and in UConn Today!
Jane O’Donnell, the manager of the diverse and significant invertebrate collection, shares the “raison d’être” and the history of EEB’s Natural History Collections with the UConn 360 Podcast crew (UConn Podcast Episode 48, 15.30 and 27 minutes). The complementary interview was featured in UConn Today. Well done Jane.
Vouchers, that is the material from which DNA was extracted for this latest study below, are deposited in the CONN herbarium. Why are such vouchers needed, now that part of their genome is sequenced? Species boundaries in bryophytes are constantly reassessed, and primarily based on inferences from molecular data. Ultimately, the structure in genetic and phylogenetic diversity should or may want to be contrasted to patterns of variation in morphological traits, which can only be gathered from the specimens. By preserving the biological material, we maintain the opportunity to integrate its genetic and morphological traits in a broader study. And technologies change. Nothing replaces an actual specimen.Who would have predicted 40 years ago that DNA could be extracted from preserved specimens for sequencing? Maybe Michael Crichton!
Dong S., C. Zhao, S. Zhang, L. Zhang, H. Wu, R. Zhu, Y. Jia, B. Goffinet & Y. Liu. 2020. Mitochondrial genomes of the early land plant lineage liverworts (Marchantiophyta): conserved genome structure, and ongoing low frequency recombination. BMC Genomics 20: 953. pdf
Abstract reads: Background: In contrast to the highly labile mitochondrial (mt) genomes of vascular plants, the architecture and composition of mt genomes within the main lineages of bryophytes appear stable and invariant. The available mt genomes of 18 liverwort accessions representing nine genera and five orders are syntenous except for Gymnomitrion concinnatumwhose genome is characterized by two rearrangements. Here, we expanded the number of assembled liverwort mt genomes to 47, broadening the sampling to 31 genera and 10 orders spanning much of the phylogenetic breadth of liverworts to further test whether the evolution of the liverwort mitogenome is overall static. Results: Liverwort mt genomes range in size from 147 Kb in Jungermanniales (clade B) to 185 Kb in Marchantiopsida, mainly due to the size variation of intergenic spacers and number of introns. All newly assembled liverwort mt genomes hold a conserved set of genes, but vary considerably in their intron content. The loss of introns in liverwort mt genomes might be explained by localized retroprocessing events. Liverwort mt genomes are strictly syntenous in genome structure with no structural variant detected in our newly assembled mt genomes. However, by screening the paired-end reads, we do find rare cases of recombination, which means multiple concurrent genome structures may exist in the vegetative tissues of liverworts. Our phylogenetic analyses of the nuclear encoded double stand break repair protein families revealed liverwort-specific subfamilies expansions. Conclusions: The low repeat recombination level, selection, along with the intensified nuclear surveillance, might together shape the structural evolution of liverwort mt genomes.
Some vouchers contributed to this study are deposited in the CONN herbarium. Dong S., C. Zhao, S. Zhang, H. Wu, W. Mu, T. Wei, N. Li, H. Liu, J. Cui, R. Zhu, B. Goffinet & Y. Liu. 2020. The amount of RNA editing sites in liverwort organellar genes is correlated with GC content and nuclear PPR protein diversity. Genome Biology and Evolution 11: 3233–3239. pdf
Abstract reads: RNA editing occurs in the organellar mRNAs of all land plants but the marchantioid liverworts, making liverworts a perfect group for studying the evolution of RNA editing. Here, we profiled the RNA editing of 42 exemplars spanning the ordinal phylogenetic diversity of liverworts, and screened for the nuclear-encoded pentatricopeptide repeat (PPR) proteins in the transcriptome assemblies of these taxa.We identified 7,428 RNA editing sites in 128 organellar genes from 31 non-marchantioid liverwort species, and characterized 25,059 PPR protein sequences. The abundance of organellar RNA editing sites varies greatly among liverwort lineages, genes, and codon positions, and shows strong positive correlations with the GC content of protein-coding genes, and the diversity of the PLS class of nuclear PPR proteins.
UConn rainforest Now Home to Collection of Unique Ginger Relatives
see press release: “UConn rainforest acquires major collection of ginger relatives”
One new exhibit at the University of Connecticut’s Ballard Institute and Museum of Puppetry entitled “Army Ants and their Guests: Works Inspired by the Carl and Marian Rettenmeyer Collection” opened last week and can be visited until February 9th. To read more about the opening, go to the article in the Daily Campus.
The BRC endowment provided opportunities for students to work in the collections during the summer. In the living plant collection, the student attended to essential horticultural task and help with the acquisition of a significant collection of Zingiberales (ginger relatives, over 200 species) which will greatly enhance the UConn living collections and directly support EEB faculty looking at a number of important questions utilizing the ginger family as a model system. A number of the recently acquired gingers are also new to science and will hopefully be described and published in the near future.
In the vertebrate collection, student completed checking the fluid levels of the spirit preserved collection of fish, reptiles and amphibians, deaccessioning specimens that were dried out, or lacking data. Finally, all peccary skulls are now kept in archival boxes.
Thank you to the supporters of the BRC that make these internships possible.
Dr. Stan Malcolm, an UCONN alum in Systematics and Entomology, has volunteered since 2017, to assist in the curation of the insect collection. He has reorganized several families of beetles, and he is shown here with his latest accomplishment: the weevils. The taxonomy of this group is now current, with all specimens transferred to new unit trays, and all trays with new labels. Great Job Dr. Malcolm!
A unique collection of mites associated with hummingbird pollinated flowers, assembled over nearly 50 years by Dr. Robert Colwell, Distinguished Emeritus Professor in EEB, is now housed in the Biodiversity Research Collection. The collection consists of thousands of specimens mounted on slides, with nearly 3000 specimens from about 50 species identified to genus and species, and 578 specimens used in original descriptions of 16 species of hummingbird flower mites.
The evo-devo model species Physcomitrella patens changes its name.
Medina, R., M. G. Johnson, Y. Liu, N.J. Wickett, A.J. Shaw & B. Goffinet. 2019. Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on nuclear targeted exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma. Journal of Systematics and Evolution 57: 404–417. pdf
Abstract reads: Selection on spore dispersal mechanisms in mosses is thought to shape the transformation of the sporophyte. The majority of extant mosses develop a sporangium that dehisces through the loss of an operculum, and regulates spore release through the movement of articulate teeth, the peristome, lining the capsule mouth. Such complexity was acquired by the Mesozoic Era, but was lost in some groups during subsequent diversification events, challenging the resolution of the affinities for taxa with reduced architectures. The Funariaceae are a cosmopolitan and diverse lineage of mostly annual mosses, and exhibit variable sporophyte complexities, spanning from long, exerted, operculate capsules with two rings of well‐developed teeth, to capsules immersed among maternal leaves, lacking a differentiated line of dehiscence (i.e., inoperculate) and without peristomes. The family underwent a rapid diversification, and the relationships of taxa with reduced sporophytes remain ambiguous. Here, we infer the relationships of five taxa with highly reduced sporophytes based on 648 nuclear loci (exons complemented by their flanking regions), based on inferences from concatenated data and concordance analysis of single gene trees. Physcomitrellopsis is resolved as nested within one clade of Entosthodon. Physcomitrella s. l., is resolved as a polyphyletic assemblage and, along with its putative relative Aphanorrhegma, nested within Physcomitrium. We propose a new monophyletic delineation of Physcomitrium, which accommodates species of Physcomitrella and Aphanorrhegma. The monophyly of Physcomitrium s. l. is supported by a small plurality of exons, but a majority of trees inferred from exons and their adjacent non‐coding regions.