From beasts to bytes:Revolutionizing zoological research with artificial intelligence

Since the late 2010s,Artificial Intelligence(AI)including machine learning,boosted through deep learning,has boomed as a vital tool to leverage computer vision,natural language processing and speech recognition in revolutionizing zoological research.This review provides an overview of the primary tasks,core models,datasets,and applications of AI in zoological research,including animal classification,resource conservation,behavior,development,genetics and evolution,breeding and health,disease models,and paleontology.Additionally,we explore the challenges and future directions of integrating AI into this field.Based on numerous case studies,this review outlines various avenues for incorporating AI into zoological research and underscores its potential to enhance our understanding of the intricate relationships that exist within the animal kingdom.As we build a bridge between beast and byte realms,this review serves as a resource for envisioning novel AI applications in zoological research that have not yet been explored.

Silencing of V-ATPase-E gene causes midgut apoptosis of Diaphorina citri and affects its acquisition of Huanglongbing pathogen

The Asian citrus psyllid,Diaphorina citri Kuwayama,is among the most im-portant pests of citrus.It is the main vector of the Huanglongbing(HLB)pathogen Can-didatus Liberibacter asiaticus(CLas),which causes severe losses in citrus crops.Control of D.citri is therefore of paramount importance to reduce the spread of HLB.In this re-gard,using RNA interference(RNAi)to silence target genes is a useful strategy to control psyllids.In this study,using RNAi,we examined the biological functions of the V-ATPase subunit E(V-ATP-E)gene of D.citri,including its effect on acquisition of CLas.The amino acid sequence of V-ATP-E from D.citri had high homology with proteins from other insects.V-ATP-E was expressed at all D.citri life stages analyzed,and the expres-sion level in mature adults was higher than that of teneral adults.Silencing of V-ATP-E resulted in a significant increase in mortality,reduced body weight,and induced cell apop-tosis of the D.citri midgut.The reduced expression of V-ATP-E was indicated to inhibit CLas passing through the midgut and into the hemolymph,leading to a majority of CLas being confined to the midgut.In addition,double-stranded RNA of D.citri V-ATP-E was safe to non-target parasitic wasps.These results suggest that V-ATP-E is an effective RNAi target that can be used in D.citri control to block CLas infection.

High-efficiency gene editing in Anopheles sinensis using ReMOT control

Dear editor,Functional genomics studies of mosquito vectors are crucial for understanding their physiological behavior,pathogen transmission,and evolution,and for providing essential molecular targets for genetic control(Severson&Behura,201l;Alphey,2014;Ruzzante et al.,2019;Hong et al.,2022).The main methods involve clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)gene editing via embryo microinjection(Criscione et al.,2015;Kistler et al.,2015).

Comparative analyses of simple sequence repeats(SSRs)in 23 mosquito species genomes:Identification,characterization and distribution(Diptera:Culicidae)

Simple sequence repeats (SSRs) exist in both eukaryotic and prokaryotic genomes and are the most popular genetic markers, but the SSRs of mosquito genomes are still not well understood. In this study, we identified and analyzed the SSRs in 23 mosquito species using Drosophila melanogaster as reference at the whole-genome level. The results show that SSR numbers (33 076-560 175/genome) and genome sizes (574.57-1342.21 Mb) are significantly positively correlated (R~= 0.8992, P < 0.01), but the correlation in individual species varies in these mosquito species. In six types of SSR, mono- to trinucleotide SSRs are dominant with cumulative percentages of 95.14%-99.00% and densities of 195.65/Mb-787.51/Mb, whereas tetra- to hexanucleotide SSRs are rare with 1.12%-4.22% and 3.76/Mb-40.23/Mb. The (A/T)n,(AC/GT)n and (AGC/GCT)n are the most frequent motifs in mononucleotide, dinucleotide and trinucleotide SSRs, respectively, and the motif frequencies of tetra- to hexanucleotide SSRs appear to be species-specific. The 10-20 bp length of SSRs are dominant with the number of 11() 561 ± 93 482 and the frequency of 87.25%± 5.73% on average, and the number and frequency decline with the increase oflength. Most SSRs(83.34%± 7.72%) are located in intergenic regions, followed by intron regions (11.59%± 5.59%), exon regions (3.74%± 1.95%), and untranslated regions (1.32%± 1.39%). The mono-, di- and trinucleotide SSRs are the main SSRs in both gene regions (98.55%± 0.85%) and exon regions (99.27%± 0.52%). An average of 42.52% of total genes contains SSRs, and the preference for SSR occurrenee in different gene subcategories are species-specific. The study provides useful insights into the SSR diversity, characteristics and distribution in 23 mosquito species of genomes.

