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DOE OSTI2024

An empirical DNA-based identification of morphologically similar snappers (Lutjanus campechanus, Lutjanus purpureus) using a versatile bioinformatics workflow for the discovery and analysis of informative single-nucleotide polymorphisms

The commercially important speciesLutjanus campechanus(Northern/Gulf red snapper) andLutjanus purpureus(Southern/Caribbean red snapper) are the protagonists of a decade’s long taxonomic debate over their species delimitation, due in part to partial habitat overlap, extensive morphological similarity, and the lack of resolution when applying canonically reliable DNA barcoding approaches. In this study, we leveraged publicly available RAD-Seq data forL. campechanusandL. purpureusto identify species-informative single‐nucleotide polymorphisms (SNPs) at the genome scale that were successful in distinguishing the Northern and Southern red snappers, while also detecting individuals exhibiting introgression. This 4-step empirical approach demonstrates the value of applying novel bioinformatics pipelines to existing genome-scale data to maximize the distillation of informative subsets. Our results facilitate economically relevant species identification in addition to confirming or challenging species identifications for specimens with data in public databases. These findings and their applications will benefit future sustainability strategies and broader research questions surrounding these overfished and evolutionarily entangled snapper species.

Environmental Sciences & Ecology↗

DOE OSTI2022

Re-evaluating the Systematics of Dendrolycopodium Using Restriction-Site Associated DNA-Sequencing

The genus Dendrolycopodium (Lycopodiaceae) includes four to five species across North America and East Asia. Species identification in Dendrolycopodium is difficult due to limited or inconsistent characters. In addition, plants with intermediate morphologies regularly occur, potentially indicative of interspecific hybridization. To determine the species relationships in Dendrolycopodium and investigate the existence of hybrids, we generated a draft genome assembly for D. obscurum and carried out double-digest restriction-site associated DNA sequencing (RADSeq) on 86 Dendrolycopodium specimens. Our sampling includes all the described species and 11 individuals with intermediate morphology. We find that the genus can be divided into four clades that largely correspond to the described taxa, as well as evidence of interspecific hybridization. Within these clades, our STRUCTURE analysis suggests that there are multiple finer subgroups, with evidence of hybridization and introgression between these subgroups. Given the limited availability of specimens collected from Asia, the status of the various Asian species remains uncertain and will require further study. In summary, our study confirms several hybrid relationships in Dendrolycopodium and provides a clear phylogenetic framework for future taxonomic revision.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Identification of a Fusarium ear rot resistance gene in maize by QTL mapping and RNA sequencing

Fusarium ear rot (FER) caused by Fusarium verticillioides is a prevalent maize disease. To comprehensively characterize the genetic basis of the natural variation in FER resistance, a recombinant inbred line (RIL) population was used to map quantitative trait loci (QTL) for FER resistance. A total of 17 QTL were identified by linkage mapping in eight environments. These QTL were located on six chromosomes and explained 3.88–15.62% of the total phenotypic variation. Moreover, qFER1.03 had the strongest effect and accounted for 4.98–15.62% of the phenotypic variation according to analyses of multiple environments involving best linear unbiased predictions. The chromosome segment substitution lines (CSSLs) derived from a cross between Qi319 (donor parent) and Ye478 (recurrent parent) were used to verify the contribution of qFER1.03 to FER resistance. The line CL171, which harbored an introgressed qFER1.03 , was significantly resistant to FER. Further fine mapping of qFER1.03 revealed that the resistance QTL was linked to insertion/deletion markers InDel 8 and InDel 2, with physical distances of 43.55 Mb and 43.76 Mb, respectively. Additionally, qFER1.03 differed from the previous resistance QTL on chromosome 1. There were three annotated genes in this region. On the basis of the RNA-seq data, which revealed the genes differentially expressed between the FER-resistant Qi319 and susceptible Ye478, GRMZM2G017792 (MPK3) was preliminarily identified as a candidate gene in the qFER1.03 region. The Pr-CMV-VIGS system was used to decrease the GRMZM2G017792 expression level in CL171 by 34–57%, which led to a significant decrease in FER resistance. Using RIL and CSSL populations combined with RNA-seq and Pr-CMV-VIGS, the candidate gene can be dissected effectively, which provided important gene resource for breeding FER-resistant varieties.

