Purifying selection drove the adaptation of mitochondrial genes along with correlation of gene rearrangements and evolutionary rates in two subfamilies of Whitefly (Insecta: Hemiptera).

Insect mitochondrial genomes (mitogenomes) are usually represented by a conserved gene order. Whiteflies exhibit gene rearrangement in their mitogenomes; however, understanding how nucleotide substitution rates shape gene rearrangement in whiteflies is unclear due to the limited number of mitogenomes. Additionally, the mechanisms by which selection pressure drives adaptations in mitochondrial genes in the two subfamilies of whiteflies are not yet known. Here, we analyzed 18 whitefly mitogenomes, including one newly generated mitogenome, to compare nucleotide substitution rates, selection pressure, and gene arrangements. The newly generated mitogenome is reported along with reannotation of Pealius mori and comparisons to other whitefly mitogenomes. Comparative studies on nucleotide composition of 18 whiteflies revealed the positive GC skewness, confirming the reversal of strand asymmetry. We found 11 rearranged gene orders within two subfamilies of whiteflies with 8-18 breakpoints of gene rearrangements. Members of the subfamily Aleyrodinae exhibit more complex pathways in the evolution of gene order as compared to the subfamily Aleurodicinae. Our findings also revealed that the increase or reduction of nucleotide substitution rates does not have an impact on any of the gene rearrangement scenarios depicting neutral correlation. Selection pressure analysis revealed that the mitogenomes from members of both the subfamilies Aleurodicinae and Aleyrodinae are characterized by intense purifying selection pressure.

Characterization of Complete Mitochondrial Genome of Badri Breed of Bos indicus (Bovidae: Bovinae): Selection Pressure and Comparative Analysis.

High-altitude mammals are often subject to specific environmental obstacles, which exert selective pressure on their physiological and morphological traits, hence driving their evolutionary processes. It is anticipated that these circumstances will lead to the adaptive evolution of protein-coding genes (PCGs) in the mitochondrial genome, which play a crucial role in the oxidative phosphorylation system. In this study, we have generated the complete mitochondrial genome of the Badri breed of Bos indicus inhabiting a high-altitude environment to test the signatures of adaptive evolution on PCGs and their phylogenetic relationships. The complete mitogenome of the Badri breed is 16,339 bp and most tRNAs showed typical clover-leaf secondary structure with a few exceptions, like trnS1 and trnS2 without DHU arm and trnK without DHU loop. Comparative analysis of PCGs indicated that cox1 is the most conserved, while atp6 is the most variable gene. Moreover, the ratios of non-synonymous to synonymous substitution rates indicated the purifying selection (Ka/Ks < 1) in the protein-coding genes that shape the diversity in mitogenome of Bos indicus. Furthermore, Branch-site model (BSM) suggested that cox1, cox2, nad3, nad4L, and nad6 underwent stronger purifying selection (ω < 1) than other PCGs in 15 breeds of 4 species, including Badri. BSM also detected 10 positive sites in PCGs and one in 13 PCGs concatenated dataset. Additional analyses in Datamonkey indicated 11 positive sites and 23 purifying sites in the concatenated dataset, a relaxation of selection strength in nad3, and no evidence of episodic diversifying selection in any PCGs. Phylogeny revealed the sister relationship of the Badri with other breeds of Bos indicus as well as Bos frontalis (Gayal-2). The mitogenome of the Badri breed is an important genomic resource for conservation genetics of this species and also contributes to the understanding of the adaptive evolution of mitochondrial protein coding genes.

Characterization of complete mitochondrial genome of three Horse flies of the genus Tabanus (Diptera: Tabanidae): comparative analysis.

