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1. Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes

   https://doi.org/10.1093/gigascience/giac021  

   Bernot, James P. ; Avdeyev, Pavel ; Zamyatin, Anton ; Dreyer, Niklas ; Alexeev, Nikita ; Pérez-Losada, Marcos ; Crandall, Keith A. ( March 2022 , GigaScience)

   The barnacles are a group of >2,000 species that have fascinated biologists, including Darwin, for centuries. Their lifestyles are extremely diverse, from free-swimming larvae to sessile adults, and even root-like endoparasites. Barnacles also cause hundreds of millions of dollars of losses annually due to biofouling. However, genomic resources for crustaceans, and barnacles in particular, are lacking.

   Using 62× Pacific Biosciences coverage, 189× Illumina whole-genome sequencing coverage, 203× HiC coverage, and 69× CHi-C coverage, we produced a chromosome-level genome assembly of the gooseneck barnacle Pollicipes pollicipes. The P. pollicipes genome is 770 Mb long and its assembly is one of the most contiguous and complete crustacean genomes available, with a scaffold N50 of 47 Mb and 90.5% of the BUSCO Arthropoda gene set. Using the genome annotation produced here along with transcriptomes of 13 other barnacle species, we completed phylogenomic analyses on a nearly 2 million amino acid alignment. Contrary to previous studies, our phylogenies suggest that the Pollicipedomorpha is monophyletic and sister to the Balanomorpha, which alters our understanding of barnacle larval evolution and suggests homoplasy in a number of naupliar characters. We also compared transcriptomes of P. pollicipes nauplius larvae and adults and found that nearly one-half of the genes in the genome are differentially expressed, highlighting the vastly different transcriptomes of larvae and adult gooseneck barnacles. Annotation of the genes with KEGG and GO terms reveals that these stages exhibit many differences including cuticle binding, chitin binding, microtubule motor activity, and membrane adhesion.

   This study provides high-quality genomic resources for a key group of crustaceans. This is especially valuable given the roles P. pollicipes plays in European fisheries, as a sentinel species for coastal ecosystems, and as a model for studying barnacle adhesion as well as its key position in the barnacle tree of life. A combination of genomic, phylogenetic, and transcriptomic analyses here provides valuable insights into the evolution and development of barnacles.

    

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2. Transcriptome Analysis of ‘Philippine Lono Tall’ Coconut (Cocos nucifera L.) Endosperm Reveals Differential Expression of Genes Involved in Oil Biosynthesis

   Osio, C.A.L. ; Aquino, G.M.B. ; Aala, W.F. ; Lado, J.P. ; Tendero, B.J.T. ; Cueto, C.A. ; Diaz, M.G.Q. ; Laude, R.P. ( January 2019 , Philippine agricultural scientist)

   null (Ed.)

   The ‘Philippine Lono Tall’ (PLNT) is a variant of the more common ‘Philippine Laguna Tall’ (LAGT), which produces fruits with soft endosperm and reported higher fat content. To understand patterns of fatty acid (FA) and oil accumulation in LAGT and PLNT fruits, transcriptomes of 6–7 month-old endosperm samples were analyzed by RNA-Seq. Quantitative PCR was performed to analyze the differential expression of selected genes related to oil biosynthesis. Further, oil samples from the PLNT endosperm were analyzed to determine their FA composition across developmental stages. A total of 416,488 contigs were de novo assembled, including 15,497 (14,356 upregulated and 1,141 downregulated) differentially expressed contigs. Several putative unigenes related to cell membrane and wall biogenesis, endosperm development, and oil biosynthesis and accumulation were identified among the assembled contigs. This first report of the complete ontogenetic FA profile revealed that medium chain fatty acids are the main components of oil from the PLNT endosperm. This pilot study is the first to suggest a molecular basis for the unique ‘Lono’ phenotype. 

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3. Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms

   https://doi.org/https://doi.org/10.1038/s42003-020-1091-1  

   Li, Y. ; Omori, A. ; Flores, R.L. ; Satterfield, S. ; Nguyen, C. ; Ota, T. ; Tsurugaya, T. ; Ikuta, T. ; Ikeo, K. ; Kikuchi, M. ; et al ( July 2020 , Communications biology)

   null (Ed.)

   Echinoderms are an exceptional group of bilaterians that develop pentameral adult symmetry from a bilaterally symmetric larva. However, the genetic basis in evolution and development of this unique transformation remains to be clarified. Here we report newly sequenced genomes, developmental transcriptomes, and proteomes of diverse echinoderms including the green sea urchin (L. variegatus), a sea cucumber (A. japonicus), and with particular emphasis on a sister group of the earliest-diverged echinoderms, the feather star (A. japonica). We learned that the last common ancestor of echinoderms retained a well-organized Hox cluster reminiscent of the hemichordate, and had gene sets involved in endoskeleton development. Further, unlike in other animal groups, the most conserved developmental stages were not at the body plan establishing phase, and genes normally involved in bilaterality appear to function in pentameric axis development. These results enhance our understanding of the divergence of protostomes and deuterostomes almost 500 Mya. 

