MSSA. However, two nonsense mutations caused by a frameshift in agrC were identified in two ST22-MSSA isolates, resulting in a significant attenuation of virulence. RT-qPCR also demonstrated that the high virulence potential of these ST22 strains may be attributed to elevated expression of agr. This study provides insight into the epidemiology of the novel and highly virulent CA-MRSA ST22 clones.

IMPORTANCEStaphylococcus aureus sequence type 22 (ST22) is the main HA-MRSA clone spreading in Europe. It has strong capacity to supplant and replace other formerly epidemic MRSA clones. Previous work has described genotypic characteristics of ST22 belonging to EMRSA-15 and Gaza clone; however, the genetic feature and virulence potential of Chinese spread of ST22 strains are still limited. We conducted a detailed analysis of genomic evolution of global ST22 strains, to clarify the genotypic features and potential transmission of MRSA ST22 strains isolated from China. Our results suggested that the Chinese subclade is highly virulent, and emerged around 2006. We also demonstrated that the ST22-SCCmec V may have evolved from the native ST22-MSSA clone rather than spread from other regions, and the high virulence potential of these ST22 strains may be attributed to the high expression of agr based on the results of virulence assays of Chinese ST22 clones. Our findings are of great importance for providing insights into the epidemiology and pathogenicity of global and Chinese ST22 clones.

A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands

Objective: To analyze the SARS-CoV-2 genomic epidemiology in the Balearic Islands, a unique setting in which the course of the pandemic has been influenced by a complex interplay between insularity, severe social restrictions and tourism travels.

Methods: Since the onset of the pandemic, more than 2,700 SARS-CoV-2 positive respiratory samples have been randomly selected and sequenced in the Balearic Islands. Genetic diversity of circulating variants was assessed by lineage assignment of consensus whole genome sequences with PANGOLIN and investigation of additional spike mutations.

Results: Consensus sequences were assigned to 46 different PANGO lineages and 75% of genomes were classified within a VOC, VUI, or VUM variant according to the WHO definitions. Highest genetic diversity was documented in the island of Majorca (42 different lineages detected). Globally, lineages B.1.1.7 and B.1.617.2/AY.X were identified as the 2 major lineages circulating in the Balearic Islands during the pandemic, distantly followed by lineages B.1.177/B.1.177.X. However, in Ibiza/Formentera lineage distribution was slightly different and lineage B.1.221 was the third most prevalent. Temporal distribution analysis showed that B.1 and B.1.5 lineages dominated the first epidemic wave, lineage B.1.177 dominated the second and third, and lineage B.1.617.2 the fourth. Of note, lineage B.1.1.7 became the most prevalent circulating lineage during first half of 2021; however, it was not associated with an increased in COVID-19 cases likely due to severe social restrictions and limited travels. Additional spike mutations were rarely documented with the exception of mutation S:Q613H which has been detected in several genomes (n = 25) since July 2021.

Conclusion: Virus evolution, mainly driven by the acquisition and selection of spike substitutions conferring biological advantages, social restrictions, and size population are apparently key factors for explaining the epidemic patterns registered in the Balearic Islands.