BACKGROUND: Tabanidae (Horse-Flies or Deer-Flies) are one of the most economically important as well as medically significant haematophagous insect family within the order Diptera. Members of this group are also responsible for the mortality of substantial number of live-stock every year. Due to their pathogen transmission potential and vector competencies makes them an important insect group to study. Till now, mitochondrial genome of 18 species of tabanids were available. METHODS AND RESULTS: The complete mitogenome of three species T. diversifrons (15,809 bp), T. rubidus (15,878 bp) and T. tenens (15,872 bp) were generated by Next generation sequencing method. They consist 37 genes, with a positive AT skew and a negative GC skew. The gene order of these three species is similar to the typical gene arrangement of infra-order Tabanomorpha. Most of the tRNAs showed typical clover-leaf secondary structure except trnS1, which lacks the DHU arm. The sliding window analysis showed that the nad4L is the most conserved while atp8, and nad6 are the most variable genes. Moreover, the ratios of non-synonymous to synonymous substitution rates indicated that all PCGs under the purifying selection. Phylogeny revealed Chrysops and Haematopota are monophyletic while species of Hybomitra are nested within the polyphyletic clade of Tabanus. T. diversifrons exhibits sister relationship with Atylotus miser. Two morphologically divergent species T. rubidus and T. tenens are found to be genetically similar and indistinguishable by mitochondrial genome. CONCLUSIONS: The hypervariable genes like atp8 and nad6 can be used as molecular markers for the identification of recently diverged lineages of family Tabanidae. Further, to address uncertainties arising from the two morphological divergent species, it is imperative to obtain data from nuclear gene markers.

Comparative analysis of the two suborders of Thysanoptera and characterization of the complete mitochondrial genome of Thrips parvispinus.

Thrips parvispinus is a serious sucking pest on a number of economically important crops in the oriental region. It has gained importance recently for its drastic range extension distribution as an invasive pest. Here, the complete mitochondrial genome (15,067 bp) of Thrips parvispinus was sequenced and characterized. It possesses 37 genes and the putative noncoding region is duplicated. Comparative analyses of nucleotide diversity, skewness, codon usage bias, and selection pressure in mitochondrial protein-coding genes of the available 31 thrips mitogenomes (24 Terebrantia + 7 Tubulifera) were performed. Phylogenetic analysis showed a sister relationship of T. parvispinus to the clade (T. florum + T. hawaiiensis). Phylogenetic analyses formed the monophyly of subfamilies Phlaeothripinae and Idolothripinae within the family Phlaeothripidae (Suborder Tubulifera). Low nucleotide diversity was indicative of reversal of strand asymmetry in the Tubulifera. Neutrality analysis showed that directional mutation plays a major role in shaping codon usage bias in both suborders. Principal component analysis indicated distinct codon usage patterns in each suborder. Our data suggested weaker selection constrains on Terebrantia than in the Tubulifera. More tubuliferan mitogenomes are required to resolve previous classification hypotheses and elucidate genome evolution in these two suborders.

Gene rearrangement in the mitogenome of whiteflies (Hemiptera: Aleyrodinae) along with their phylogeny and characterization of complete mitogenome of Aleurodicus rugioperculatus.

BACKGROUND: Mitochondrial genome rearrangements have been used for defining evolutionary relationships, but there have been incidences of convergences at different taxonomic levels. To gain new insights into whitefly mitogenome evolution, gene arrangement and phylogeny, we sequenced the complete mitogenome of Aleurodicus rugioperculatus (Aleyrodidae: Aleurodicinae) and conducted a comparative analysis with the previously published mitogenomes across the family Aleyrodidae. METHODS AND RESULTS: The complete mitogenome of Aleurodicus rugioperculatus was generated by Next generation sequencing method. It is 15,060 bp circular molecule with 86.5 A + T and 5.5% G + C content. It contains 37 genes (13 PCGs, two rRNAs, 22 tRNAs) and a non-coding control region (CR). Comparative analysis of codon usage indicated that the subfamily Aleyrodinae have weaker bias than Aleurodicinae. Bayesian Inference (BI) and Maximum Likelihood (ML) phylogenetic analyses yielded similar topologies supporting the monophyly of Aleyrodinae and Aleurodicinae. The gene order of 13 whiteflies was compared with ancestor to examine the plesiomorphies, synapomorphies and autapomorphies. We identified five gene blocks (I-V) in the whitefly ancestor that are shared plesiomorphies retained in different whitefly lineages. Gene block I is conserved in all whiteflies except three species. Conversely, we detected 83 derived gene boundaries within the family. Mapping these gene boundaries onto a phylogenetic tree revealed that 16 were symplesiomorphies for two subfamilies; 9 were synapomorphies between the species, and 28 autapomorphies for individual species. CONCLUSIONS: Comparative analyses of gene order of whiteflies revealed the derived gene boundaries which can be further investigated with more mitogenome data to examine the genome evolution in whiteflies.

