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1. Stachydrine Catabolism Contributes to an Optimal Root Nodule Symbiosis Between Sinorhizobium meliloti and Medicago sativa

   https://doi.org/10.1094/MPMI-02-25-0021-SC  

   Levin, Garrett J; Kearsley, Jason_V S; Finan, Turlough M; Geddes, Barney A (August 2025, Molecular Plant-Microbe Interactions®)

   Sinorhizobium meliloti forms a robust N₂-fixing root-nodule symbiosis with Medicago sativa. We are interested in identifying the minimal symbiotic genome of the model strain S. meliloti Rm1021. This gene set refers to the minimal genetic determinants required to form a robust N₂-fixing symbiosis. Many symbiotic genes are located on the 1,354 kb pSymA megaplasmid of S. meliloti Rm1021. We recently constructed a minimalized pSymA, minSymA2.1, that lacked over 90% of the pSymA genes. Relative to the wild-type, minSymA2.1 showed a reduction in M. sativa shoot biomass production and nodule size with an increase in total nodule number. Here we show that the addition of either the stachydrine (stc) or trigonelline (trc) catabolism genes from pSymA to minSymA2.1 restores nodule size and total nodule number to levels indistinguishable from the wild-type but does not restore reduced shoot biomass production. In the context of the complete Rm1021 genome, removing the stc genes reduced nodule size and increased total nodule number while removal of the trc genes alone had no apparent effect. Together, these observations implicate stachydrine catabolism as an important determinant of root nodule symbiosis between S. meliloti and M. sativa while trigonelline catabolism seems to contribute in a more conditional manner, in the context of the minimized genome. These findings highlight the minimal symbiotic genome as a tool for investigating the impact individual genetic determinants have in conferring an optimal symbiosis. Factors whose impact, in the context of a complete genome, may be hidden or dampened due to redundancies. 

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2. The complete mitochondrial genome of the pink shrimp Farfantepenaeus duorarum (Burkenroad, 1939) (Decapoda: Dendrobranchiata: Penaeidae)

   https://doi.org/10.1093/jcbiol/ruac007  

   Collins, Stormie B; Bracken-Grissom, Heather D; Baeza, J Antonio (March 2022, Journal of Crustacean Biology)

   Abstract Farfantepenaeus duorarum (Burkenroad, 1939) is a commercially harvested decapod shrimp that ranges from the eastern coast of the United States, through the Gulf of Mexico, and as far south as Isla Mujeres, Mexico. We report for the first time the complete mitochondrial genome of F. duorarum. The mitochondrial genome is 15,971 base pairs in length and is comprised of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. An intergenic space 982 bp in length located between the rrnS (12S) and trnI (Isoleucine) genes is presumed to be the D-loop. The mitochondrial gene order in F. duorarum is identical to that reported for congeners. To assess selection pressures within the mitochondrial genome, KA/KS ratios were calculated for all PCGs, and show values < 1, indicating that all genes are evolving under purifying selection. This work contributes one more mitochondrial genome to the penaeid shrimps, an economically targeted group. 

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3. Comparative analyses of the banded alder borer ( Rosalia funebris ) and Asian longhorned beetle ( Anoplophora glabripennis ) genomes reveal significant differences in genome architecture and gene content among these and other Cerambycidae

   https://doi.org/10.1093/jhered/esae021  

   Sylvester, Terrence; Adams, Richard; Mitchell, Robert_F; Ray, Ann_M; Shen, Rongrong; Shin, Na_Ra; McKenna, Duane_D; Blackmon, ed., Heath (March 2024, Journal of Heredity)

   Abstract Rosalia funebris (RFUNE; Cerambycidae), the banded alder borer, is a longhorn beetle whose larvae feed on the wood of various economically and ecologically significant trees in western North America. Adults are short-lived and not known to consume plant material substantially. We sequenced, assembled, and annotated the RFUNE genome using HiFi and RNASeq data. We documented genome architecture and gene content, focusing on genes putatively involved in plant feeding (phytophagy). Comparisons were made to the well-studied genome of the Asian longhorned beetle (AGLAB; Anoplophora glabripennis) and other Cerambycidae. The 814 Mb RFUNE genome assembly was distributed across 42 contigs, with an N50 of 30.18 Mb. Repetitive sequences comprised 60.27% of the genome, and 99.0% of expected single-copy orthologous genes were fully assembled. We identified 12,657 genes, fewer than in the four other species studied, and 46.4% fewer than for Aromia moschata (same subfamily as RFUNE). Of the 7,258 orthogroups shared between RFUNE and AGLAB, 1,461 had more copies in AGLAB and 1,023 had more copies in RFUNE. We identified 240 genes in RFUNE that putatively arose via horizontal transfer events. The RFUNE genome encoded substantially fewer putative plant cell wall degrading enzymes than AGLAB, which may relate to the longer-lived plant-feeding adults of the latter species. The RFUNE genome provides new insights into cerambycid genome architecture and gene content and provides a new vantage point from which to study the evolution and genomic basis of phytophagy in beetles. 

