“Co-construction” to “Symbiosis”: Research on the Integrated Governance Mechanism of Industrial Colleges in Higher Vocational Colleges

Industrial colleges are the connection point between higher vocational colleges and enterprises to carry out in-depth collaborative education. At present, there are three forms of industrial colleges: surface cooperative industrial college focusing on order cooperation, middle-level industrial college relying on industry development, and deep cooperative industrial college with integrated development. There are several common problems among the three forms of industrial colleges, such as vague positioning, unclear division of responsibilities and rights between both parties, and “free riding” at all levels. In order to establish symbiotic industrial colleges, there is a need to change the concept first, then establish and improve the system, and finally, establish a cross-border teacher pool.

Chromosomal-level genome assembly of the bioluminescent cardinalfish Siphamia tubifer, an emerging model for symbiosis research

The bioluminescent symbiosis between the sea urchin cardinalfish Siphamia tubifer (Kurtiformes: Apogonidae) and the luminous bacterium Photobacterium mandapamensis is an emerging vertebrate-bacteria model for the study of microbial symbiosis. However, there is little genetic data available for the host fish, limiting the scope of potential research that can be carried out with this association. In this study, we present a chromosomal-level genome assembly of S. tubifer using a combination of PacBio HiFi sequencing and Hi-C technologies. The final genome assembly was 1.2 Gb distributed on 23 chromosomes and contained 32,365 protein coding genes with a BUSCO completeness score of 99%. A comparison of the S. tubifer genome to that of another non-luminous cardinalfish revealed a high degree of synteny, whereas a similar comparison to a more distant relative in the Gobiiformes order revealed a fusion of two chromosomes in the cardinalfish genomes. An additional comparison of orthologous clusters among these three genomes revealed a set of 710 clusters that were unique to S. tubifer in which 23 GO pathways were significantly enriched, including several relating to host-microbe interactions and one involved in visceral muscle development, which could be related to the musculature involved in the gut-associated light organ of S. tubifer. We also assembled the complete mitogenome of S. tubifer and discovered both an inversion in the WANCY tRNA gene region resulting in a WACNY gene order as well as heteroplasmy in the length of the control region for this individual. A phylogenetic analysis based on the whole mitochondrial genome indicated that S. tubifer is divergent from the rest of the cardinalfish family, bringing up questions of the involvement of the bioluminescent symbiosis in the initial divergence of the ancestral Siphamia species. This draft genome assembly of S. tubifer will enable future studies investigating the evolution of bioluminescence in fishes as well as candidate genes involved in the symbiosis and will provide novel opportunities to use this system as a vertebrate-bacteria model for symbiosis research.

Finding Needles in Haystacks and Inferring Their Function: Challenges and Successes in Beneficial Symbiosis Research

ABSTRACT Symbioses between hosts and beneficial microbes are key drivers of biological innovation and diversity. While a range of systems have emerged that provide foundational insights into how symbioses function and evolve, we still have a limited understanding of the vast diversity of organisms that engage in such interactions. Recent advances in molecular tools, theory, and interdisciplinary approaches now permit researchers to expand our knowledge and to press forward the frontiers of symbiosis research. As described in a recent issue of mSystems, Myers and colleagues (K. N. Myers, D. Conn, and A. M. V. Brown, mSystems, 6:e01048-20, 2021, https://doi.org/10.1128/mSystems.01048-20) conducted a genome skimming approach to understand the role of obligate beneficial symbionts in plant-parasitic dagger nematodes. Nematodes are extraordinarily abundant and key players in ecosystem function and health. However, they are difficult to harness in the lab. The approach used by Myers et al. ameliorates these challenges to illustrate a relatively complete picture of a poorly understood beneficial symbiosis.

Toyohashi University of Technology: The Direction the Center for Human-Robot Symbiosis Research Should Take and its Achievements to Date

In the preface of this special issue, we will discuss the achievements of the Toyohashi University of Technology and the Center for Human-Robot Symbiosis Research so far and the direction they should proceed in hereafter. In particular, the history of the establishment of the center, research results until now, future activity plans, and this special issue are described.