Gene arrangement, phylogeny and divergence time estimation of mitogenomes in Thrips.

BACKGROUND: The metazoan mitogenomes usually display conserved gene arrangement while thrips are known for their extensive gene rearrangement, and duplication of the control region. METHODS AND RESULT: We sequenced complete mitogenomes of eight species of thrips to determine the gene arrangement, phylogeny and divergence time estimation. All contain 37 genes and one control region, (CR) except four species with two CRs. Duplicated tRNAs were detected in Mycterothrips nilgiriensis and Thrips florum. nad4-nad4L were not found adjacent to each other in Phibalothrips peringueyi and Plicothrips apicalis. Both Bayesian and likelihood phylogenetic analyses of thrips mitogenomes supported the monophyly of two suborders (Terebrantia and Tubulifera) and the two largest families (Phlaeothripidae and Thripidae). Out of seven earlier proposed ancestral gene blocks, six are conserved in Panchaetothripinae, three in Thripinae and two in Phlaeothripidae. Additionally, eight Thrips Gene Blocks were identified, of which, three conserved in Tubulifera, four in Terebrantia, and one only in Aeolothripidae. Forty-two gene boundaries (15 from previous study + 27 new) were identified. The molecular divergence time is estimated for the order Thysanoptera and suggested that these insects may have been diversified from hemipterans in the late Permian period. The most recent ancestors belong to family Thripidae and Phlaeothripidae, which were diversified in upper Cretaceous period and showed higher rates of rearrangement from the ancestral gene order. CONCLUSIONS: The current study is the first largest effort to provide the new insights into the mitogenomic features, gene arrangement, phylogeny and divergence time estimation of thrips belonging to the order Thysanoptera.

Complete Mitochondrial Genome of Great Frigatebird (Fregata minor): Phylogenetic Position and Gene Rearrangement.

The complete mitogenome sequence of the Great Frigatebird, Fregata minor was sequenced for the first time in this study. The mitogenome (16,899 bp) comprises of 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes, and a control region (CR). The mitogenome was AT-rich (55.60%) with 11 overlapping and 18 intergenic spacer regions. Most of the PCGs were started by a typical ATG initiation codon except for cox1 and nad3. A maximum-likelihood phylogeny of concatenated PCGs resulted in a well-resolved phylogeny of all the species of Suliformes and illuminates the sister relationship of F. minor with F. magnificens. The present mitogenome-based phylogeny clearly enlightens the evolutionary position of Suliformes and Pelecaniformes species. Unique tandem repeats were identified in both F. minor and F. magnificens, which can be employed as a species-specific marker. To illuminate the population structure of this migratory seabirds, the present study advocate more sampling and the generation of additional molecular data to clarify their genetic diversity. The present study also rejects an earlier hypothesis on the mitochondrial gene order of Suliformes and corroborated the typical avian gene order in frigatebirds.

Morphological and DNA Barcoding Evidence for Invasive Pest Thrips, Thrips parvispinus (Thripidae: Thysanoptera), Newly Recorded From India.

South East Asia pest thrips species, Thrips parvispinus (Karny), is a serious pest on a number of agricultural and horticultural crops in a number of plant families. Based on an integrated approach of morphology and DNA barcoding, invasion of this serious pest is reported first time from India on papaya plantations. Molecular data have corroborated with the morphological identification. Haplotyping data suggested that the Indonesia may be a probable source of invasion of this pest to India.

The Poaceae-associated genus Bamboosiella (Thysanoptera, Phlaeothripidae) from India with one new species.

