Molecular And Genome Evolution Download [VERIFIED].zip

Following the discovery of the SARS-CoV-2 Omicron variant (B.1.1.529), the global COVID-19 outbreak has resurfaced after appearing to be relentlessly spreading over the past 2 years. This new variant showed marked degree of mutation, compared with the previous SARS-CoV-2 variants. This study investigates the evolutionary links between Omicron variant and recently emerged SARS-CoV-2 variants. The entire genome sequences of SARS-CoV-2 variants were obtained, aligned using Clustal Omega, pairwise comparison was computed, differences, identity percent, gaps, and mutations were noted, and the identity matrix was generated. The phylogenetics of Omicron variants were determined using a variety of evolutionary substitution models. The ultrametric and metric clustering methods, such as UPGMA and neighbor-joining (NJ), using nucleotide substitution models that allowed the inclusion of nucleotide transitions and transversions as Kimura 80 models, revealed that the Omicron variant forms a new monophyletic clade that is distant from other SARS-CoV-2 variants. In contrast, the NJ method using a basic nucleotide substitution model such as Jukes-Cantor revealed a close relationship between the Omicron variant and the recently evolved Alpha variant. Based on the percentage of sequence identity, the closest variants were in the following order: Omicron, Alpha, Gamma, Delta, Beta, Mu, and then the SARS-CoV-2 USA isolate. A genome alignment with other variants indicated the greatest number of gaps in the Omicron variant's genome ranging from 43 to 63 gaps. It is possible, given their close relationship to the Alpha variety, that Omicron has been around for much longer than predicted, even though they created a separate monophyletic group. Sequencing initiatives in a systematic and comprehensive manner is highly recommended to study the evolution and mutations of the virus.

Comparative genome analyses reveal that most functional domains of human genes have homologs in widely divergent species. These shared functional domains, however, are differentially shuffled among evolutionary lineages to produce an increasing number of domain architectures. Combined with duplication and adaptive evolution, domain shuffling is responsible for the great phenotypic complexity of higher eukaryotes. Although the domain-shuffling hypothesis is generally accepted, determining the molecular mechanisms that lead to domain shuffling and novel gene creation has been challenging, as sequence features accompanying the formation of known genes have been obscured by accumulated mutations. The growing availability of genome sequences and EST databases allows us to study the characteristics of newly emerged genes. Here we review recent genome-wide DNA and EST analyses, and discuss the three major molecular mechanisms of gene formation: (1) atypical spicing, both within and between genes, followed by adaptation, (2) tandem and interspersed segmental duplications, and (3) retrotransposition events.

The comparison of genome content variation and levels of SNPs in domesticated and wild clades (Supplementary Fig. 28) shows higher SNP density (median 0.55% versus 0.41%) and lower genome content variation (median 115 ORFs that are not shared, versus 161 shared ORFs) in wild versus domesticated clades, respectively (Supplementary Fig. 28 and Supplementary Tables 9, 10). These findings suggest a shift in evolutionary mechanisms during the domestication process. The wild clades share similar genome content, and their evolution is mainly driven by the accumulation of SNPs. The specific artificial environments colonized by domesticated clades probably promote rapid ORF expansion and/or loss, leading to considerable variation in genome content and CNVs. Some domesticated clades also exhibit high copy numbers of Ty1 and Ty2 transposable elements (Supplementary Fig. 29).

Host-symbiont co-speciation and reductive genome evolution have been commonly observed among obligate endocellular insect symbionts, while such examples have rarely been identified among extracellular ones, the only case reported being from gut symbiotic bacteria of stinkbugs of the family Plataspidae. Considering that gut symbiotic communities are vulnerable to invasion of foreign microbes, gut symbiotic associations have been thought to be evolutionarily not stable. Stinkbugs of the family Acanthosomatidae harbor a bacterial symbiont in the midgut crypts, the lumen of which is completely sealed off from the midgut main tract, thereby retaining the symbiont in the isolated cryptic cavities. We investigated histological, ecological, phylogenetic, and genomic aspects of the unique gut symbiosis of the acanthosomatid stinkbugs.