Research advances and new challenges in overcoming triple-negative breast cancer

Triple-negative breast cancer (TNBC) is a pathological term used to identify invasive breast cancers that lack expression of estrogen and progesterone receptors and do not have pathologic overexpression of the HER2 receptor or harbor ERBB2 gene amplification. TNBC includes a collection of multiple distinct disease entities based upon genomic, transcriptomic and phenotypic characterization. Despite improved clinical outcomes with the development of novel therapeutics, TNBC still yields the worst prognosis among all clinical subtypes of breast cancer. We will systematically review evidence of the genomic evolution of TNBC, as well as potential mechanisms of disease progression and treatment resistance, defined in part by advances in next-generation DNA sequencing technology (including single cell sequencing), providing a new perspective on treatment strategies, and promise to reveal new potential therapeutic targets. Moreover, we review novel therapies aimed at homologous recombination deficiency, PI3 kinase/AKT/PTEN pathway activation, androgen receptor blockade, immune checkpoint inhibition, as well as antibody-drug conjugates engaging novel cell surface targets, including recent progress in pre-clinical and clinical studies which further validate the role of targeted therapies in TNBC. Despite major advances in treatment for TNBC, including FDA approval of 2 PARP inhibitors for metastatic TNBC, the crossing of the superiority boundary in a phase 3, placebo-controlled study of adjuvant olaparib in early-stage patients with germline BRCA-mutated high-risk HER2-negative early breast cancer, the FDA approval of 2 PD-(L)1 checkpoint antibodies for metastatic TNBC, and the FDA approval of the first antibody drug conjugate for TNBC, significant challenges remain. For example, despite the dawn of immunotherapy in metastatic TNBC, durable responses are limited to a small subset of patients, definitive biomarkers for patient selection are lacking, and the Oncology Drug Advisory Committee to the FDA has recently voted against approval of an anti-PD-1 checkpoint antibody high risk early-stage TNBC in the neoadjuvant setting. Also, despite early positive randomized phase 2 studies of AKT inhibition in metastatic TNBC, a recent phase 3 registration trial failed to validate earlier phase 2 data. Finally, we note that level one evidence for clinical efficacy of androgen receptor blockade in TNBC is still lacking. To meet these and other challenges, we will catalogue the ongoing exponential increase in interest in basic, translational, and clinical research to develop new treatment paradigms for TNBC.

Genomic Evolution and Variation of SARS-CoV-2 in the Early Phase of COVID-19 Pandemic in Guangdong Province, China

Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) with unknown origin spread rapidly to 222 countries, areas or territories. To investigate the genomic evolution and variation in the early phase of COVID-19 pandemic in Guangdong, 60 specimens of SARS-CoV-2 were used to perform whole genome sequencing, and genomics, amino acid variation and Spike protein structure modeling analyses. Phylogenetic analysis suggested that the early variation in the SARS-CoV-2 genome was still intra-species, with no evolution to other coronaviruses. There were one to seven nucleotide variations (SNVs) in each genome and all SNVs were distributed in various fragments of the genome. The Spike protein bound with human receptor, an amino acid salt bridge and a potential furin cleavage site were found in the SARS-CoV-2 using molecular modeling. Our study clarified the characteristics of SARS-CoV-2 genomic evolution, variation and Spike protein structure in the early phase of local cases in Guangdong, which provided reference for generating prevention and control strategies and tracing the source of new outbreaks.

Recombination Events Shape the Genomic Evolution of Infectious Bronchitis Virus in Europe

Infectious bronchitis of chicken is a high morbidity and mortality viral disease affecting the poultry industry worldwide; therefore, a better understanding of this pathogen is of utmost importance. The primary aim of this study was to obtain a deeper insight into the genomic diversity of field infectious bronchitis virus (IBV) strains using phylogenetic and recombination analysis. We sequenced the genome of 20 randomly selected strains from seven European countries. After sequencing, we created a genome sequence data set that contained 36 European origin field isolates and 33 vaccine strains. When analyzing these 69 IBV genome sequences, we identified 215 recombination events highlighting that some strains had multiple recombination breaking points. Recombination hot spots were identified mostly in the regions coding for non-structural proteins, and multiple recombination hot spots were identified in the nsp2, nsp3, nsp8, and nsp12 coding regions. Recombination occurred among different IBV genotypes and involved both field and vaccine IBV strains. Ninety percent of field strains and nearly half of vaccine strains showed evidence of recombination. Despite the low number and the scattered geographical and temporal origin of whole-genome sequence data collected from European Gammacoronaviruses, this study underlines the importance of recombination as a major evolutionary mechanism of IBVs.

