The complete sequence of the W chromosome, which carries feminization activity in the silkworm, is crucial for understanding the sex-determination system in Lepidoptera. However, extensive accumulation of transposons due to lack of recombination, the very rare protein-coding genes and almost no information about molecular markers has hindered full W sequencing. We report the first complete silkworm W sequence (T2T_W, 11683305 bp) obtained by combining sequencing-assembly technologies and newly developed error detection methods, evaluated with genetically mapped W-RAPD markers, W-mutants, and W-derived BAC clones. The T2T_W sequence showed that the W is composed of a massive 92% accumulation of transposons and repeat sequences, among which the main constituents are intact LTR/LINE retrotransposons indicating recent expansions. In addition to Fem clusters producing Fem piRNA (Feminizer-derived PIWI-interacting RNA), we found 26 protein-coding genes in the W sequence. These include four gene pairs encoding zinc-finger motifs designated z1:z20 and a gene encoding serine/arginine repetitive matrix protein 1-like (SRRM1-like). To identify candidate genes for female sex-determination and differentiation we also sequenced the shortest W (3.8 Mb) from a translocation mutant with feminizing activity, which harbored four conventional genes: a Fem cluster, a pair of z1:z20 isoforms, z20-S, and a SRRM1-like gene. Phylogenetic analysis revealed that z1:z20 originated from a copy of an autosomal zinc-finger gene pair, z2:z21, translocated onto the W around 2.43 Mya and subsequently amplified to yield 4 W-linked zinc-finger gene pairs. The complete W sequence revealed that large-scale deletions and amplifications played a significant role in W chromosome evolution.

Gene expression profiling is vital for deciphering immune responses in insects, especially for genes involved in pathogen defense, stress adaptation, and immune regulation. The muga silkworm, Antheraea assamensis Helfer (A. assamensis), a species of considerable economic and cultural significance in Northeast India, is vulnerable to bacterial and viral infections that severely impact silk production. Despite its importance, no prior studies have validated suitable reference genes for reverse-transcription quantitative PCR (RT-qPCR) based expression analysis under pathogenic stress in this species. Given that reference gene expression may vary with tissue type, developmental stage, and infection status, rigorous validation of stable reference genes is essential for accurate normalization. Eight candidate housekeeping genes (EF1α, GAPDH, RPS3A, RPL13A, Actin-A1, Tub1, SDHA, and EIF4A) were selected for evaluation. RT-qPCR assays were conducted on fat body and midgut tissues under bacterial and viral infection conditions. Gene expression stability was assessed using the geNorm, NormFinder, and RefFinder algorithms. Results indicated that GAPDH was the most stable gene in the fat body during bacterial infection, whereas Actin-A1 and RPS3A exhibited the highest stability under viral infection. In the midgut, GAPDH showed the highest stability during bacterial infection, while both GAPDH and Tub1 were stable under viral infection conditions. Overall, RPS3A demonstrated the most consistent expression stability across all tissues and infection conditions. This study provides the first validated reference gene set for A. assamensis under pathogenic stress, highlighting RPS3A as the most reliable gene for RT-qPCR normalization. These findings will improve the accuracy of gene expression studies and support future transcriptomic and functional genomic research in this economically important silkmoth species.

The Indian tasar silkworm Antheraea mylitta (A. mylitta) is an economically important silkmoth and is native to tropical India. Our current research has deciphered the mitochondrial genome (mitogenome) of A. mylitta by recovering the complete genome sequence from the NCBI-SRA database and comparing it with other mitogenomes from the order Lepidoptera. The mitogenome is a double-stranded circular molecule spanning 15,354 bp with an A & thorn; T content of roughly 80.4%. It consists of a total of 37 genes, comprising 13 protein- coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs), along with a 337 bp long control region. The arrangement of PCGs is similar to other Lepidoptera mitogenomes, with the exception of Cox1 and Cox2, which have different initiation codons. The control region of A. mylitta contains a conserved five bp ATAGA motif as seen in other Antheraea species. Phylogenetic analysis supports previous morphological hypotheses that Bombycoidea, Noctuoidea, Geometroidea, Papilionoidea, and Torticoidea are monophyletic. The divergence time analysis of 13 protein-coding genes reported that A. mylitta diverged from the last common ancestor w 23 million years ago. As per our knowledge, this is the first documented record of the entire mitogenome of A. mylitta. (c) 2024 National Science Museum of Korea (NSMK) and Korea National Arboretum (KNA), Publishing Services by Elsevier. This is an open access article under the CC BY-NC-ND license (http:// creativecommons.org/licenses/by-nc-nd/4.0/).