Phylogenetic analyses showed that the acanthosomatid symbionts constitute a distinct clade in the γ-Proteobacteria, whose sister groups are the obligate endocellular symbionts of aphids Buchnera and the obligate gut symbionts of plataspid stinkbugs Ishikawaella. In addition to the midgut crypts, the symbionts were located in a pair of peculiar lubricating organs associated with the female ovipositor, by which the symbionts are vertically transmitted via egg surface contamination. The symbionts were detected not from ovaries but from deposited eggs, and surface sterilization of eggs resulted in symbiont-free hatchlings. The symbiont-free insects suffered retarded growth, high mortality, and abnormal morphology, suggesting important biological roles of the symbiont for the host insects. The symbiont phylogeny was generally concordant with the host phylogeny, indicating host-symbiont co-speciation over evolutionary time despite the extracellular association. Meanwhile, some local host-symbiont phylogenetic discrepancies were found, suggesting occasional horizontal symbiont transfers across the host lineages. The symbionts exhibited AT-biased nucleotide composition, accelerated molecular evolution, and reduced genome size, as has been observed in obligate endocellular insect symbionts.

Comprehensive studies of the acanthosomatid bacterial symbiosis provide new insights into the genomic evolution of extracellular symbiotic bacteria: host-symbiont co-speciation and drastic genome reduction can occur not only in endocellular symbiotic associations but also in extracellular ones. We suggest that many more such cases might be discovered in future surveys.

However, the conventional view was countered by a recent study on stinkbugs of the family Plataspidae. These insects, which harbor a γ-proteobacterial symbiont named Ishikawaella capsulata in their midgut crypts, had been known for their unique mechanism for vertical transmission, so-called 'capsule transmission' [24, 25], wherein mother insects deposit symbiont-filled particles (symbiont capsules) in association with eggs, and hatchlings probe the content of the capsules to acquire the symbiont. In the plataspid symbiosis, strict host-symbiont co-cladogenesis and reductive symbiont genome evolution were identified despite the extracellular association [19]. Now it is of evolutionary interest whether similar cases are to be found in other insect-microbe extracellular symbioses or the case of plataspid stinkbugs is an orphan exception.

Here we report a novel group of insect gut bacteria that exhibit host-symbiont co-cladogenesis and reductive genome evolution. The host insects are stinkbugs of the family Acanthosomatidae, which are known for their social behavior such as maternal guarding of eggs and nymphs against predators [26, 27]. Rosenkranz [28] described unique histological structures called 'isolated midgut crypts' and 'lubricating organs' for harboring symbiotic bacteria in these insects. In most plant-sucking stinkbugs, the lumen of the midgut crypts is connected to the midgut main tract, and thus the insects are able to excrete the symbiotic bacteria from the anus for vertical transmission to their eggs by surface contamination [2, 18, 29]. In acathosomatid stinkbugs, by contrast, the lumen of the crypts is completely sealed off, thereby retaining the symbiotic bacteria in the isolated cryptic cavities. The female ovipositor is equipped with a pair of peculiar lubrication organs of unknown developmental origin, which consist of numerous bacteria-filled tubulets. These highly-developed symbiotic organs suggest intimacy of the host-symbiont relationship, but there have been no studies on the acanthosomatid gut symbionts except for the early histological description by Rosenkranz [28].

Table 3 summarizes the results of relative rate tests for the 16S rRNA gene from the lineages of acanthosomatid gut symbionts, obligate aphid endosymbionts Buchnera, plataspid gut symbionts Ishikawaella, and related free-living bacteria. The molecular evolutionary rates in the lineage of acanthosomatid symbionts were significantly higher than those of the free-living bacteria, and were similar to those in the lineages of Buchnera and Ishikawaella. Table 4 shows the results of relative rate tests for the groEL gene sequences, which exhibited similar evolutionary patterns.

The symbiont is associated with stinkbugs of the family Acanthosomatidae, including E. humeralis, E. nubilus, Elasmostethus brevis, L. gramineus, E. putoni, Elasmucha dorsalis, E. signoreti, S. esakii, S. scutellata, A. labiduroides, A. denticaudum, A. forficula, A. giganteum, and A. haemorrhoidale (Additional file 1). Early histological descriptions [28] suggest that the symbiont is also found in other acanthosomatid species including Elasmostethus interstinctus, Elasmostethus minor, Elasmucha ferrugata, Elasmucha fieberi, Elasmucha grisea, Cyphostethus tristiatus, Planois bimaculata, and Ditomotarsus gayi, although no molecular data are available for them. The host phylogeny is largely concordant with the symbiont phylogeny (Figure 7), suggesting stable host-symbiont association over evolutionary time. Elimination of the symbiont results in retarded growth, elevated mortality, and abnormal coloration of the host insects (Figure 6). The symbiont has not been cultured outside the host insects. 2b1af7f3a8

Molecular And Genome Evolution Download [VERIFIED].zip

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