Meta-Transcriptomic Analysis Reveals the Virome and Viral Genomic Evolution of Medically Important Mites

Mites are notorious for being vectors transmitting infectious pathogens and source of allergens causing allergic conditions in animals and humans. However, despite their huge impact on public health, the virome of mites remains unknown. Here we characterized the virus diversity and abundance of 14 species of medically important mites based on total RNA sequencing data sets generated in this study as well as those deposited in the Sequence Read Archive (SRA) database. A total of 47 genetically distinct viruses were identified and classified into 17 virus families or virus super-groups, and the viral sequences accounted for as much as 29.67% of total non-rRNA transcriptome in one mite library. The most commonly identified viruses are members of Picornavirales, among which we revealed more than one type of viruses that are evolutionarily related to dicistronic viruses but contain a single open reading frame, thus likely representing a recent example of host (i.e., mite)-related parallel evolution from dicistronic to monocistronic genomic form within the family Dicistroviridae To our best knowledge, this is the first time to perform comprehensive and systematic screening of RNA virome in medically important mites including house dust mites (HDM). Overall, the RNA virome identified here provides not only significant insights into the diversity and evolution of RNA viruses in mites, but also a solid knowledge base for studying their roles in human diseases.IMPORTANCE Mites are important group of arthropods that are associated with a variety of human diseases including scrub typhus and asthma. However, it remains unclear whether or not mites carry viruses that might play a role in human infections or allergic disease. In this study, we used a total transcriptomics approach to characterize and compare the complete RNA virome within mites that are relevant to human health and diseases. Specifically, our data revealed a large diversity, a high abundance, and a flexible genomic evolution for these viruses. Although most of the viruses identified here are unknown to associate with human infectious disease, the abundant presence of viral RNAs may play an immunomodulatory role in the development of allergic reactions such as asthma during environmental exposure to mite allergens, and therefore provide important insights into the mite-induced allergy and preparation of mite allergen vaccines.

The origin and evolution of the diosgenin biosynthetic pathway in yam

Diosgenin, mainly produced by Dioscorea species, is a traditional precursor of most hormonal drugs in the pharmaceutical industry. The mechanisms that underlie the origin and evolution of diosgenin biosynthesis in plants remain unclear. After sequencing the whole genome of Dioscorea zingiberensis, we revealed the evolutionary trajectory of the diosgenin biosynthetic pathway in Dioscorea and demonstrated the de novo biosynthesis of diosgenin in a yeast cell factory. First, we found that P450 gene duplication and neo-functionalization, driven by positive selection, played important roles in the origin of the diosgenin biosynthetic pathway. Subsequently, we found that the enrichment of diosgenin in the yam lineage was regulated by CpG islands, which evolved to regulate gene expression in the diosgenin pathway and balance the carbon flux between the biosynthesis of diosgenin and starch. Finally, by integrating genes from plants, animals, and yeast, we heterologously synthesized diosgenin to 10 mg/l in genetically-engineered yeast. Our study not only reveals the origin and evolutionary mechanisms of the diosgenin biosynthetic pathway in Dioscorea, but also introduces an alternative approach for the production of diosgenin through synthetic biology.

Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen

Horizontal gene transfer is of major evolutionary importance as it allows for the redistribution of phenotypically important genes among lineages. Such genes with essential functions include those involved in resistance to antimicrobial compounds and virulence factors in pathogenic bacteria. Understanding gene turnover at microevolutionary scales is critical to assess the pace of this evolutionary process. Here, we characterized and quantified gene turnover for the epidemic lineage of a bacterial plant pathogen of major agricultural importance worldwide. Relying on a dense geographic sampling spanning 39 years of evolution, we estimated both the dynamics of single nucleotide polymorphism accumulation and gene content turnover. We identified extensive gene content variation among lineages even at the smallest phylogenetic and geographic scales. Gene turnover rate exceeded nucleotide substitution rate by three orders of magnitude. Accessory genes were found preferentially located on plasmids, but we identified a highly plastic chromosomal region hosting ecologically important genes such as transcription activator-like effectors. Whereas most changes in the gene content are probably transient, the rapid spread of a mobile element conferring resistance to copper compounds widely used for the management of plant bacterial pathogens illustrates how some accessory genes can become ubiquitous within a population over short timeframes.

Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates

Long considered to be a consequence of human antibiotics use by deduction, antibiotic resistance mechanisms appear to be in fact a much older phenomenon as antibiotic resistance genes have previously been detected from millions of year-old permafrost samples. As these specimens guarantee the viability of archaic bacteria, we herein propose to apply the culturomics approach to recover the bacterial content of a Siberian permafrost sample dated, using the in situ-produced cosmogenic nuclide chlorine36 (36Cl), at 2.7 million years to study the dynamics of bacterial evolution in an evolutionary perspective. As a result, we cultured and sequenced the genomes of 28 ancient bacterial species including one new species. To perform genome comparison between permafrost strains and modern isolates we selected 7 of these species (i.e., Achromobacter insolitus, Bacillus idriensis, Brevundimonas aurantiaca, Janibacter melonis, Kocuria rhizophila, Microbacterium hydrocarbonoxydans and Paracoccus yeei). We observed a high level of variability in genomic content with a percentage of shared genes in the core genomes ranging from 21.23% to 55.59%. In addition, the Single Nucleotide Polymorphism (SNP) comparison between permafrost and modern strains for the same species did not allow a dating of ancient strains based on genomic content. There were no significant differences in antibiotic resistance profiles between modern and ancient isolates of each species. Acquired resistance to antibiotics was phenotypically detected in all gram-negative bacterial species recovered from permafrost, with a significant number of genes coding for antibiotic resistance detected. Taken together, these findings confirm previously obtained data that antibiotic resistance predates humanity as most of antimicrobial agents are natural weapons used in inter-microbial conflicts within the biosphere.

Evolution of Multi-Resistance to Vancomycin, Daptomycin, and Linezolid in Methicillin-Resistant Staphylococcus aureus Causing Persistent Bacteremia

The genomic evolution in vivo in persistent infection was critical information for understanding how methicillin-resistant Staphylococcus aureus (MRSA) was adapted to host environments with high antibiotic selective pressure. Thirty-two successive MRSA blood isolates with incremental non-susceptibility to vancomycin (VISA), daptomycin (DRSA), and/or linezolid (LRSA) were isolated from a patient failing multiple courses of antimicrobial therapy during 1,356 days of bacteremia. Whole genome sequencing (WGS) for all consecutive isolates were conducted to characterize the evolutionary pathways, resistance-associated mutations and their temporal relationship with antimicrobial treatment. The WGS-based phylogeny categorized the isogenic strains into three major clades, I (22 isolates), II (7 isolates), and III (3 isolates), respectively, harboring a median (range) of 7 (1–30), 62 (53–65), and 118 (100–130) non-synonymous mutations when compared to the very first isolate. Clade I strains were further grouped into early and late subclades, which, respectively, shared the most recent common ancestor with Clade III strains at day 393.7 and Clade II strain at day 662.5. Clade I and Clade III strains were characterized, respectively, with high rates of VISA (9/22, 40.9%) and VISA-and-DRSA phenotype (2/3, 66.7%). Linezolid-resistance including VISA-DRSA-and-LRSA phenotype was exclusively identified in Clade II strains after eight courses of linezolid treatment. The LRSA displayed a small colony variant phenotype and were associated with G2576T mutations in domain V region of 23S rRNA. Substantial loss of mobile elements or alleles mediating resistance or virulence were identified during the evolution of multi-resistance. However, the gene loss might not be correlated to the development of VISA, DRSA, or LRSA phenotype. In conclusion, MRSA in persistent bacteremia was adapted to harsh host environment through multiple pathways involving both resistance-associated mutations and extensive gene loss.