First report of complete mitochondrial genome in the subfamily Alleculinae and mitochondrial genome-based phylogenetics in Tenebrionidae(Coleoptera:Tenebrionoidea)

Despite worldwide distribution and rich diversity,the knowledge of mitochondrial genome(mtgenome)characteristics within the family Tenebrionidae(Coleoptera)is still very limited,and phylogenetics remain unresolved for the family.In this study,the mtgenomes for 12 species are newly sequenced and annotated.Three of the species represent the first report of complete mtgenomes from the subfamily Alleculinae.Comparative analysis of 36 tenebrionid mtgenomes finds that gene composition and order are the same as a theoretical ancestral insect mtgenome,and AT bias,length variation,and codon usage are consistent with other reported beetle mtgenomes.Some intergenic overlap and gap sequences may contain phylogenetically informative information,whereas neither the conserved nor repeat sequences in the control region do.The subfamilies Lagriinae,Pimeliinae,Stenochiinae,and Alleculinae are found to be monophyletic,and the subfamilies Diaperinae and Tenebrioninae polyphyletic in our study.Furthermore,Lagriinae is sister to the rest of the subfamilies.At the tribal level,the tribes Lagriini in the subfamily Lagrrinae;Strongyliini in Stenochiinae;Cteniopodini in Alleculinae;and Triboliini,Opatrini,and Amarygmini in Tenebrioninae are monophyletic;while Diaperini in Diaperinae,and Tenebrionini in Tenebrioninae are polyphyletic.

piggyBac-mediated germline transformation of the malaria mosquito Anopheles sinensis (Diptera:Culicidae)

Dear Editor,Anopheles sinensis is the primary vector of vivax malaria in China.Given the risks posed by An.sinensis,many methods have been used to control this vector,most commonly chemical prevention.However,the extensive use of insecticides has subjected mosquitoes to intense selection pressure,resulting in the development of resistance,variations in mosquito behavior.

Physicochemical properties, molecular structure, antioxidant activity, and biological function of extracellular melanin from Ascosphaera apis

Ascosphaera apis spores containing a dark-colored pigment infect honeybee larvae,resulting in a large-scale collapse of the bee colony due to chalkbrood disease.However,little is known about the pigment or whether it plays a role in bee infection caused by A.apis.In this study,the pigment was isolated by alkali extraction,acid hydrolysis,and repeated precipitation.Ultraviolet(UV)analysis revealed that the pigment had a color value of 273,a maximum absorption peak at 195 nm,and a high alkaline solubility(7.67%)and acid precipitability.Further chemical structure analysis of the pigment,including elemental composition,Fourier transform infrared(FTIR)spectroscopy,Raman spectroscopy,mass spectrometry,and nuclear magnetic resonance(NMR),proved that it was a eumelanin with a typical indole structure.The molecular formula of melanin is C10H6O4N2,and its molecular weight is 409 Da.Melanin has hydroxyl,carboxyl,amino,and phenolic groups that can potentially chelate to metal ions.Antioxidant function analyses showed that A.apis melanin had a high scavenging activity against superoxide,hydroxyl,and 2,2-diphenyl-1-picrylhydrazyl(DPPH)radicals,and a high reducing ability to Fe3+.Indirect immunofluorescence assay(IFA),scanning electron microscopy(SEM),and transmission electron microscopy(TEM)analyses showed that A.apis melanin was located on the spore wall.The spore wall localization,antioxidant activity,and metal ion chelating properties of fungal melanin have been suggested to contribute to spore pathogenicity.However,further infection experiments showed that melanin-deficient spores did not reduce the mortality of bee larvae,indicating that melanin does not increase the virulence of A.apis spores.This study is the first report on melanin produced by A.apis,providing an important background reference for further study on its role in A.apis.

Mitogenome-based phylogeny of mosquitoes(Diptera:Culicidae)

Mosquitoes are of great medical significance as vectors of many deadly diseases.Mitogenomes have been widely used in phylogenetic studies,but mitogenome knowledge within the family Culicidae is limited,and Culicidae phylogeny is far from resolved.In this study,we surveyed the mitogenomes of 149 Culicidae species,including 7 newly sequenced species.Comparative analysis of 149 mosquito mitogenomes shows gene composition and order to be identical to that of an ancestral insect,and the AT bias,length variation,and codon usage are all consistent with that of other reported Dipteran mitogenomes.Phylogenetic analyses based on the DNA sequences of the 13 protein-coding genes from the 149 species robustly support the monophyly of the subfamily Anophelinae and the tribes Aedini,Culicini,Mansonini,Sabethini,and Toxorhynchitini.To resolve ambiguous relationships between clades within the subfamily Culicinae,we performed topological tests and show that Aedini is a sister to Culicini and that Uranotaenini is a sister to(Mansonini)+(Toxorhynchitini+Sabethini).In addition,we estimated divergence times using a Bayesian relaxation clock based on the sequence data and 3 fossil calibration points.The results show mosquitoes diverged during the Early Jurassic with massive Culicinae radiations during the Cretaceous,coincident with the emergence of angiosperms and the burst of mammals and birds.Overall,this study,which uses the largest number of Culicidae mitogenomes sequenced to date,comprehensively reveals the mitogenome characteristics and mitogenome-based phylogeny and divergence times of Culicidae,providing information for further studies on the mitogenome,phylogeny,evolution,and taxonomic revision of Culicidae.