Bamboosiella venkataramani sp. n. is described from India based on specimens collected on grass clumps from the Karnataka State of India. A key is provided for identification of seven Indian species of the genus Bamboosiella.

The genus Rhamphothrips in India (Thysanoptera: Thripidae) with description of a new species .

Rhamphothrips bhattii sp.n. is described from India based on specimens collected on flowers and leaves of Tabernaemontana divaricata (Apocynaceae) in the States of West Bengal and Odisha. The pronotum of this species is longer than any other known member of the genus. A key to the six species of Rhamphothrips recorded from India is provided.

Frankliniella species from India (Thysanoptera: Thripidae), with a new generic synonym and an unusual new species.

Frankliniella genus-group is one of the most important group in the sub-family Thripinae comprising, more than 270 species in nine genera. A morphological-based cladistic analysis of genus-level relationships within this group was performed, based on 54 morphological character states for 26 species, including Thrips physapus as an outgroup. This analysis recovered Pseudanaphothrips as monophyletic and sister-group to a group of five Old World genera: Firmothrips, Kakothrips, Parabaliothrips, Sitothrips and Yaobinthrips. It also showed a sister relationship between eight species of Poaceae-associated Old World species in Frankliniella plus Iridothrips, and a group of five New World species in Frankliniella and Guerothrips. As a result, Iridothrips is here considered a new synonym of Frankliniella, and Frankliniella insolitum sp. n. is described from northern India. A key to the six species of Frankliniella recorded from India is also provided. Images and notes of F. unicolor Morgan based on a paratype of the synonym F. andropogoni Moulton & Andre are also provided.

A new genus and species of subfamily Dendrothripinae (Thysanoptera: Thripidae) from India.

Jammuthrips paikulensis gen. et sp. n. is described from Jammu Kashmir, Union territory of India and the morphological relationships among the closely related genera of subfamily Dendrothripinae are discussed. Key to Indian genera of subfamily Dendrothripinae is provided. Two DNA barcodes of new species were generated and submitted to The Barcode of Life Data Systems (BOLD).

A new species of Psephenothrips (Thysanoptera:Phlaeothripidae) with one new record from India.

Psephenothrips uttarakhandensis sp. n. is described and illustrated from India. Also, Neohydatothrips xestosternitus (Han Cui) is newly recorded from India. The DNA barcode data using partial mitochondrial cytochrome c oxidase subunit I (mtCOI) from the holotype of the new species and one sequence of Neohydatothrips xestosternitus were generated and submitted to The Barcode of Life Data Systems (BOLD).

Complete mitogenome of the endangered and endemic Nicobar treeshrew (Tupaia nicobarica) and comparison with other Scandentians.

The Nicobar treeshrew (Tupaia nicobarica) is an endangered small mammal endemic to the Nicobar Island of the Andaman Sea, India regarded as an alternative experimental animal model in biomedical research. The present study aimed to assemble the first mitochondrial genome of T. nicobarica to elucidate its phylogenetic position with respect to other Scandentians. The structure and variation of the novel mitochondrial genome were analyzed and compared with other Scandentians. The complete mitogenome (17,164 bp) encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs), and one control region (CR). Most of the genes were encoded on majority strand, except nad6 and eight tRNAs. The nonsynonymous/synonymous ratio in all PCGs indicates strong negative selection among all Tupaiidae species. The comparative study of CRs revealed the occurrence of tandem repeats (CGTACA) found in T. nicobarica. The phylogenetic analyses (Maximum Likelihood and Bayesian Inference) showed distinct clustering of T. nicobarica with high branch supports and depict a substantial divergence time (12-19 MYA) from the ancestor lineage of Tupaiidae. The 16S rRNA dataset corroborates the taxonomic rank of two subspecies of T. nicobarica from the Great and Little Nicobar Islands. In the future, whole nuclear genome sequencing is necessary to further improve our understanding of evolutionary relationships among treeshrews, and will have implications for biomedical research.

Gut microbial composition in developmental stages of gall inducing thrips Gynaikothrips uzeli and associated plant pathogenesis.

