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1. Long-Read Genome Assemblies Reveal Extraordinary Variation in the Number and Structure of MHC Loci in Birds

   https://doi.org/10.1093/gbe/evaa270  

   He, Ke; Minias, Piotr; Dunn, Peter O (February 2021, Genome Biology and Evolution)

   Eyre-Walker, Adam (Ed.)

   Abstract Our knowledge of the Major Histocompatibility Complex (MHC) in birds is limited because it often consists of numerous duplicated genes within individuals that are difficult to assemble with short read sequencing technology. Long-read sequencing provides an opportunity to overcome this limitation because it allows the assembly of long regions with repetitive elements. In this study, we used genomes based on long-read sequencing to predict the number and location of MHC loci in a broad range of bird taxa. From the long-read-based genomes of 34 species, we found that there was extremely large variation in the number of MHC loci between species. Overall, there were greater numbers of both class I and II loci in passerines than nonpasserines. The highest numbers of loci (up to 193 class II loci) were found in manakins (Pipridae), which had previously not been studied at the MHC. Our results provide the first direct evidence from passerine genomes of this high level of duplication. We also found different duplication patterns between species. In some species, both MHC class I and II genes were duplicated together, whereas in most species they were duplicated independently. Our study shows that the analysis of long-read-based genomes can dramatically improve our knowledge of MHC structure, although further improvements in chromosome level assembly are needed to understand the evolutionary mechanisms producing the extraordinary interspecific variation in the architecture of the MHC region. 

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2. New insights into the genome and transmission of the microsporidian pathogen Nosema muscidifuracis

   https://doi.org/10.3389/fmicb.2023.1152586  

   Xiong, Xiao; Geden, Christopher J.; Bergstralh, Dan T.; White, Roxie L.; Werren, John H.; Wang, Xu (April 2023, Frontiers in Microbiology)

   IntroductionNosemais a diverse genus of unicellular microsporidian parasites of insects and other arthropods.Nosema muscidifuracisinfects parasitoid wasp species ofMuscidifurax zaraptorandM. raptor(Hymenoptera: Pteromalidae), causing ~50% reduction in longevity and ~90% reduction in fecundity. Methods and ResultsHere, we report the first assembly of theN. muscidifuracisgenome (14,397,169 bp in 28 contigs) of high continuity (contig N50 544.3 Kb) and completeness (BUSCO score 97.0%). A total of 2,782 protein-coding genes were annotated, with 66.2% of the genes having two copies and 24.0% of genes having three copies. These duplicated genes are highly similar, with a sequence identity of 99.3%. The complex pattern suggests extensive gene duplications and rearrangements across the genome. We annotated 57 rDNA loci, which are highly GC-rich (37%) in a GC-poor genome (25% genome average).Nosema-specific qPCR primer sets were designed based on 18S rDNA annotation as a diagnostic tool to determine its titer in host samples. We discovered highNosematiters inNosema-curedM. raptorandM. zaraptorusing heat treatment in 2017 and 2019, suggesting that the remedy did not completely eliminate theNosemainfection. Cytogenetic analyses revealed heavy infections ofN. muscidifuraciswithin the ovaries ofM. raptorandM. zaraptor, consistent with the titer determined by qPCR and suggesting a heritable component of infection and per ovum vertical transmission. DiscussionThe parasitoids-Nosemasystem is laboratory tractable and, therefore, can serve as a model to inform future genome manipulations ofNosema-host system for investigations of Nosemosis. 

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3. Genome assembly and annotation of Acropora pulchra from Mo’orea, French Polynesia

   https://doi.org/10.1101/2025.03.27.645822  

   Conn, Trinity; Ashey, Jill; Cunning, Ross; Putnam, Hollie (April 2025, Gigabyte)