Reprogramming of Retrotransposon Activity during Speciation of the Genus Citrus

Speciation of the genus Citrus from a common ancestor has recently been established to begin ∼8 Ma during the late Miocene, a period of major climatic alterations. Here, we report the changes in activity of Citrus LTR retrotransposons during the process of diversification that gave rise to the current Citrus species. To reach this goal, we analyzed four pure species that diverged early during Citrus speciation, three recent admixtures derived from those species and an outgroup of the Citrus clade. More than 30,000 retrotransposons were grouped in ten linages. Estimations of LTR insertion times revealed that retrotransposon activity followed a species-specific pattern of change that could be ascribed to one of three different models. In some genomes, the expected pattern of gradual transposon accumulation was suddenly arrested during the radiation of the ancestor that gave birth to the current Citrus species. The individualized analyses of retrotransposon lineages showed that in each and every species studied, not all lineages follow the general pattern of the species itself. For instance, in most of the genomes, the retrotransposon activity of elements from the SIRE lineage reached its highest level just before Citrus speciation, while for Retrofit elements, it has been steadily growing. Based on these observations, we propose that Citrus retrotransposons may respond to stressful conditions driving speciation as a part of the genetic response involved in adaptation. This proposal implies that the evolving conditions of each species interact with the internal regulatory mechanisms of the genome controlling the proliferation of mobile elements.

Genomic Evolution of Staphylococcus aureus During Artificial and Natural Colonization of the Human Nose

Staphylococcus aureus can colonize the human vestibulum nasi for many years. It is unknown whether and, how S. aureus adapts to this ecological niche during colonization. We determined the short (1 and 3 months) and mid-term (36 months) genomic evolution of S. aureus in natural carriers and artificially colonized volunteers. Eighty-five S. aureus strains were collected from 6 natural carriers during 3 years and 6 artificially colonized volunteers during 1 month. Multi-locus sequence typing (MLST) and single nucleotide polymorphism (SNP) analysis based on whole-genome sequencing (WGS) were carried out. Mutation frequencies within resident bacterial populations over time were quantified using core genome SNP counts (comparing groups of genomes) and pairwise SNP divergence assessment (comparing two genomes from strains originating from one host and sharing identical MLST). SNP counts (within 1–3 months) in all naturally colonizing strains varied from 0 to 757 (median 4). These strains showed random and independent patterns of pairwise SNP divergence (0 to 44 SNPs, median 7). When the different core genome SNP counts over a period of 3 years were considered, the median SNP count was 4 (range 0–26). Host-specific pairwise SNP divergence for the same period ranged from 9 to 57 SNPs (median 20). During short term artificial colonization the mutation frequency was even lower (0–7 SNPs, median 2) and the pairwise SNP distances were 0 to 5 SNPs (median 2). Quantifying mutation frequencies is important for the longitudinal follow-up of epidemics of infections and outbreak management. Random pattern of pairwise SNP divergence between the strains isolated from single carriers suggested that the WGS of multiple colonies is necessary in this context. Over periods up to 3 years, maximum median core genome SNP counts and SNP divergence for the strains studied were 4 and 20 SNPs or lower. During artificial colonization, where median core genome SNP and pairwise SNP distance scores were 2, there is no early stage selection of different genotypes. Therefore, we suggest an epidemiological cut off value of 20 SNPs as a marker of S. aureus strain identity during studies on nasal colonization and also outbreaks of infection.

Identification of Disease Risk DNA Variations is Shaping the Future of Precision Health

In recent years, the knowledge generated by decoding the human genome has allowed groundbreaking genetic research to better understand genomic architecture and heritability in healthy and disease states. The vast amount of data generated over time and yet to be generated provides the basis for translational research towards the development of preventive and therapeutic strategies for many conditions. In this special issue, we highlight the discoveries of disease-associated and protective DNA variations in common human diseases and developmental disorders.

Genetic diversity and evolutionary features of type VI secretion systems in Salmonella

AIM

Type VI secretion systems (T6SS) play key roles in bacterial pathogenesis, but their evolutionary features remain largely unclear. In this study, we conducted systematic comparisons among the documented T6SSs in Salmonella and determined their structural diversity, phylogenetic distribution and lineage-specific properties.

