Transcript and protein profiling identify candidate gene sets of potential adaptive significance in New Zealand Pachycladon

<p>Abstract</p> <p>Background</p> <p>Transcript profiling of closely related species provides a means for identifying genes potentially important in species diversification. However, the predictive value of transcript profiling for inferring downstream-physiological processes has been unclear. In the present study we use shotgun proteomics to validate inferences from microarray studies regarding physiological differences in three <it>Pachycladon </it>species. We compare transcript and protein profiling and evaluate their predictive value for inferring glucosinolate chemotypes characteristic of these species.</p> <p>Results</p> <p>Evidence from heterologous microarrays and shotgun proteomics revealed differential expression of genes involved in glucosinolate hydrolysis (myrosinase-associated proteins) and biosynthesis (methylthioalkylmalate isomerase and dehydrogenase), the interconversion of carbon dioxide and bicarbonate (carbonic anhydrases), water use efficiency (ascorbate peroxidase, 2 cys peroxiredoxin, 20 kDa chloroplastic chaperonin, mitochondrial succinyl CoA ligase) and others (glutathione-S-transferase, serine racemase, vegetative storage proteins, genes related to translation and photosynthesis). Differences in glucosinolate hydrolysis products were directly confirmed. Overall, prediction of protein abundances from transcript profiles was stronger than prediction of transcript abundance from protein profiles. Protein profiles also proved to be more accurate predictors of glucosinolate profiles than transcript profiles. The similarity of species profiles for both transcripts and proteins reflected previously inferred phylogenetic relationships while glucosinolate chemotypes did not.</p> <p>Conclusions</p> <p>We have used transcript and protein profiling to predict physiological processes that evolved differently during diversification of three <it>Pachycladon </it>species. This approach has also identified candidate genes potentially important in adaptation, which are now the focus of ongoing study. Our results indicate that protein profiling provides a valuable tool for validating transcript profiles in studies of adaptive divergence.</p

Evidence for both long-distance dispersal and isolation in the Southern Oceans: molecular phylogeny of <i>Sophora</i> sect <i>Edwardsia</i> (Fabaceae)

<p>We examined the phylogenetic relationships within <i>Sophora</i> sect. <i>Edwardsia</i> using DNA sequences from the chloroplast <i>trnQ-5′rps16</i> and <i>trnH^GUG-psbA</i> intergenic spacers and the nuclear-encoded chloroplast-expressed glutamine synthetase gene. Sequences were analysed with median-joining networks and phylogenetic approaches. Low sequence diversity was detected, which is consistent with past genetic studies of the section. Chloroplast and nuclear sequences are shared across large geographic distances. The New Zealand species did not form a monophyletic group, nor did the species from Chile. However, species on some Pacific Islands (Lord Howe Island, Easter Island, Hawaii and French Polynesia) and Réunion Island in the Indian Ocean appear to have unique chloroplast haplotypes, indicating isolation. The <i>S. chrysophylla</i> chloroplast haplotype derives from the French Polynesian haplotype rather than <i>S. denudata</i> from Réunion Island, with which it shares morphological characters. In the nuclear phylogeny <i>Sophora macrocarpa</i> was sister to the remaining species that were sequenced in the section, a relationship that has been previously suggested from morphological analysis.</p

Three new species of 'Gingidia' (Apiaceae: Apioideae) from Australia and New Zealand segregated from 'G. montana'

Three new species of 'Gingidia' (Apiaceae: Apioideae) segregated from the 'G. montana' (J.R.Forst. &amp; G.Forst.) J.W.Dawson complex are named, with 'G. montana' now regarded as a New Zealand endemic. The new Australian endemic, 'G. rupicola' I.Telford &amp; J.J.Bruhl, is restricted to the eastern escarpment of the New England Tableland, New South Wales. With few populations and limited numbers of plants, the conservation assessment of 'G. rupicola' is Endangered. 'G. haematitica' Heenan is described as a new species from North-West Nelson, South Island, New Zealand, where it is restricted to base-rich substrates in the Burnett Range. Because of its restricted distribution and the continued mining for dolomite at the site of the largest population, 'G. haematitica' is considered to have a conservation assessment of Nationally Critical. The second New Zealand endemic, 'G. amphistoma' Heenan, is known from alpine habitats in the Southern Alps, South Island. Distributions of the three new species are mapped, habitats noted, and a table compares attributes of these species and 'G. montana'

Mesorhizobium waimense sp. nov. isolated from Sophora longicarinata root nodules and Mesorhizobium cantuariense sp. nov. isolated from Sophora microphylla root nodules

In total 14 strains of Gram-stain-negative, rod-shaped bacteria were isolated from Sophora longicarinata and Sophora microphylla root nodules and authenticated as rhizobia on these hosts. Based on the 16S rRNA gene phylogeny, they were shown to belong to the genus Mesorhizobium, and the strains from S. longicarinata were most closely related to Mesorhizobium amorphae ACCC 19665(T) (99.8-99.9 %), Mesorhizobium huakuii IAM 14158(T) (99.8-99.9 %), Mesorhizobium loti USDA 3471(T) (99.5-99.9 %) and Mesorhizobium septentrionale SDW 014(T) (99.6-99.8 %), whilst the strains from S. microphylla were most closely related to Mesorhizobium ciceri UPM-Ca7(T) (99.8-99.9 %), Mesorhizobium qingshengii CCBAU 33460(T) (99.7 %) and Mesorhizobium shangrilense CCBAU 65327(T) (99.6 %). Additionally, these strains formed two distinct groups in phylogenetic trees of the housekeeping genes glnll, recA and rpoB. Chemotaxonomic data, including fatty acid profiles, supported the assignment of the strains to the genus Mesorhizobium and allowed differentiation from the closest neighbours. Results of DNA-DNA hybridizations, MALDI- TOF MS analysis, ERIC-PCR, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from their closest neighbouring species. Therefore, the strains isolated from S. longicarinata and S. microphylla represent two novel species for which the names Mesorhizobium waimense sp. nov. (ICMP 19557(T)=LMG 28228(T)=HAMBI 3608(T)) and Mesorhizobium cantuariense sp. nov. (ICMP 19515(T)=LMG 28225(T)=HAMBI 3604(T)), are proposed respectively

Brian Peter John Molloy (12 August 1930–31 July 2022): field ecologist, botanist and conservationist

Brian Peter John Molloy (12 August 1930–31 July 2022): field ecologist, botanist and conservationis