Correction
Plant Sciences
Todd G. B. McLay, Michael J. Bayly, Michael R. Whitehead, Rachael M. Fowler
Summary: By comparing the plastome genomes of two species in the genus Dipodium, it was found that there was no degradation of photosynthesis genes in the putative mycoheterotroph species, and both species had undergone loss or pseudogenisation of all plastid ndh genes. This contrasts with most other comparisons between photosynthetic and mycoheterotrophic relatives, suggesting that the leafless Dipodium species may still be capable of photosynthesis and in the early stages of transitioning to a fully heterotrophic lifestyle.
AUSTRALIAN JOURNAL OF BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Ardashir Kharabian-Masouleh, Agnelo Furtado, Bader Alsubaie, Othman Al-Dossary, Alex Wu, Ibrahim Al-Mssalem, Robert Henry
Summary: Plant plastid genomes are usually highly conserved, but the desert plant jojoba has lost five essential NADH dehydrogenase subunit genes in its plastid. Jojoba has evolved mechanisms to cope with extreme desert conditions and survive with abundant sunlight and limited water.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Ecology
Deyi Wang, Gerhard Gebauer, Hans Jacquemyn, Franziska E. Zahn, Sofia I. F. Gomes, Johanna Lorenz, Harrie van der Hagen, Menno Schilthuizen, Vincent S. F. T. Merckx
Summary: The symbiotic associations between orchids and various ecological guilds of fungi provide an ideal study system for understanding the evolution and ecophysiology of mycorrhizal symbiosis. This research investigated the mycorrhizal communities and isotope signatures of a terrestrial orchid, Neottia ovata, growing in different light conditions in Europe. The results suggest that rhizoctonia fungi played a major functional role in carbon and nutrient supply for the orchids, while ectomycorrhizal fungi did not substantially contribute to the plants' carbon budget.
FUNCTIONAL ECOLOGY
(2023)
Article
Plant Sciences
Huan-Wen Peng, Lian Lian, Jun Zhang, Andrey S. Erst, Wei Wang
Summary: This study provides a comprehensive analysis of the evolutionary origin and plastome degradation of mycoheterotrophy in the tribe Neottieae. The results indicate that autotrophy is the ancestral state, mixotrophy originated independently multiple times, and the transition from mixotrophy to mycoheterotrophy occurred independently three times. Plastome degradation is irreversible in mycoheterotrophic lineages, which limits their habitat to understories with low light levels. The Pleistocene climatic fluctuations and resulting migration caused the disjunction between the Loess Plateau and Changbai Mountains in Diplandrorchis.
Article
Plant Sciences
Li-Hsuan Ho, Yung- Lee, Shu-Ying Hsieh, I-Shiuan Lin, Yun-Chien Wu, Han-Yu Ko, Patrick A. Klemens, H. Ekkehard Neuhaus, Yi-Min Chen, Tzu-Pi Huang, Chih-Hsin Yeh, Woei-Jiun Guo
Summary: Gastrodia elata, a mycoheterotrophic orchid, relies on symbiotic fungus Armillaria for carbon distribution, with sucrose identified as a major sugar transported. The high-affinity sucrose transporter gene GeSUT4 plays a key role in active sucrose transport and carbon allocation, highlighting the evolutionary importance of sucrose transporters in plant-microbe interactions. Transgenic Arabidopsis overexpressing GeSUT4 showed larger leaves but were sensitive to excess sucrose, demonstrating the regulation role of GeSUT4 in sugar allocation.
PLANT CELL AND ENVIRONMENT
(2021)
Article
Biochemistry & Molecular Biology
Xiong-De Tu, Ding-Kun Liu, Shao-Wei Xu, Cheng-Yuan Zhou, Xu-Yong Gao, Meng-Yao Zeng, Sai Zhang, Jin-Liao Chen, Liang Ma, Zhuang Zhou, Ming-Zhong Huang, Shi-Pin Chen, Zhong-Jian Liu, Si-Ren Lan, Ming-He Li
Summary: Goodyerinae is a phylogenetically unresolved group within Orchidaceae. This study utilized large-scale phylogenomic data to compare plastome structure between two main clades, revealing unique features in plastome structure among different genera. The findings provide insights into orchid phylogenetics and plastome evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Plant Sciences
Kenji Suetsugu, Jun Matsubayashi
Summary: Most land plants form mutualistic mycorrhizal symbioses with fungal partners, but mycoheterotrophs exploit fungal partners by reversing carbon movement. This study focused on a photosynthetic orchid, Apostasia nipponica, and found that it gains carbon through both photosynthesis and fungal cheating (partial mycoheterotrophy), shedding light on the evolution of mycoheterotrophy in orchids.
