A comparison of freezer-stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming

Premise

The use of DNA from herbarium specimens is an increasingly important source for evolutionary studies in plant biology, particularly in cases where species are rare or difficult to obtain. Here we compare the utility of DNA from herbarium tissues to their freezer-stored DNA counterparts via the Hawaiian Plant DNA Library.

Methods

Plants collected for the Hawaiian Plant DNA Library were simultaneously accessioned as herbarium specimens at the time of collection, from 1994-2019. Paired samples were sequenced using short-read sequencing and assessed for chloroplast assembly and nuclear gene recovery.

Results

Herbarium specimen-derived DNA was statistically more fragmented than freezer-stored DNA derived from fresh tissue, leading to poorer chloroplast assembly and overall lower coverage. The number of nuclear targets recovered varied mostly by total sequencing reads per library and age of specimen, but not by storage method (herbarium or long-term freezer). Although there was evidence of DNA damage in the samples, there was no evidence that it was related to the length of time in storage, whether frozen or as herbarium specimens.

Discussion

DNA extracted from herbarium tissues will continue to be invaluable, despite being highly fragmented and degraded. Rare floras would benefit from both traditional herbarium storage methods and extracted DNA freezer banks.

Introduction to the Special Issue: Advances in island plant biology since Sherwin Carlquist's Island Biology

Sherwin Carlquist's seminal publications-in particular his classic Island Biology, published in 1974-formulated hypotheses specific to island biology that remain valuable today. This special issue brings together some of the most interesting contributions presented at the First Island Biology Symposium hosted in Honolulu on 7-11 July 2014. We compiled a total of 18 contributions that present data from multiple archipelagos across the world and from different disciplines within the plant sciences. In this introductory paper, we first provide a short overview of Carlquist's life and work and then summarize the main findings of the collated papers. A first group of papers deals with issues to which Carlquist notably contributed: long-distance dispersal, adaptive radiation and plant reproductive biology. The findings of such studies demonstrate the extent to which the field has advanced thanks to (i) the increasing availability and richness of island data, covering many taxonomic groups and islands; (ii) new information from the geosciences, phylogenetics and palaeoecology, which allows us a more realistic understanding of the geological and biological development of islands and their biotas; and (iii) the new theoretical and methodological advances that allow us to assess patterns of abundance, diversity and distribution of island biota over large spatial scales. Most other papers in the issue cover a range of topics related to plant conservation on islands, such as causes and consequences of mutualistic disruptions (due to pollinator or disperser losses, introduction of alien predators, etc.). Island biologists are increasingly considering reintroducing ecologically important species to suitable habitats within their historic range and to neighbouring islands with depauperate communities of vertebrate seed dispersers, and an instructive example is given here. Finally, contributions on ecological networks demonstrate the usefulness of this methodological tool to advancing conservation management and better predicting the consequences of disturbances on species and interactions in the fragile insular ecosystems.

Development and characterization of microsatellite markers for analysis of population differentiation in the tree legume Acacia koa (Fabaceae: Mimosoideae) in the Hawaiian Islands

The aim of this research was to develop and use microsatellite markers to characterize the high-value timber tree Acacia koa (koa), which is endemic to the Hawaiian Islands. Genomic DNA fragments of 300-1000 bp were cloned and sequenced following enrichment for microsatellite motifs by PCR using 7 oligonucleotide repeat primers in separate reactions. Among 96 sequences analyzed, 63 contained unique microsatellite motifs flanked by variable sequences. A dual PCR method involving a primer walking step was used to develop 15 primer pairs. Another 16 primer pairs were developed directly from the variable sequences on both sides of the microsatellite motifs. These 31 primer pairs were tested on 172 koa plants representing 11 populations collected from 4 of the major Hawaiian Islands. Nine of the primers that identified polymorphic microsatellite loci and 3 that detected unique alleles exclusively in some populations were used for genetic diversity studies of koa. Cluster analysis and multidimensional scaling of the allelic phenotype data revealed that koa from Kauai formed a distinct group separate from koa of the neighboring islands of Oahu, Maui, and Hawaii. The oldest of the four islands, Kauai, also had the most diverse populations of koa.

Combinatorial analysis of the structural requirements of the Escherichia coli hemolysin signal sequence

We have investigated the substrate specificity of the Escherichia coli hemolysin transporter system. Translocation of hemolysin is dependent on a C-terminal signal sequence located within the last 60 amino acids of this protein. Previous comparative studies of the signal sequence have revealed a conserved helix(alpha1)-linker-helix(alpha2) motif, suggesting that secondary structure is important for transport. In this study, we generated three random libraries in the alpha1, linker, and alpha2 regions, as well as an alpha1-amphiphilic helical library to identify features buried within the structural motif that contribute to transport. Combinatorial variants were generated by altering the primary sequence of specific regions, and correlation between the genotype and phenotype of the mutant populations allowed us to objectively identify any functional features involved. It was found that the alpha1-amphiphilic helix and the linker are both important for function. To our surprise, the second helix of the conserved structural motif was not essential for transport. The finding that a predicted amphiphilic helix and hydrophobicity, rather than primary sequence, contribute to transport in the alpha1 region allows us to speculate on the mechanism of multiple substrate recognition. This may have implications for understanding the broad substrate specificity common among other ATP-binding cassette transporters.

Phylogenetics of the plant genera Dracaena and Pleomele (Asparagaceae)

This research focuses on the biodiversity and the evolutionary history of the world-wide medicinal plant genus, Dracaena, and the plant genus Pleomele. The debate concerning the relationship between Dracaena and Pleomele has continued till date - some botanists continue to include Pleomele within Dracaena but others claimed to separate the two genera. Dracaena is a genus comprising of about 40-100 species world wide, mainly in tropics and subtropics, with the exception of America. Pleomele is a genus that has been circumscribed consisting of 10-50 species in Asia. Till date, its center of biodiversity is unknown. Pleomele is only classified well in Hawaii, but confused with Dracaena in the other parts of Asia. Phylogenetic relationship among the 33 taxa within the Dracaena and Pleomele were reconstructed. DNA sequences from the chloroplast DNA intergenic spacer, trnL-trnF and trnH-psbA were analyzed. A phylogeny was reconstructed using neighbor-joining, maximum parsimony in PAUP*, and likelihood criteria in RAxML, and Bayesian inference in MrBayes. The phylogeny with Agave missionum and Agave attenuata as outgroup taxa indicates that Pleomele is mixed with Dracaena. This study provides the first phylogenetic reconstruction with taxonomic sampling of the Dracaena and Pleomele to resolve their questionable placement. The relationships of the climate change adaptation, biogeography, and conservation with the two plant genera will be further discussed in this study. Some suggestions for the benefits of the biodiversity and natural resource conservation in Himalaya regions will be addressed. One significant contribution of this research will be in promoting molecular taxonomy to solve problems in systematics especially in cases when the classification is in debate. Key-words: Phylogeny; chloroplast DNA; Asparagaceae; Dracaena; Pleomele. DOI: 10.3126/botor.v7i0.4385Botanica Orientalis – Journal of Plant Science (2010) 7: 64-72