MATERIALS & METHODS

We screened 295 Salmonella genomes for 13 T6SS core components by hidden Markov models and identified 363 T6SS clusters covering types i1, i2, i3 and i4a.

RESULTS

Type i3 and i4a T6SSs were restricted to Salmonella enterica subspecies enterica and Salmonella bongori, respectively. whereas type i2 T6SSs were conserved between S. enterica subspecies, arizonae and diarizonae. S. enterica subspecies salamae, indica and houtenae harbored only type i1 T6SSs, which had wide distribution and high sequence diversity.

CONCLUSION

The diverse Salmonella T6SSs have undergone purifying selection pressures during the bacterial evolution and may be involved in host adaptation.

The roles of homologous recombination and the immune system in the genomic evolution of cancer

A variety of factors, whether extracellular (mutagens/carcinogens and viruses in the environment, chronic inflammation and radiation associated with the environment and/or electronic devices/machines) and/or intracellular (oxidative metabolites of food, oxidative stress due to inflammation, acid production, replication stress, DNA replication/repair errors, and certain hormones, cytokines, growth factors), pose a constant threat to the genomic integrity of a living cell. However, in the normal cellular environment multiple biological pathways including DNA repair, cell cycle, apoptosis and the immune system work in a precise, regulated (tightly controlled), timely and concerted manner to ensure genomic integrity, stability and proper functioning of a cell. If damage to DNA takes place, it is efficiently and accurately repaired by the DNA repair systems. Homologous recombination (HR) which utilizes either a homologous chromosome (in G1 phase) or a sister chromatid (in G2) as a template to repair the damage, is known to be the most precise repair system. HR in G2 which utilizes a sister chromatid as a template is also called an error free repair system. If DNA damage in a cell is so extensive that it overwhelms the repair system/s, the cell is eliminated by apoptosis. Thus, multiple pathways ensure that genome of a cell is intact and stable. However, constant exposure to DNA damage and/or dysregulation of DNA repair mechanism/s poses a risk of mutation and cancer. Oncogenesis, which seems to be a multistep process, is associated with acquisition of a number of genomic changes that enable a normal cell to progress from benign to malignant transformation. Transformed/cancer cells are recognized and killed by the immune system. However, the ongoing acquisition of new genomic changes enables cancer cells to survive/escape immune attack, evolve into a more aggressive phenotype, and eventually develop resistance to therapy. Although DNA repair (especially the HR) and the immune system play unique roles in preserving genomic integrity of a cell, they can also contribute to DNA damage, genomic instability and oncogenesis. The purpose of this article is to highlight the roles of DNA repair (especially HR) and the immune system in genomic evolution, with special focus on gastrointestinal cancer.

Comparative Analysis of Repetitive DNA between the Main Vectors of Chagas Disease: Triatoma infestans and Rhodnius prolixus

Chagas disease or American trypanosomiasis affects six to seven million people worldwide, mostly in Latin America. This disease is transmitted by hematophagous insects known as “kissing bugs” (Hemiptera, Triatominae), with Triatoma infestans and Rhodnius prolixus being the two most important vector species. Despite the fact that both species present the same diploid chromosome number (2n = 22), they have remarkable differences in their total DNA content, chromosome structure and genome organization. Variations in the DNA genome size are expected to be due to differences in the amount of repetitive DNA sequences. The T. infestans genome-wide analysis revealed the existence of 42 satellite DNA families. BLAST searches of these sequences against the R. prolixus genome assembly revealed that only four of these satellite DNA families are shared between both species, suggesting a great differentiation between the Triatoma and Rhodnius genomes. Fluorescence in situ hybridization (FISH) location of these repetitive DNAs in both species showed that they are dispersed on the euchromatic regions of all autosomes and the X chromosome. Regarding the Y chromosome, these common satellite DNAs are absent in T. infestans but they are present in the R. prolixus Y chromosome. These results support a different origin and/or evolution in the Y chromosome of both species.