Xia, Yusheng↗

DOE OSTI2022

Factors influencing pregnancy, litter size, and reproductive parameters of invasive wild pigs

Abstract Reproduction is the most energetically expensive life stage with the demands of productivity representing a balance between physiological requirements and environmental conditions. Wild pigs ( Sus scrofa ) throughout most of North America are genetic hybrids of feral domestic pigs and wild boar and have the highest reproductive potential of any wild ungulate. The phenology of reproduction, extent of multiple reproductive events per year, how individual and extrinsic factors contribute to variability in productivity, and impact of genetic lineage on these parameters is not well understood in wild pigs. We quantified reproductive parameters in wild pigs relative to a suite of individual and environmental attributes across seasons and multiple years in South Carolina, USA, from March 2017 and May 2020. We hypothesized that individual attributes (mass, age class, number of teats, rump fat, relative genetic association to wild boar vs. domestic pigs) and extrinsic factors (mast availability) would influence probability of pregnancy and fetal litter size. Wild pigs produced offspring throughout all months with peaks in conception corresponding to a seasonal pulse in food availability. The likelihood of pregnancy was influenced by female mass and nutritional condition and was greatest during years with abundant resources. Similarly, litter size increased with female mass and age, implying larger and older females represent the most important group for population recruitment. In evaluating the relationship between reproductive output and ancestral associations to domestic pigs versus wild boar, the proportion of wild boar ancestry was not an important influence on productivity in our population. We determined juveniles reach a physiological threshold of sexual maturity at approximately 30 kg. Average litter size was comparable to other populations, and wild pigs maintain an average fetal litter size of 5.43 offspring despite 13.6% embryonic mortality. A thorough understanding of biotic and extrinsic factors influencing reproduction are important for realistic population models, which are necessary for identifying areas to focus management needs and implementation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Plastome evolution in annual Brachypodium species reveals widespread heteroplasmy and chloroplast capture, lineage-specific codon usage bias, and low positive selection

Comparative genomics and plastome phylogenomics have advanced significantly in recent years, highlighting the diversity, possible admixture, and non-neutral evolution of the predominantly considered non-recombinant chloroplast genomes in angiosperms. The grass genus Brachypodium serves as a powerful model for studying evolutionary processes in monocots. We analyzed 287 plastomes across the native circum-Mediterranean range of the three annual Brachypodium species ( B. distachyon, B. stacei, B. hybridum ), focusing on their structural variation, selection patterns and phylogenomic relationships. Our analyses confirmed the differentiation of the S and D plastomes, inherited respectively from the diploid progenitor species B. stacei and B. distachyon . We identified novel structural rearrangements and indels, and unique repeat motifs, along with widespread heteroplasmy, particularly in ancestral B. hybridum -D plastotypes. SNP diversity varied among plastotypes, reflecting population dynamics and evolutionary histories, with B. hybridum -D plastotypes showing the highest normalized diversity and B. hybridum -S the lowest. Positive selection was detected in 29 plastid genes by Tajima’s neutrality test, and in nine genes by site and branch-site evolutionary models, including matK, ndhF, rbcL, and rpoC2. Phylogenomic analyses revealed well-supported clades corresponding to the S and D plastome lineages, with frequent chloroplast capture events and long-distance dispersals shaping their evolutionary trajectories.

allopolyploidy↗

DOE OSTI2022

Editorial: Genomic insights on fungal hybrids

Hybrids are chimeric organisms that result from the crossing of two genetically divergent lineages. Compared to their parents, hybrids sometimes show higher adaptive capacities towards specific niches, thereby contributing to diversification (Abbott et al., 2013). Fungal hybrids have been neglected by formal studies for a long time due to the inherent challenges of the microbial species concept and the difficulty of identifying hybrids based on morphological characters (Gabaldon, 2020a; Boekhout et al., 2021). Although the first fungal hybrids were identified in Saccharomyces, thanks to careful dissection of metabolic properties (Morales and Dujon, 2012) and emerging genome sequencing technologies (Hittinger, 2013), it was the spread of these sequencing technologies that revealed the true pervasiveness of hybrids across the fungal tree of life (Naranjo-Ortiz and Gabaldon, 2020; Gabaldon, 2020b). Sequencing techniques, particularly genomic approaches, have not only unearthed the hybrid nature of many fungal organisms, but also serve as ideal tools for the study of hybrids. Hybrids have chimeric genomes, which usually display high instability and are subject to evolutionary pressures that are different from that of non-hybrid genomes (Runemark et al., 2019). Understanding how hybrids are formed, how they cope with their chimeric genomes, and how they evolve and adapt to distinct environments is a matter of intensive research. This Research Topic gathers six outstanding contributions that use genomic approaches to tackle diverse questions that relate to fungal hybrids.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population

Bacterial species often undergo rampant recombination yet maintain cohesive genomic identity. Ecological differences can generate recombination barriers between species and sustain genomic clusters in the short term. But can these forces prevent genomic mixing during long-term coevolution? Cyanobacteria in Yellowstone hot springs comprise several diverse species that have coevolved for hundreds of thousands of years, providing a rare natural experiment. By analyzing more than 300 single-cell genomes, we show that despite each species forming a distinct genomic cluster, much of the diversity within species is the result of hybridization driven by selection, which has mixed their ancestral genotypes. This widespread mixing is contrary to the prevailing view that ecological barriers can maintain cohesive bacterial species and highlights the importance of hybridization as a source of genomic diversity.

Evolutionary Biology↗