Sweep spread carrier (S2C) acoustic communication uses wideband chirp waveforms as they are well suited for communicating in an undersea multipath environment. While the gradient heterodyne receivers in the S2C systems can handle the multipath arrivals, we show that they are extremely sensitive to a time scaling of the communication waveform induced by the Doppler effect or carrier frequency offset. The time-scaling can be estimated, and compensated for by re-scaling the received waveform. However, estimation errors leave out a residual timescale even in the re-scaled waveform. We show that even a timescale estimation error of the order of +/- 10(-5) can lead to deleterious variations in the symbol phases within a received S2C frame. We also show the existence of multiple, frequency-dependent, approximately affine symbol phase migration trajectories in a received frame in the presence of small residual time-scales and timing errors. Motivated by this observation, we propose a parallel bank of low complexity decision-aided progressive symbol phase (DAPSP) equalizers to effectively suppress the symbol phase migration in the S2C receiver.

Antimicrobial peptides (AMPs) are essential components of insect immunity, yet the attacin gene family remains poorly studied in Saturniidae. Despite comprehensive functional studies on AMPs across various lepidopteran taxa, the attacin gene family remains insufficiently characterized in Antheraea assamensis (A. assamensis) and related saturniid silkmoths. Here, we present a comprehensive genome-wide analysis across five saturniid silkmoths, identifying 10 attacin genes in A. assamensis, 9 in Antheraea pernyi (A. pernyi), 5 in Antheraea mylitta (A. mylitta), 4 in Antheraea yamamai (A. yamamai), and 10 in Samia ricini (S. ricini). Domain analysis revealed that while most Attacins possess both N- and C-terminal glycine-rich domains, several encode truncated isoforms and some with extended polypeptide lengths. Phylogenetic analysis demonstrated lineage-specific expansions, and aBSREL analysis identified positive selection acting on certain clades, particularly those encoding C-terminal-only isoforms. Conserved microsynteny with Bombyx mori (B. mori) supports a shared evolutionary origin despite scaffold variation. In silico structural modelling and molecular docking predicted high-affinity interactions between Attacin peptides and bacterial lipopolysaccharides (LPS), implicating their role in membrane disruption. Finally, qRT-PCR analysis revealed that several attacin paralogs, particularly attacin5 to attacin8, were significantly upregulated in both the fat body and midgut of A. assamensis following E. coli infection. Notably, attacin2 and attacin10 exhibited higher expression levels in the midgut, highlighting their potential roles in both systemic and gut-localized immune responses.

Muga silkworm (Antheraea assamensis), one of the economically important wild silkmoths, is unique among saturniid silkmoths. It is confined to the North-eastern part of India. Muga silk has the highest value among the other silks. Unlike other silkmoths, A. assamensis has a low chromosome number (n = 15), and ZZ/ZO sex chromosome system. Here, we report the first high-quality draft genome of A. assamensis, assembled by employing the Illumina and PacBio sequencing platforms. The assembled genome of A. assamensis is 501.18 Mb long, with 2697 scaffolds and an N50 of 683.23 Kb. The genome encompasses 18,385 protein-coding genes, 86.29% of which were functionally annotated. Phylogenetic analysis of A. assamensis revealed its divergence from other Antheraea species approximately 28.7 million years ago. Moreover, an investigation into detoxification-related gene families, CYP450, GST, and ABC-transporter, revealed a significant expansion in A. assamensis as compared to the Bombyx mori. This expansion is comparable to Spodoptera litura, suggesting adaptive responses linked to the polyphagous behavior observed in these insects. This study provides valuable insights into the molecular basis of evolutionary divergence and adaptations in muga silkmoth. The genome assembly reported in this study will significantly help in the functional genomics studies on A. assamensis and other Antheraea species along with comparative genomics analyses of Bombycoidea insects.