Inter- and intracontinental migrations and local differentiation have shaped the contemporary epidemiological landscape of canine parvovirus in South America

Canine parvovirus (CPV) is a fast-evolving single-stranded DNA virus that causes one of the most significant infectious diseases of dogs. Although the virus dispersed over long distances in the past, current populations are considered to be spatially confined and with only a few instances of migration between specific localities. It is unclear whether these dynamics occur in South America where global studies have not been performed. The aim of this study is to analyze the patterns of genetic variability in South American CPV populations and explore their evolutionary relationships with global strains. Genomic sequences of sixty-three strains from South America and Europe were generated and analyzed using a phylodynamic approach. All the obtained strains belong to the CPV-2a lineage and associate with global strains in four monophyletic groups or clades. European and South American strains from all the countries here analyzed are representative of a widely distributed clade (Eur-I) that emerged in Southern Europe during 1990–98 to later spread to South America in the early 2000s. The emergence and spread of the Eur-I clade were correlated with a significant rise in the CPV effective population size in Europe and South America. The Asia-I clade includes strains from Asia and Uruguay. This clade originated in Asia during the late 1980s and evolved locally before spreading to South America during 2009–10. The third clade (Eur-II) comprises strains from Italy, Brazil, and Ecuador. This clade appears in South America as a consequence of an early introduction from Italy to Ecuador in the middle 1980s and has experienced extensive local genetic differentiation. Some strains from Argentina, Uruguay, and Brazil constitute an exclusive South American clade (SA-I) that emerged in Argentina in the 1990s. These results indicate that the current epidemiological scenario is a consequence of inter- and intracontinental migrations of strains with different geographic and temporal origins that set the conditions for competition and local differentiation of CPV populations. The coexistence and interaction of highly divergent strains are the main responsible for the drastic epidemiological changes observed in South America in the last two decades. This highlights the threat of invasion from external sources and the importance of whole-genome resolution to robustly infer the origin and spread of new CPV variants. From a taxonomic standpoint, the findings herein show that the classification system that uses a single amino acid to identify variants (2a, 2b, and 2c) within the CPV-2a lineage does not reflect phylogenetic relationships and is not suitable to analyze CPV evolution. In this regard, the identification of clades or sublineages within circulating CPV strains is the first step towards a genetic and evolutionary classification of the virus.

Different Genomic Changes Underlie Adaptive Evolution in Populations of Contrasting History

Experimental evolution is a powerful tool to understand the adaptive potential of populations under environmental change. Here, we study the importance of the historical genetic background in the outcome of evolution at the genome-wide level. Using the natural clinal variation of Drosophila subobscura, we sampled populations from two contrasting latitudes (Adraga, Portugal and Groningen, Netherlands) and introduced them in a new common environment in the laboratory. We characterized the genome-wide temporal changes underlying the evolutionary dynamics of these populations, which had previously shown fast convergence at the phenotypic level, but not at chromosomal inversion frequencies. We found that initially differentiated populations did not converge either at genome-wide level or at candidate SNPs with signs of selection. In contrast, populations from Portugal showed convergence to the control population that derived from the same geographical origin and had been long-established in the laboratory. Candidate SNPs showed a variety of different allele frequency change patterns across generations, indicative of an underlying polygenic basis. We did not detect strong linkage around candidate SNPs, but rather a small but long-ranging effect. In conclusion, we found that history played a major role in genomic variation and evolution, with initially differentiated populations reaching the same adaptive outcome through different genetic routes.