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4. Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses

   https://doi.org/10.1128/mBio.02027-20  

   Myers, J. M. ; Bonds, A. E. ; Clemons, R. A. ; Thapa, N. A. ; Simmons, D. R. ; Carter-House, D. ; Ortanez, J. ; Liu, P. ; Miralles-Durán, A. ; Desirò, A. ; et al ( October 2020 , mBio)

   Taylor, John W. (Ed.)

   ABSTRACT Mycoviruses are widespread and purportedly common throughout the fungal kingdom, although most are known from hosts in the two most recently diverged phyla, Ascomycota and Basidiomycota, together called Dikarya. To augment our knowledge of mycovirus prevalence and diversity in underexplored fungi, we conducted a large-scale survey of fungi in the earlier-diverging lineages, using both culture-based and transcriptome-mining approaches to search for RNA viruses. In total, 21.6% of 333 isolates were positive for RNA mycoviruses. This is a greater proportion than expected based on previous taxonomically broad mycovirus surveys and is suggestive of a strong phylogenetic component to mycoviral infection. Our newly found viral sequences are diverse, composed of double-stranded RNA, positive-sense single-stranded RNA (ssRNA), and negative-sense ssRNA genomes and include novel lineages lacking representation in the public databases. These identified viruses could be classified into 2 orders, 5 families, and 5 genera; however, half of the viruses remain taxonomically unassigned. Further, we identified a lineage of virus-like sequences in the genomes of members of Phycomycetaceae and Mortierellales that appear to be novel genes derived from integration of a viral RNA-dependent RNA polymerase gene. The two screening methods largely agreed in their detection of viruses; thus, we suggest that the culture-based assay is a cost-effective means to quickly assess whether a laboratory culture is virally infected. This study used culture collections and publicly available transcriptomes to demonstrate that mycoviruses are abundant in laboratory cultures of early-diverging fungal lineages. The function and diversity of mycoviruses found here will help guide future studies into mycovirus origins and ecological functions. IMPORTANCE Viruses are key drivers of evolution and ecosystem function and are increasingly recognized as symbionts of fungi. Fungi in early-diverging lineages are widespread, ecologically important, and comprise the majority of the phylogenetic diversity of the kingdom. Viruses infecting early-diverging lineages of fungi have been almost entirely unstudied. In this study, we screened fungi for viruses by two alternative approaches: a classic culture-based method and by transcriptome-mining. The results of our large-scale survey demonstrate that early-diverging lineages have higher infection rates than have been previously reported in other fungal taxa and that laboratory strains worldwide are host to infections, the implications of which are unknown. The function and diversity of mycoviruses found in these basal fungal lineages will help guide future studies into mycovirus origins and their evolutionary ramifications and ecological impacts. 

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5. Noise during mouthbrooding impairs maternal care behaviors and juvenile development and alters brain transcriptomes in the African cichlid fish Astatotilapia burtoni

   https://doi.org/10.1111/gbb.12692  

   Butler, Julie M. ; Maruska, Karen P. ( September 2020 , Genes, Brain and Behavior)

   Anthropogenic noise has increased underwater ambient sound levels in the range in which most fishes detect and produce acoustic signals. Although the impacts of increased background noise on fish development have been studied in a variety of species, there is a paucity of information on how noise affects parental care. Mouthbrooding is an energetically costly form of parental care in which the brooding fish carries developing larvae in the buccal cavity for the duration of development. In the African cichlidAstatotilapia burtoni, females carry their brood for ~2 weeks during which time they do not eat. To test the hypothesis that increased background noise impacts maternal care behaviors and brood development, we exposed brooding females to a 3‐h period of excess noise (~140 dB) played through an underwater speaker. Over half of noise‐exposed brooding females cannibalized or pre‐maturely released their brood, but 90% of control females exhibited normal brooding behaviors. RNA‐seq analysis revealed that transcripts related to feeding and parental care were differentially expressed in the brains of noise‐exposed females. Juveniles that were exposed to noise during their brood period within the mother's mouth had lower body condition factors, higher mortality and altered head transcriptomes compared with control broods. Furthermore, onset of adult‐typical coloration and behaviors was delayed compared with control fish. Together, these data indicate that noise has severe impacts on reproductive fitness in mouthbrooding females. Our results, combined with past studies, indicate that parental care stages are extremely susceptible to noise‐induced perturbations with detrimental effects on species persistence.

    

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