Insect gut microbiomes play a fundamental role in various aspects of insect physiology, including digestion, nutrient metabolism, detoxification, immunity, growth and development. The wild Muga silkworm, Antheraea assamensis Helfer holds significant economic importance, as it produces golden silk. In the current investigation, we deciphered its intricate gut bacteriome through high-throughput 16S rRNA amplicon sequencing. Further, to understand bacterial community dynamics among silkworms raised under outdoor environmental conditions, we compared its gut bacteriomes with those of the domesticated mulberry silkworm, Bombyx mori L. Most abundant bacterial phyla identified in the gut of A. assamensis were Proteobacteria (78.1

A new variable bandwidth multicarrier (VBMC) waveform was presented in [1] for communicating over wideband rapidly time-varying multi-scale multi-lag (MSML) channels. Perfect channel state information was assumed to be available at the receiver in [1]. In this work, we address the problem of channel estimation for VBMC based communications over wideband MSML channels. Using the Variational Bayesian (VB) inference framework, we estimate the channel from short preamble and postamble waveforms that are primarily used for timing and carrier frequency synchronization, and then decode the data symbols in VBMC communications. We also derive the Bayesian Cramér-Rao bound (BCRB) of the channel estimate as a benchmark for assessing the normalized mean squared error (NMSE) performance of the estimators. We numerically illustrate the efficacy of our approach in the context of underwater acoustic channel estimation.

Abstract Background Peepal/Bodhi tree (Ficus religiosa L.) is an important, long-lived keystone ecological species. Communities on the Indian subcontinent have extensively employed the plant in Ayurveda, traditional medicine, and spiritual practices. The Peepal tree is often thought to produce oxygen both during the day and at night by Indian folks. The goal of our research was to produce molecular resources using whole-genome and transcriptome sequencing techniques. Results The complete genome of the Peepal tree was sequenced using two next-generation sequencers Illumina HiSeq1000 and MGISEQ-2000. We assembled the draft genome of 406 Mb, using a hybrid assembly workflow. The genome annotation resulted in 35,093 protein-coding genes; 53% of its genome consists of repetitive sequences. To understand the physiological pathways in leaf tissues, we analyzed photosynthetically distinct conditions: bright sunny days and nights. The RNA-seq analysis supported the expression of 26,479 unigenes. The leaf transcriptomic analysis of the diurnal and nocturnal periods revealed the expression of the significant number of genes involved in the carbon-fixation pathway. Conclusions This study presents a draft hybrid genome assembly for F. religiosa and its functional annotated genes. The genomic and transcriptomic data-derived pathways have been analyzed for future studies on the Peepal tree.

Fusarium wilt is a major devastating fungal disease of tomato (Solanum lycopersicum L.) caused by Fusarium oxysporum f. sp. lycopersici (Fol) which reduces the yield and production. Xylem sap protein 10 (XSP10) and Salicylic acid methyl transferase (SlSAMT) are two putative negative regulatory genes associated with Fusarium wilt of tomato. Fusarium wilt tolerance in tomato can be developed by targeting these susceptible (S) genes. Due to its efficiency, high target specificity, and versatility, CRISPR/Cas9 has emerged as one of the most promising techniques for knocking out disease susceptibility genes in a variety of model and agricultural plants to increase tolerance/resistance to various plant diseases in recent years. Though alternative methods, like RNAi, have been attempted to knock down these two S genes in order to confer resistance in tomato against Fusarium wilt, there has been no report of employing the CRISPR/Cas9 system for this specific intent. In this study, we provide a comprehensive downstream analysis of the two S genes via CRISPR/Cas9-mediated editing of single (XSP10 and SlSAMT individually) and dual-gene (XSP10 and SlSAMT simultaneously). Prior to directly advancing on to the generation of stable lines, the editing efficacy of the sgRNA-Cas9 complex was first validated using single cell (protoplast) transformation. In the transient leaf disc assay, the dual-gene editing showed strong phenotypic tolerance to Fusarium wilt disease with INDEL mutations than single-gene editing. In stable genetic transformation of tomato at the GE1 generation, dual-gene CRISPR transformants of XSP10 and SlSAMT primarily exhibited INDEL mutations than single-gene-edited lines. The dual-gene CRISPR-edited lines (CRELs) of XSP10 and SlSAMT at GE1 generation conferred a strong phenotypic tolerance to Fusarium wilt disease compared to single-gene-edited lines. Taken together, the reverse genetic studies in transient and stable lines of tomato revealed that, XSP10 and SlSAMT function together as negative regulators in conferring genetic tolerance to Fusarium wilt disease.