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4. The Genome Architecture of the Copepod Eurytemora carolleeae —  the Highly Invasive Atlantic Clade of the Eurytemora affinis Species Complex

   https://doi.org/10.1093/gpbjnl/qzae066  

   Du, Zhenyong; Gelembiuk, Gregory; Moss, Wynne; Tritt, Andrew; Lee, Carol Eunmi (October 2024, Genomics, Proteomics & Bioinformatics)

   Jiang, Yu (Ed.)

   Abstract Copepods are among the most abundant organisms on the planet and play critical functions in aquatic ecosystems. Among copepods, populations of the Eurytemora affinis species complex are numerically dominant in many coastal habitats and serve as food sources for major fisheries. Intriguingly, certain populations possess the unusual capacity to invade novel salinities on rapid time scales. Despite their ecological importance, high-quality genomic resources have been absent for calanoid copepods, limiting our ability to comprehensively dissect the genome architecture underlying the highly invasive and adaptive capacity of certain populations. Here, we present the first chromosome-level genome of a calanoid copepod, from the Atlantic clade (Eurytemora carolleeae) of the E. affinis species complex. This genome was assembled using high-coverage PacBio long-read and Hi-C sequences of an inbred line, generated through 30 generations of full-sib mating. This genome, consisting of 529.3 Mb (contig N50 = 4.2 Mb, scaffold N50 = 140.6 Mb), was anchored onto four chromosomes. Genome annotation predicted 20,262 protein-coding genes, of which ion transport-related gene families were substantially expanded based on comparative analyses of 12 additional arthropod genomes. Also, we found genome-wide signatures of historical gene body methylation of the ion transport-related genes and the significant clustering of these genes on each chromosome. This genome represents one of the most contiguous copepod genomes to date and is among the highest quality marine invertebrate genomes. As such, this genome provides an invaluable resource to help yield fundamental insights into the ability of this copepod to adapt to rapidly changing environments. 

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5. The Iron-Responsive Genome of the Chiton Acanthopleura granulata

   https://doi.org/10.1093/gbe/evaa263  

   Varney, Rebecca M; Speiser, Daniel I; McDougall, Carmel; Degnan, Bernard M; Kocot, Kevin M (January 2021, Genome Biology and Evolution)

   Venkatesh, B (Ed.)

   Abstract Molluscs biomineralize structures that vary in composition, form, and function, prompting questions about the genetic mechanisms responsible for their production and the evolution of these mechanisms. Chitons (Mollusca, Polyplacophora) are a promising system for studies of biomineralization because they build a range of calcified structures including shell plates and spine- or scale-like sclerites. Chitons also harden the calcified teeth of their rasp-like radula with a coat of iron (as magnetite). Here we present the genome of the West Indian fuzzy chiton Acanthopleura granulata, the first from any aculiferan mollusc. The A. granulata genome contains homologs of many genes associated with biomineralization in conchiferan molluscs. We expected chitons to lack genes previously identified from pathways conchiferans use to make biominerals like calcite and nacre because chitons do not use these materials in their shells. Surprisingly, the A. granulata genome has homologs of many of these genes, suggesting that the ancestral mollusc may have had a more diverse biomineralization toolkit than expected. The A. granulata genome has features that may be specialized for iron biomineralization, including a higher proportion of genes regulated directly by iron than other molluscs. A. granulata also produces two isoforms of soma-like ferritin: one is regulated by iron and similar in sequence to the soma-like ferritins of other molluscs, and the other is constitutively translated and is not found in other molluscs. The A. granulata genome is a resource for future studies of molluscan evolution and biomineralization. 

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