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Jawless vertebrates possess an alternative adaptive immune system in which antigens are recognized by variable lymphocyte receptors (VLRs) generated by combinatorial assembly of leucine-rich repeat (LRR) cassettes. Three types of receptors, VLRA, VLRB, and VLRC, have been previously identified. VLRA- and VLRC-expressing cells are T cell-like, whereas VLRB-expressing cells are B cell-like. Here, we report two types of VLRs in lampreys, VLRD and VLRE, phylogenetically related to VLRA and VLRC. The germline VLRD and VLRE genes are flanked by 39 LRR cassettes used in the assembly of mature VLRD and VLRE, with cassettes from chromosomes containing the VLRA and VLRC genes also contributing to VLRD and VLRE assemblies. VLRD and VLRE transcription is highest in the triple-negative (VLRA−/VLRB−/VLRC−) population of lymphocytes, albeit also detectable in VLRA+ and VLRC+ populations. Tissue distribution studies suggest that lamprey VLRD+ and VLRE+ lymphocytes comprise T-like sublineages of cells. 

Quantification of environmental impacts through life cycle assessment is essential when evaluating bioenergy systems as potential replacements for fossil-based energy systems. Bioenergy systems employing localized fast pyrolysis combined with electrocatalytic hydrogenation followed by centralized hydroprocessing (Py-ECH) can have higher carbon and energy efficiencies than traditional cellulosic biorefineries. A cradle-to-grave life cycle assessment was performed to compare the performance of Py-ECH versus cellulosic fermentation in three environmental impact categories: climate change, water scarcity, and eutrophication. Liquid hydrocarbon production using Py-ECH was found to have much lower eutrophication potential and water scarcity footprint than cellulosic ethanol production. Greater amounts of renewable electricity led to lower greenhouse gas emissions for the Py-ECH processing. When the renewable fraction of grid electricity is higher than 87%, liquid hydrocarbon production using Py-ECH has lower greenhouse gas emissions than cellulosic ethanol production. A sensitivity analysis illustrates the major role of annual soil carbon sequestration in determining system-wide net greenhouse gas emissions. 

Maximizing fossil fuel displacement and limiting atmospheric carbon dioxide levels require a high efficiency of carbon incorporation in bioenergy systems. The availability of biomass carbon is a constraint globally, and strategies to increase the efficiency of bioenergy production and biogenic carbon use are needed. Previous studies have shown that “energy upgrading” of biomass by coupling with renewable electricity through electrocatalytic hydrogenation offers a potential pathway to near full petroleum fuel displacement in the U.S., even when annual U.S. biomass production is limited to 1.2 billion dry tonnes. Commercialization of such technology requires economic feasibility. A technoeconomic model of decentralized, depot-based pyrolysis with electrocatalytic hydrogenation and centralized upgrading (Py-ECH), producing liquid hydrocarbon fuel is presented and compared to a cellulosic ethanol pathway using consistent assumptions. Using a discounted cash flow approach, a minimum fuel selling price (MFSP) of $3.62 per gallon gasoline equivalent (GGE) or $0.96 per gasoline liter equivalent (GLE) is estimated for Py-ECH fuel derived from corn stover, considering n th plant economics and a fixed internal rate of return of 10%. This is comparable to the MFSP for cellulosic ethanol from fermentation with the same feedstock ($3.71 per GGE or $0.98 per GLE) and is in the range of gasoline prices over the last 20 years of $1 per GGE ($0.26 per GLE) to $4.44 per GGE ($1.17 per GLE) in 2018. Optimization studies on depot sizing identified a trade-off between transportation and economies-of-scale costs, with an optimum size of 500 tpd. Sensitivity analyses showed that electricity cost, raw material costs, bio-oil yields, and cell efficiencies are the key parameters that affect the Py-ECH MFSP. With system improvements, a pathway to less than $3 per GGE or $0.79 per GLE is articulated for liquid hydrocarbon fuel from corn stover using Py-ECH. 

Three types of variable lymphocyte receptor (VLR) genes, VLRA , VLRB , and VLRC, encode antigen recognition receptors in the extant jawless vertebrates, lampreys and hagfish. The somatically diversified repertoires of these VLRs are generated by serial stepwise copying of leucine-rich repeat (LRR) sequences into an incomplete germline VLR gene. Lymphocytes that express VLRA or VLRC are T cell–like, while VLRB-expressing cells are B cell–like. Here, we analyze the composition of the VLRB locus in different jawless vertebrates to elucidate its configuration and evolutionary modification. The incomplete germline VLRB genes of two hagfish species contain short noncoding intervening sequences, whereas germline VLRB genes in six representative lamprey species have much longer intervening sequences that exhibit notable genomic variation. Genomic clusters of potential LRR cassette donors, fragments of which are copied to complete VLRB gene assembly, are identified in Japanese lamprey and sea lamprey. In the sea lamprey, 428 LRR cassettes are located in five clusters spread over a total of 1.7 Mbp of chromosomal DNA. Preferential usage of the different donor cassettes for VLRB assemblage is characterized in our analysis, which reveals evolutionary modifications of the lamprey VLRB genes, elucidates the organization of the complex VLRB locus, and provides a comprehensive catalog of donor VLRB cassettes in sea lamprey and Japanese lamprey. 

Abstract Polyploidy or whole-genome duplication (WGD) is a major event that drastically reshapes genome architecture and is often assumed to be causally associated with organismal innovations and radiations. The 2R hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution. However, the timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved and whether these WGD events underlie vertebrate phenotypic diversification remains elusive. Here we present the genome of the inshore hagfish,Eptatretus burgeri. Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and 2R occurred in the gnathostome stem-lineage, maximally in the late Cambrian–earliest Ordovician, after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced an additional independent genome triplication. Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only in the gnathostome but not in the cyclostome lineage, calling into question the general expectation that WGDs lead to leaps of bodyplan complexity. 

Abstract The Zinc Fingers and Homeoboxes (Zhx) proteins, Zhx1, Zhx2, and Zhx3, comprise a small family of proteins containing two amino-terminal C2–H2 zinc fingers and four or five carboxy-terminal homeodomains. These multiple homeodomains make Zhx proteins unusual because the majority of homeodomain-containing proteins contain a single homeodomain. Studies in cultured cells and mice suggest that Zhx proteins can function as positive or negative transcriptional regulators. Zhx2 regulates numerous hepatic genes, and all three Zhx proteins have been implicated in different cancers. Because Zhx proteins contain multiple predicted homeodomains, are associated with interesting physiological traits, and seem to be only present in the vertebrate lineage, we investigated the evolutionary history of this small family by comparing Zhx homologs from a wide range of chordates. This analysis indicates that the zinc finger motifs and homeodomains are highly similar among all Zhx proteins and also identifies additional Zhx-specific conserved regions, including a 13 amino acid amino-terminal motif that is nearly identical among all gnathostome Zhx proteins. We found single Zhx proteins in the sea lamprey (Petromyzon marinus) and in the nonvertebrate chordates sea squirt (Ciona intestinalis) and lancelet (Branchiostoma floridae); these Zhx proteins are most similar to gnathostome Zhx3. Based on our analyses, we propose that a duplication of the primordial Zhx gene gave rise to Zhx3 and the precursor to Zhx1 and Zhx2. A subsequent tandem duplication of this precursor generated Zhx1 and Zhx2 found in gnathostomes.