Additional file 5: Text File S1.1. The statistics of IlluminaMGI reads mapped to Peepal hybrid whole genome

The present study was conducted to screen the suitable castor (Ricinus communis) cultivar for use in commercial chawki (young age silkworms) rearing of eri silkworm (Samia ricini D.).Five commercially available cultivars of castor viz., NBR-1, Kalpi-6, DCH-519, ICH-66 and DCS-9 were sown in the field and standard package of practices were followed to select the economically viable cultivar in terms of plant growth and yield parameters.The results revealed varying degrees of growth and yield parameters in all five cultivars in terms of plant height, number of leaves per plant and leaf yield at different days after sowing.Among all the cultivars, higher growth and yield parameters was recorded in two cultivars (NBR-1 and Kalpi-6).Further, these two cultivars (NBR-1 and Kalpi-6) were selected for analysis of biochemical constituents.Higher moisture retention capacity (82.65%), protein content (20.60%), carbohydrate content (17.12%) and other leaf quality parameters which are essential for eri young age silkworms (chawki) were recorded in NBR-1.Among the two castor cultivars fed to eri-silkworm, NBR-1 fed worms recorded higher larval weight and more uniformity compared to Kalpi-6 fed worms.The results indicate suitability of NBR-1 cultivar in terms of growth, yield, biochemical constituents and eri young age silkworm rearing.Therefore, NBR-1 is recommended for commercial eri chawki rearing in view of the higher leaf yield obtained at different intervals in a year and superior in improving the rearing performance of eri chawki.Based on these findings a standard package of practice to raise NBR-1 cultivar for chawki rearing has been developed.

In delay-scale spread channels, modulation schemes like orthogonal frequency division multiplexing, orthogonal time frequency space, and the recently proposed orthogonal delay-scale space modulation schemes need to use computationally expensive MMSE receivers to obtain reasonable performance. The MMSE receiver is required to equalize the severe inter-carrier interference caused by the Doppler scale in harsh wideband channels. In this paper, we first develop a variational Bayesian inference (VBI) based a low-complexity variational soft symbol decoding (VSSD) algorithm under the availability of perfect channel state information at the receiver and present a comparative study of the improvement in the BER obtained by using the VSSD algorithm with these waveforms. Second, we propose a two-stage iterative algorithm for the delay-scale spread wideband channel estimation and data detection and show its performance advantage over a direct channel estimation followed by data detection, in the context of underwater acoustic communications. We also present a comparative study of the performance of orthogonal matching pursuit and VBI based channel estimations.

In this paper, we develop a new waveform for communicating over a delay and time-scale spread wideband channel. This waveform, named Variable Bandwidth Multicarrier (VBMC) waveform, comprises multiple subcarriers that are constructed from chirp pulses used in radars and sonars, and is a multicarrier analogue of the sweep spread carrier waveform that time multiplexes the digital symbols onto a single chirp pulse. We design the subcarrier chirps to occupy progressively increasing, frequency-dependent bandwidth from the lower to upper frequency edge of the communication band. Due to this, the subcarriers of the VBMC waveform maintain their near mutual orthogonality even after passing through a delay and scale spread channel, resulting in low inter-carrier interference, and thereby facilitating a low complexity subcarrier-by-subcarrier decoding at the receiver. Numerical simulation of the bit error rate over delay-scale channels shows that the VBMC waveform outperforms the widely used Cyclic Prefix Orthogonal Frequency Division Multiplexing (CP-OFDM) and the recently developed Orthogonal Time-Frequency Space (OTFS) waveforms.