   Abstract Reef-building corals are integral ecosystem engineers in tropical coral reefs worldwide but are increasingly threatened by climate change and rising ocean temperatures. Consequently, there is an urgency to identify genetic, epigenetic, and environmental factors, and how they interact, for species acclimatization and adaptation. The availability of genomic resources is essential for understanding the biology of these organisms and informing future research needs for management and and conservation. The highly diverse coral genusAcroporaboasts the largest number of high-quality coral genomes, but these remain limited to a few geographic regions and highly studied species. Here we present the assembly and annotation of the genome and DNA methylome ofAcropora pulchrafrom Mo’orea, French Polynesia. The genome assembly was created from a combination of long-read PacBio HiFi data, from which DNA methylation data were also called and quantified, and additional Illumina RNASeq data forab initiogene predictions. The work presented here resulted in the most completeAcroporagenome to date, with a BUSCO completeness of 96.7% metazoan genes. The assembly size is 518 Mbp, with 174 scaffolds, and a scaffold N50 of 17 Mbp. Structural and functional annotation resulted in the prediction of a total of 40,518 protein-coding genes, and 16.74% of the genome in repeats. DNA methylation in the CpG context was 14.6% and predominantly found in flanking and gene body regions (61.7%). This reference assembly of theA. pulchragenome and DNA methylome will provide the capacity for further mechanistic studies of a common coastal coral in French Polynesia of great relevance for restoration and improve our capacity for comparative genomics inAcroporaand cnidarians more broadly. 

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4. Jekyll or Hyde? The genome (and more) of Nesidiocoris tenuis , a zoophytophagous predatory bug that is both a biological control agent and a pest

   https://doi.org/10.1111/imb.12688  

   Ferguson, K_B; Visser, S.; Dalíková, M.; Provazníková, I.; Urbaneja, A.; Pérez‐Hedo, M.; Marec, F.; Werren, J_H; Zwaan, B_J; Pannebakker, B_A; et al (December 2020, Insect Molecular Biology)

   Abstract Nesidiocoris tenuis(Reuter) is an efficient predatory biological control agent used throughout the Mediterranean Basin in tomato crops but regarded as a pest in northern European countries. From the family Miridae, it is an economically important insect yet very little is known in terms of genetic information and no genomic or transcriptomic studies have been published. Here, we use a linked‐read sequencing strategy on a single femaleN. tenuis. From this, we assembled the 355 Mbp genome and delivered anab initio, homology‐based and evidence‐based annotation. Along the way, the bacterial “contamination” was removed from the assembly. In addition, bacterial lateral gene transfer (LGT) candidates were detected in theN. tenuisgenome. The complete gene set is composed of 24 688 genes; the associated proteins were compared to other hemipterans (Cimex lectularis,Halyomorpha halysandAcyrthosiphon pisum). We visualized the genome using various cytogenetic techniques, such as karyotyping, CGH and GISH, indicating a karyotype of 2n= 32. Additional analyses include the localization of 18S rDNA and unique satellite probes as well as pooled sequencing to assess nucleotide diversity and neutrality of the commercial population. This is one of the first mirid genomes to be released and the first of a mirid biological control agent. 

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5. CiFi: accurate long-read chromosome conformation capture with low-input requirements

   https://doi.org/10.1038/s41467-025-66918-y  

   McGinty, Sean_P; Kaya, Gulhan; Sim, Sheina_B; Makunin, Alex; Corpuz, Renée_L; Quail, Michael_A; Abuelanin, Mohamed; Lawniczak, Mara_K_N; Geib, Scott_M; Korlach, Jonas; et al (December 2025, Nature Communications)

   Abstract Hi-C characterizes three-dimensional chromatin organization, facilitates haplotype phasing, and enables genome-assembly scaffolding, but encounters difficulties across complex regions. By coupling chromosome conformation capture (3C) with PacBio HiFilong-read sequencing, here we develop a method (CiFi) that enables analysis of genomic interactions across repetitive regions. Starting with as little as 60,000 cells (sub-microgram DNA), the method produces multi-kilobasepair HiFi reads that contain multiple interacting, concatenated segments (~350 bp to 2 kbp). This multiplicity and increase in segment length versus standard short-read-based Hi-C improves read-mapping efficiency and coverage in repetitive regions and enhances haplotype phasing. CiFi pairwise interactions are largely concordant with Hi-C from a human lymphoblastoid cell line, with gains in assigning topologically associating domains across centromeres, segmental duplications, and human disease-associated genomic hotspots. As CiFi requires less input versus established methods, we apply the approach to characterize single small insects: assaying chromatin interactions across the genome from anAnopheles coluzziimosquito and producing a chromosome-scale scaffolded assembly from aCeratitis capitataMediterranean fruit fly. Together, CiFi enables assessment of chromosome-scale interactions of previously recalcitrant low-complexity loci, low-input samples, and small organisms. 

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