Gut bacteria play a crucial role in the several metabolic activity of the insects. In the present work, effort has been made to decipher the gut microbiota associated with the developmental stages of Gynaikothrips uzeli a gall inducing thrips along with their predicted functional role. Further, an effort has been made to correlate the bacterial communities with plant pathogenesis and thelytoky behaviour of G. uzeli. Findings obtained revealed that genus Arsenophonus dominated the total bacterial diversity and was transmitted vertically through the developmental stages. Further, it was observed that the high abundance of genus Arsenophonus promotes the thelytoky behaviour in G. uzeli and results in the killing of males. Furthermore, strong connecting link between Arsenophonus abundance and gall induction in F. benjamina was observed in the current dataset. G. uzeli being in the category of phloem sucking insect was known for the induction of galls and the current findings for the first time unveiled the facts that high abundance of genus Arsenophonus a well-known plant pathogen may be one of the major reason for inducing galls in F. benjamina. Moreover, PICRUSt2 analysis revealed that predicted functional pathways like biosynthesis of amino acids, and metabolism of carbon, nitrogen, carbohydrates and amino acids (e.g. Arginine, Alanine, Aspartate, Glutamate, Proline, Cysteine, Methionine, Glycine, Threonine, and Serine) were frequently noticed in profiles associated with all the developmental stages of G. uzeli. More to this, the high abundance of Arsenophonus in G. uzeli suggest that representatives of this genus may be resistant and/or tolerant to different antibacterial agents, alkaloids, flavonoids, and glycosides (e.g. quercetin). The correlation of bacterial diversity in pathogenicity can be extrapolated in different pest and vector species of other arthropods.

GIS-based impact assessment and spatial distribution of air and water pollutants in mining area.

Mining is a significant part of the transforming economy, which is generally considered as essential as well as social evil at the same time. It is one of the potential contributors to air and water pollution and possesses long-term impact on their quality. Keeping in view the exponential mining activities, we have selected an iron mine area in Bailadila, Chhattisgarh, India, as a sampling site and investigated the impact of mining activities on the air as well as water quality by setting up seven air quality and thirty water quality monitoring stations. From the results obtained, it was observed that concentration of air pollutants such as SO2, NO2, PM2.5 and PM10 for the year 2015 lies in the range of 11.5-13.0 µg/m3, 11.5-13.0 µg/m3, 24.9-33.4 ppm and 61.6-74.2 ppm, respectively, while for the year 2018, it lies in the range of 10.3-11.7 µg/m3, 10.5-14.7 µg/m3, 18.3-50.8 ppm and 23.7-60.7 ppm, respectively. Furthermore, results obtained revealed that air pollutants such as SO2, NO2, PM2.5 and PM10 were within the permissible limits but they contributed towards the light air pollution (air pollution index: 25-50) at all the air monitoring stations. Moreover, PM10 was considered as criterion pollutant in the Bailadila, Chhattisgarh region. On the other hand, it was observed that groundwater quality was deteriorated in the subsequent years. Most of the water quality parameters were in the permissible limits except iron (Fe). Moreover, on the basis of water quality indexing, water quality was classified as "poor" in ~ 30% of the sites and "very poor" in ~ 34% sites. The water quality was "unhealthy for drinking" in 3% and 6% sites in the year 2015 and 2018, respectively.

Nanoporous carbon materials as a sustainable alternative for the remediation of toxic impurities and environmental contaminants: A review.

