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1. High‐contiguity genome assembly of the chemosynthetic gammaproteobacterial endosymbiont of the cold seep tubeworm Lamellibrachia barhami

   https://doi.org/10.1111/1755-0998.13220  

   Breusing, Corinna ; Schultz, Darrin T. ; Sudek, Sebastian ; Worden, Alexandra Z. ; Young, Curtis Robert ( July 2020 , Molecular Ecology Resources)

   Symbiotic relationships between vestimentiferan tubeworms and chemosynthetic Gammaproteobacteria build the foundations of many hydrothermal vent and hydrocarbon seep ecosystems in the deep sea. The association between the vent tubewormRiftia pachyptilaand its endosymbiontCandidatusEndoriftia persephone has become a model system for symbiosis research in deep‐sea vestimentiferans, while markedly fewer studies have investigated symbiotic relationships in other tubeworm species, especially at cold seeps. Here we sequenced the endosymbiont genome of the tubewormLamellibrachia barhamifrom a cold seep in the Gulf of California, using short‐ and long‐read sequencing technologies in combination with Hi‐C and Dovetail Chicago libraries. Our final assembly had a size of ~4.17 MB, a GC content of 54.54%, 137X coverage, 4153 coding sequences, and aCheckMcompleteness score of 97.19%. A single scaffold contained 99.51% of the genome. Comparative genomic analyses indicated that theL. barhamisymbiont shares a set of core genes and many metabolic pathways with other vestimentiferan symbionts, while containing 433 unique gene clusters that comprised a variety of transposases, defence‐related genes and a lineage‐specific CRISPR/Cas3 system. This assembly represents the most contiguous tubeworm symbiont genome resource to date and will be particularly valuable for future comparative genomic studies investigating structural genome evolution, physiological adaptations and host‐symbiont communication in chemosynthetic animal‐microbe symbioses.
2. Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis

   https://doi.org/10.1093/jhered/esad037  

   Bishop, Anusha P. ; Westeen, Erin P. ; Yuan, Michael L. ; Escalona, Merly ; Beraut, Eric ; Fairbairn, Colin ; Marimuthu, Mohan P. A. ; Nguyen, Oanh ; Chumchim, Noravit ; Toffelmier, Erin ; et al ( June 2023 , Journal of Heredity)

   Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis, the species status of the Californiamore »endemic island fence lizard (S. becki), and the spectacular radiation of Sceloporus lizards.

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3. A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology.

   https://doi.org/10.1093/gigascience/giab066  

   Westfall, A. K. ; Telemeco, R. S. ; Grizante, M. B. ; Waits, D. S. ; Clark, A. D. ; Simpson D. Y. ; Klabacka, R. L. ; Sullivan, A. P. ; Perry, G. H. ; Sears, M. W. ; et al ( October 2021 , GigaScience)

   Background High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources. Findings We present a high-quality chromosome-level reference genome assembly, SceUnd1.0 (using 10X Genomics Chromium, HiC, and Pacific Biosciences data), and tissue/developmental stage transcriptomes for the eastern fence lizard, Sceloporus undulatus. We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to provide improved reference-based genome assemblies for 34 additional Sceloporus species. Finally, we used RNAseq and whole-genome resequencing data to compare 3 assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium, HiRise Assembly that added data from HiC, and PBJelly Assembly that added data from Pacific Biosciences sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and single-nucleotide polymorphism calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole-genome associationmore »mapping analyses. The subsequent addition of PacBio data doubled the contig N50 but provided negligible gains in scaffold length. Conclusions These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.« less
4. Improved Reference Genome for Cyclotella cryptica CCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta)

   https://doi.org/10.1534/g3.120.401408  

   Roberts, Wade R ; Downey, Kala M ; Ruck, Elizabeth C ; Traller, Jesse C ; Alverson, Andrew J ( September 2020 , G3 Genes|Genomes|Genetics)

   Abstract The diatom, Cyclotella cryptica, is a well-established model species for physiological studies and biotechnology applications of diatoms. To further facilitate its use as a model diatom, we report an improved reference genome assembly and annotation for C. cryptica strain CCMP332. We used a combination of long- and short-read sequencing to assemble a high-quality and contaminant-free genome. The genome is 171 Mb in size and consists of 662 scaffolds with a scaffold N50 of 494 kb. This represents a 176-fold decrease in scaffold number and 41-fold increase in scaffold N50 compared to the previous assembly. The genome contains 21,250 predicted genes, 75% of which were assigned putative functions. Repetitive DNA comprises 59% of the genome, and an improved classification of repetitive elements indicated that a historically steady accumulation of transposable elements has contributed to the relatively large size of the C. cryptica genome. The high-quality C. cryptica genome will serve as a valuable reference for ecological, genetic, and biotechnology studies of diatoms.
5. The reference genome assembly of the bright cobblestone lichen, Acarospora socialis

   https://doi.org/10.1093/jhered/esad052  

   Adams, Julia N. ; Escalona, Merly ; Marimuthu, Mohan P. A. ; Fairbairn, Colin W. ; Beraut, Eric ; Seligmann, William ; Nguyen, Oanh ; Chumchim, Noravit ; Stajich, Jason E. ; Olsen, ed., Kenneth ( September 2023 , Journal of Heredity)

   Acarospora socialis, the bright cobblestone lichen, is commonly found in southwestern North America. This charismatic yellow lichen is a species of key ecological significance as it is often a pioneer species in new environments. Despite their ecological importance virtually no research has been conducted on the genomics of A. socialis. To address this, we used long-read sequencing to generate the first high-quality draft genome of A. socialis. Lichen thallus tissue was collected from Pinkham Canyon in Joshua Tree National Park, California and deposited in the UC Riverside herbarium under accession #295874. The de novo assembly of the mycobiont partner of the lichen was generated from Pacific Biosciences HiFi long reads and Dovetail Omni-C chromatin capture data. After removing algal and bacterial contigs, the fungal genome was approximately 31.2 Mb consisting of 38 scaffolds with contig and scaffold N50 of 2.4 Mb. The BUSCO completeness score of the assembled genome was 97.5% using the Ascomycota gene set. Information on the genome of A. socialis is important for California conservation purposes given that this lichen is threatened in some places locally by wildfires due to climate change. This reference genome will be used for understanding the genetic diversity, population genomics, andmore »comparative genomics of A. socialis species. Genomic resources for this species will support population and landscape genomics investigations, exploring the use of A. socialis as a bioindicator species for climate change, and in studies of adaptation by comparing populations that occur across aridity gradients in California.

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