Availability of quality seeds in muga culture for commercial rearing during May-June and Oct-Nov seasons is the biggest challenge, which severely affects the total muga silk production.Both the commercial seasons are preceded by seed and pre-seed seasons with highly unfavourable weather conditions, which affects the availability of quality Disease Free Layings (DFLs) due to low cocoon yield, reduced fecundity, poor hatching and male sterility.Therefore, there is an urgent need to develop an integrated approach to improve the availability of quality DFLs during commercial seasons.Towards this end different strategies are being developed and tested.Breeding for selecting muga lines with high fecundity has been taken up.To avoid unfavourable weather conditions during seed crops especially during summer months June-September, efforts are being made to identify the cooler regions in Northeastern states and to take up seed rearing in the selected regions.Wild muga that exhibit winter hibernation are being studied to identify the linked gene and to introgress it into cultivated population to completely avoid rearing during winter season.Adual-purpose cold reeling procedure has been developed, which has also been tested field level, to reel the silk and obtain live pupae for use in grainage.Through biotechnological approaches the realized fecundity has been increased.Improved mountages that provide enough space, aeration and reduced temperature are being tested for increasing the number of good cocoons and also reducing the male sterility due to high temperature.Other approaches such as rearing of seed cocoons in non-traditional areas having muga host plants such an Uttarakhand state, cold preservation of both DFLs and cocoons, new plantations in cooler regions, effective utilization of grainages developed under different government schemes through state governments, etc., are being explored to effectively increase the quality DFL production for use during commercial seasons in muga ecosystem.These approaches are of great promise and help in achieving 'Sustainability Development Goals 2020' of Central Silk Board.

Orthogonal Time Frequency Space (OTFS) modulation is a recently proposed scheme for time-varying narrowband channels in terrestrial radio-frequency communications. Underwater acoustic (UWA) and ultra-wideband (UWB) communication systems, on the other hand, confront wideband time-varying channels. Unlike narrowband channels, for which time contractions or dilations due to Doppler effect can be approximated by frequency-shifts, the Doppler effect in wideband channels results in frequency-dependent non-uniform shift of signal frequencies across the band. In this paper, we develop an OTFS-like modulation scheme - Orthogonal Delay Scale Space (ODSS) modulation - for handling wideband time-varying channels. We derive the ODSS transmission and reception schemes from first principles. In the process, we introduce the notion of omega-convolution in the delay-scale space that parallels the twisted convolution used in the time-frequency space. The preprocessing 2D transformation from the Fourier-Mellin domain to the delay-scale space in ODSS, which plays the role of inverse symplectic Fourier transform (ISFFT) in OTFS, improves the bit error rate performance compared to OTFS and Orthogonal Frequency Division Multiplexing (OFDM) in wideband time-varying channels. Furthermore, since the channel matrix is rendered near-diagonal, ODSS retains the advantage of OFDM in terms of its low-complexity receiver structure.

Brown spot disease (BSD) of rice (Oryza sativa L.) caused by Bipolaris oryzae is one of the major and neglected fungal diseases worldwide affecting rice production. Despite its significance, very limited knowledge on genetics and genomics of rice in response to B. oryzae available. Our study firstly identified moderately resistant (Gitesh) and susceptible (Shahsarang) North-East Indian rice cultivars in response to a native Bipolaris oryzae isolate BO1. Secondly, a systematic comparative RNA seq was performed for both cultivars at four different time points viz. 12, 24, 48, and 72 hours post infestation (hpi). Differential gene expression analysis revealed the importance of early response to the pathogen in suppressing disease progression. The pathogen negatively regulates the expression of photosynthetic-related genes at early stages in both cultivars. Of the cell wall modification enzymes, cellulose synthase and callose synthase are important for signal transduction and defense. Cell wall receptors OsLYP6, OsWAK80 might positively and OsWAK25 negatively regulate disease resistance. Jasmonic acid and/or abscisic acid signaling pathways are presumably involved in disease resistance, whereas salicylic acid pathway, and an ethylene response gene OsEBP-89 in promoting disease. Surprisingly, pathogenesis-related proteins showed no antimicrobial impact on the pathogen. Additionally, transcription factors OsWRKY62 and OsWRKY45 together might negatively regulate resistance to the pathogen. Taken together, our study has identified and provide key regulatory genes involved in response to B. oryzae which serve as potential resources for functional genetic analysis to develop genetic tolerance to BSD of rice.