The subclonal structure and genomic evolution of oral squamous cell carcinoma revealed by ultra-deep sequencing

Recent studies suggest that head and neck squamous cell carcinomas are very heterogeneous between patients; however the subclonal structure remains unexplored mainly due to studies using only a single biopsy per patient. To deconvolute the clonal structure and describe the genomic cancer evolution, we applied whole-exome sequencing combined with ultra-deep targeted sequencing on oral squamous cell carcinomas (OSCC). From each patient, a set of biopsies was sampled from distinct geographical sites in primary tumor and lymph node metastasis.We demonstrate that the included OSCCs show a high degree of inter-patient heterogeneity but a low degree of intra-tumor heterogeneity. However, some OSCC cancers contain complex subclonal architectures comprising distinct subclones only found in geographically distinct regions of the primary tumors. In several cases we find mutations in the primary tumor that are not present in the lymph node metastasis. We conclude that metastatic potential in our population is acquired early in tumor evolution as evident by the ongoing parallel evolution in several primary tumors.

Unraveling the evolutionary scenario of the hobo element in populations of Drosophila melanogaster and D. simulans in South America using the TPE repeats as markers

Transposable elements (TEs) are nucleotide sequences found in most studied genomes. These elements are highly diversified and have a large variation in nucleotide structure and mechanisms of transposition. hobo is a member of class II, belonging to hAT superfamily, described inDrosophila melanogaster, and it presents in its Open Reading Frame, a repetitive region encoding the amino acids threonine-proline-glutamic acid (TPE), which shows variability in the number of repeats in some regions of the world. Due to this variability some evolutionary scenarios of the hobo element are discussed, such as the scenario of the invasion of hobo element in populations ofD. melanogaster. In the present study, we investigated 22 DNA sequences of D. melanogaster and seven sequences ofD. simulans, both from South America, to check the number of repetitions of TPE, in order to clarify the evolutionary scenario of thehobo element in these populations. Our results showed a monomorphism in populations of both species in South America, with only three TPE repeats. Hence, we discuss and propose an evolutionary scenario of the invasion of the hobo element in populations of D. melanogaster and D. simulans.

The molecular biology of vertebrate olfaction

The importance of chemosensation for vertebrates is reflected in the vast and variable nature of their chemosensory tissues, neurons, and genes, which we explore in this review. Immense progress has been made in elucidating the molecular biology of olfaction since the discovery of the olfactory receptor genes by Buck and Axel, which eventually won the authors the Nobel Prize. In particular, research linking odor ligands to olfactory receptors (ORs) is truly revolutionizing our understanding of how a large but limited number of chemosensory receptors can allow us to perceive the massive diversity of odors in our habitat. This research is providing insight into the evolution of genomes and providing the raw data needed to explore links between genotype and phenotype, still a grand challenge in biology. Research into olfaction is still developing and will no doubt continue until we have a clear understanding of how all odors are detected and the evolutionary forces that have molded the chemosensory subgenome in vertebrates. This knowledge will not only be a huge step in elucidating olfactory function, advancing scientific knowledge and techniques, but there are also commercial applications for this research. This review focuses on the molecular basis of chemosensation, particularly olfaction, its evolution across vertebrates and the recent molecular advances linking odors to their cognate receptors.

Strong links between genomic and anatomical diversity in both mammalian olfactory chemosensory systems

Mammalian olfaction comprises two chemosensory systems: the odorant-detecting main olfactory system (MOS) and the pheromone-detecting vomeronasal system (VNS). Mammals are diverse in their anatomical and genomic emphases on olfactory chemosensation, including the loss or reduction of these systems in some orders. Despite qualitative evidence linking the genomic evolution of the olfactory systems to specific functions and phenotypes, little work has quantitatively tested whether the genomic aspects of the mammalian olfactory chemosensory systems are correlated to anatomical diversity. We show that the genomic and anatomical variation in these systems is tightly linked in both the VNS and the MOS, though the signature of selection is different in each system. Specifically, the MOS appears to vary based on absolute organ and gene family size while the VNS appears to vary according to the relative proportion of functional genes and relative anatomical size and complexity. Furthermore, there is little evidence that these two systems are evolving in a linked fashion. The relationships between genomic and anatomical diversity strongly support a role for natural selection in shaping both the anatomical and genomic evolution of the olfactory chemosensory systems in mammals.