Due to rapidly deteriorating water resources, the world is looking forward to a sustainable alternative for the remediation of noxious pollutants such as heavy metals and organic and gaseous contaminants. To address this global issue of environmental pollution, nanoporous carbon materials (NPCMs) can be used as a one-stop solution. They are widely applied as adsorbents for many toxic impurities and environmental contaminants. The present review provides a detailed overview of the role of different synthesis factors on the porous characteristics of carbon materials, activating agents, reagent-precursor ratio and their potential application in the remediation. Findings revealed that synthetic parameters result in the formation of microporous NPCMs (SBET: >4000 m3/g; VTotal (cm3/g) ≥ 2; VMicro (cm3/g) ≥ 1), micromesoporous (SBET: >2500 m3/g; VTotal (cm3/g) ≥ 1.5; VMicro (cm3/g) ≥ 0.7) and mesoporous (SBET: >2500 m3/g; VTotal (cm3/g) ≥ 1.5; VMicro (cm3/g) ≥ 0.5) NPCMs. Moreover, it was observed that a narrow pore size distribution (0.5-2.0 nm) yields excellent results in the remediation of noxious contaminants. Further, chemical activating agents such as NaOH, KOH, ZnCl2, and H3PO4 were compared. It was observed that activating agents KОН, H3PO4, and ZnCl2 were generally used and played a significant role in the possible large-scale production and commercialization of NPCMs. Thus, it can be interpreted that with a well-planned strategy for the synthesis, NPCMs with a "tuned" porosity for a specific application, in particular, microporosity for the accumulation and adsorption of energetically important gases (CO2, CH4, H2), micro-mesoporosity and mesoporosity for high adsorption capacity for towards metal ions and a large number of dyes, respectively.

Complete mitochondrial genome of critically endangered Crocidura nicobarica (Soricidae: Eulipotyphla) from the Great Nicobar Island, India.

The mitogenome (17,388 bp) of the Nicobar shrew, Crocidura nicobarica was determined in the present study. The mitogenome comprises 13 PCGs (11,427 bp), 22 tRNAs (1507 bp), two rRNAs (2538 bp), and a major non-coding control region (1932 bp). The Maximum Likelihood phylogeny clearly discriminates all the studied Crocidura species with high bootstrap support by concatenated PCGs. The studied species, C. nicobarica shows a close relationship with Crocidura orientalis, distributed in Java, Indonesia. The lineage diversification and zoogeographic patterns are congruent in the present analyses and encouraged further sampling and more molecular data to elucidate their in-depth evolutionary relationship.

Insights into the gut bacterial communities of spider from wild with no evidence of phylosymbiosis.

In the present study, an effort has been made to elucidate the gut bacterial diversity of twelve species of the family Araneidae under three subfamilies collected from 5 states of India along with their predicted metabolic role in functional metabolism. Further, we also compared the host species phylogeny based on partial cytochrome c oxidase subunit I (COI) sequences with the gut bacteria composition dendrogram to decipher the phylosymbiotic relationships. Analysis revealed the presence of 22 bacterial phyla, 145 families, and 364 genera in the gut, with Proteobacteria, Firmicutes, Actinobacteria, and Deinococcus-Thermus as the highest abundant phyla. Moreover, phylum Bacteriodetes was dominated only in Cyclosa mulmeinensis and Chlamydiae in Neoscona bengalensis. At the genus level, Bacillus, Acinetobacter, Cutibacterium, Pseudomonas, and Staphylococcus were the most dominant genera. Furthermore, the genus Prevotella was observed only in Cyclosa mulmeinensis, and endosymbiont Wolbachia only in Eriovixia laglaizei. The differential abundance analysis (DeSeq2) revealed the 19 significant ASVs represented by the genera like Acinetobacter, Vagoccoccus, Prevotella, Staphylococcus, Curvibacter, Corynebacterium, Paracoccus, Streptococcus, Microbacterium, and Pseudocitrobacter. The inter- and intra-subfamilies comparison based on diversity indices (alpha and beta diversity) revealed that the subfamily Araneinae have high richness and diversity than Argiopinae and Gasteracanthinae. The phylosymbiotic analysis revealed that there is no congruence between the gut bacteria composition dendrogram with their host phylogeny.

A new species of Mycterothrips Trybom (Thysanoptera: Thripidae) from India with new record of the genus Paithrips Nonaka amp; Jangvitaya.

Mycterothrips nainiae sp. n. (Thripinae) is described and illustrated from India, and one genus and species, Paithrips circularis Nonaka and Jangvitaya, is newly recorded from India. A key to species of Mycterothrips from India is also provided. The DNA barcode data using partial mitochondrial cytochrome c oxidase subunit I (mtCOI) from the holotype also five sequences of Paithrips circularis were generated.