Voracious feeding, trans-continental migration and insecticide resistance make Spodoptera litura among the most difficult Asian agricultural pests to control. Larvae exhibit strong circadian behavior, feeding actively at night and hiding in soil during daytime. The daily pattern of larval metabolism was reversed, with higher transcription levels of genes for digestion (amylase, protease, lipase) and detoxification (CYP450s, GSTs, COEs) in daytime than at night. To investigate the control of these processes, we annotated nine essential clock genes and analyzed their transcription patterns, followed by functional analysis of their coupling using siRNA knockdown of interlocked negative feedback system core and repressor genes (SlituClk, SlituBmal1 and SlituCwo). Based on phase relationships and overexpression in cultured cells the controlling mechanism seems to involve direct coupling of the circadian processes to E-boxes in responding promoters. Additional manipulations involving exposure to the neonicotinoid imidacloprid suggested that insecticide application must be based on chronotoxicological considerations for optimal effectiveness.

Bombyx mori, the domesticated silkworm, is an economically important insect owing to the billion-dollar sericulture industry. It is dominant amongst the other silkworm species due to its short generation time, larger progeny size and good quality of silk fibres suitable for silk production. However, B. mori is susceptible to attack by various pathogens such as bacteria, fungi, protozoa, and viruses leading to larval mortality and causing enormous economic loss to the sericulture industry. In the past decade, microRNAs (miRNAs), a group of small non-coding RNAs that function at the post-transcriptional level, have been involved in fine-tuning many biological processes, including host-pathogen interaction. Recent studies have revealed the hitherto unknown layer of host-pathogen interaction through miRNAs in many insect species. Upon infection with the virus, the insect host produces various miRNAs that manipulate gene expression of the virus, while the virus produces several miRNAs using the host small RNA machinery to surpass the host defence mechanism and successfully infect the host. This miRNA-mediated cross-talk is a subject of study to understand better the virus infection mechanism in B. mori. The present chapter highlights various B. mori as well as pathogen-encoded miRNAs involved in host-pathogen interaction. A detailed understanding of miRNAs functioning in B. mori-pathogen interactions would undoubtedly help us design effective strategies to combat pathogen attacks on the insect population.

Fusarium wilt caused by Fusarium oxysporum f. sp. lycopersici ( Fol ) is a major fungal disease of tomato ( Solanum lycopersicum L.). Xylem sap protein 10 ( XSP10) and Salicylic acid methyl transferase ( SlSAMT) have been identified as putative negative regulatory genes associated with Fusarium wilt of tomato. Despite their importance as potential genes for developing Fusarium wilt disease tolerance, very little knowledge is available about their expression, cell biology, and functional genomics. Semi-quantitative and quantitative real-time PCR expression analysis of XSP10 and SlSAMT, in this study, revealed higher expression in root and flower tissue respectively in different tomato cultivars viz. Micro-Tom (MT), Arka Vikas (AV), and Arka Abhed (AA). Therefore, the highly up-regulated expression of XSP10 and SlSAMT in biotic stress susceptible tomato cultivar (AV) than a multiple disease resistant cultivar (AA) suggested the disease susceptibility nature of these genes for Fusarium wilt. Sub-cellular localization analysis through the expression of gateway cloning constructs in tomato protoplasts and seedlings showed the predominant localization of XSP10 in the nucleus and SlSAMT at the cytoplasm. A strong in vivo protein–protein interaction of XSP10 with SlSAMT at cytoplasm from bi-molecular fluorescent complementation study suggested that these two proteins function together in regulating responses to Fusarium wilt tolerance in tomato.