A Century of Synergy in Termite Symbiosis Research: Linking the Past with New Genomic Insights

Termites have long been studied for their symbiotic associations with gut microbes. In the late nineteenth century, this relationship was poorly understood and captured the interest of parasitologists such as Joseph Leidy; this research led to that of twentieth-century biologists and entomologists including Cleveland, Hungate, Trager, and Lüscher. Early insights came via microscopy, organismal, and defaunation studies, which led to descriptions of microbes present, descriptions of the roles of symbionts in lignocellulose digestion, and early insights into energy gas utilization by the host termite. Focus then progressed to culture-dependent microbiology and biochemical studies of host–symbiont complementarity, which revealed specific microhabitat requirements for symbionts and noncellulosic mechanisms of symbiosis (e.g., N2 fixation). Today, knowledge on termite symbiosis has accrued exponentially thanks to omic technologies that reveal symbiont identities, functions, and interdependence, as well as intricacies of host–symbiont complementarity. Moving forward, the merging of classical twentieth-century approaches with evolving omic tools should provide even deeper insights into host–symbiont interplay.

What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen

Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are poor candidates for experimentation. Obtaining contiguous, high-quality genomes for such symbiotic communities is technically challenging. Here, we present the first assembly of a lichen holo-genome from metagenomic whole-genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis—the fungus Umbilicaria pustulata (33 Mb) and the green alga Trebouxia sp. (53 Mb)—were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of ∼20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with nonrandom sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.

What is in a lichen? A metagenomic approach to reconstruct the holo-genome of Umbilicaria pustulata

Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are generally poor candidates for experimentation. Obtaining contiguous, high quality genomes for such symbiotic communities is technically challenging. Here we present the first assembly of a lichen holo-genome from metagenomic whole genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis – the fungus Umbilicaria pustulata (33 Mbp) and the green alga Trebouxia sp. (53 Mbp) – were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative cellular abundance of approximately 20:1 (fungus:alga). Gap-free, circular sequences for all organellar genomes were obtained. The community of lichen-associated bacteria is dominated by Acidobacteriaceae, and the two largest bacterial contigs belong to the genus Acidobacterium. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that G/C-rich inverted repeats paired with non-random sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.

Exaiptasia diaphana from the Great Barrier Reef: a valuable resource for coral symbiosis research

The sea anemone, Exaiptasia diaphana, commonly known as Exaiptasia pallida or Aiptasia pallida, has become increasingly popular as a model for cnidarian-microbiome symbiosis studies due to its relatively rapid growth, ability to reproduce sexually and asexually, and symbiosis with diverse prokaryotes and the same microalgal symbionts (family Symbiodiniaceae) as its coral relatives. Clonal E. diaphana strains from Hawaii, the Atlantic Ocean, and Red Sea are now established for use in research. Here, we introduce Great Barrier Reef (GBR)-sourced E. diaphana strains as additions to the model repertoire. Sequencing of the 18S rRNA gene confirmed the anemones to be E. diaphana while genome-wide single nucleotide polymorphism analysis revealed four distinct genotypes. Based on Exaiptasia-specific inter-simple sequence repeat (ISSR)-derived sequence characterized amplified region (SCAR) marker and gene loci data, these four E. diaphana genotypes are distributed across several divergent phylogenetic clades with no clear phylogeographical pattern. The GBR E. diaphana genotypes comprised three females and one male, which all host Breviolum minutum as their homologous Symbiodiniaceae endosymbiont. When acclimating to an increase in light levels from 12 to 28 μmol photons m-2 s-1, the genotypes exhibited significant variation in maximum quantum yield of Symbiodiniaceae photosystem II and Symbiodiniaceae cell density. The comparatively high levels of physiological and genetic variability among GBR anemone genotypes makes these animals representative of global E. diaphana diversity and thus excellent model organisms. The addition of these GBR strains to the worldwide E. diaphana collection will contribute to cnidarian symbiosis research, particularly in relation to the climate resilience of coral reefs.