Article
Biochemistry & Molecular Biology
Xiao-Jian Qu, Xue-Jie Zhang, Dong-Ling Cao, Xiu-Xiu Guo, Jeffrey P. Mower, Shou-Jin Fan
Summary: Koenigia, a genus proposed by Linnaeus, has a contentious taxonomic history. The relationships among species and the circumscription of the genus relative to Aconogonon remain uncertain. In this study, genome skimming was used to explore the phylogenetic relationships of Koenigia and to establish the timing of major evolutionary diversification events. The results showed that K. delicatula has lost functional copies of certain genes and has gene rearrangements in its plastome. The conflicting relationships among plastome and mitochondrial trees and among gene trees complicate the circumscription of Koenigia, which may be due to rapid diversification within a short period of time. Furthermore, the study revealed correlated variation in substitution rates among Persicarieae species, suggesting a shared underlying mechanism promoting evolutionary rate variation in both organellar genomes. The divergence of K. delicatula from other Koenigia species may be associated with climatic events and the uplift of certain geographical areas.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Plant Sciences
Deyi Wang, Hans Jacquemyn, Sofia I. F. Gomes, Rutger A. Vos, Vincent S. F. T. Merckx
Summary: Research has shown that shifts in trophic mode in orchids often coincide with changes in fungal symbionts, indicating that the loss of photosynthesis selects for different fungal communities. By analyzing changes in fungal partners and the evolution of plant trophic modes, it is revealed that symbiotic associations and ecophysiological traits are tightly correlated throughout the diversification of orchids.
Article
Plant Sciences
Janice Valencia-D, W. Mark Whitten, Kurt Neubig
Summary: The chloroplast plays a crucial role in controlling carbon uptake in land plants, with its DNA sequence and function highly conserved. However, for plants with alternative carbon supplies, the plastid genome is prone to mutations. Fully mycoheterotrophic plants do not photosynthesize and exhibit albino characteristics, but mutations in the plastid genome do not seem to affect their photosynthetic capability.
Article
Biochemistry & Molecular Biology
Jeffrey P. Mower, Wenhu Guo, Raghavendran Partha, Weishu Fan, Nick Levsen, Kirsten Wolff, Jacqueline M. Nugent, Natalia Pabon-Mora, Favio Gonzalez
Summary: Plantagineae tribe comprises approximately 270 species in three genera, with Plantago being the most diverse. Plastomes from Plantago exhibit atypical features, and phylogenomic analyses provided strong support for relationships among major lineages. General plastid features reinforced major divisions within Plantagineae.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Kalman Konyves, Jordan Bilsborrow, Maria D. Christodoulou, Alastair Culham, John David
Summary: Amaryllidaceae is a widespread plant family that contributes both food and ornamental plants. A survey of plastomes in the family showed structural rearrangements and gene losses, with some taxa displaying gains in plastome length and evidence of gene loss in others. Further sampling across the family could provide valuable new information on plastome variation and evolution.
Article
Plant Sciences
Chung-Shien Wu, Chung-I. Chen, Shu-Miaw Chaw
Summary: Convolvulaceae is a large family of plants with economic value. However, the phylogenetic relationships within this family and the complexity of plastid genomes are still not well understood. In this study, we analyzed 78 plastomes from different genera within Convolvulaceae and found various plastomic rearrangements, including inversions, duplications, and loss of genes and introns. Our findings also shed light on the uncertain positions of the genera Cuscuta and Erycibe and provide a rare example of gene transfer from mitochondria to plastids in angiosperms.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Erton Mendonca de Almeida, Mariela Analia Sader, Pablo Emanuel Rodriguez, Benoit Loeuille, Leonardo P. Felix, Andrea Pedrosa-Harand
Summary: Discocactus and Melocactus are representatives of the Core Cactoideae II BCT clade, consisting of 14 and 50 species, respectively. While both genera are found in South America, Melocactus also extends into Central America and the West Indies. Comparative analysis of their plastomes revealed a significant number of gene rearrangements within the subfamily Cactoideae.
BRAZILIAN JOURNAL OF BOTANY
(2021)
Article
Biochemistry & Molecular Biology
Young-Kee Kim, Se-Hwan Cheon, Ja-Ram Hong, Ki-Joong Kim
Summary: This study decoded the chloroplast genomes of six vanilloid species and compared them with other vanilloid plastomes. Different evolutionary patterns and gene losses were observed among the vanilloid species. Photosynthetic vanilloids lost most of their photosynthesis-related genes, while mycoheterotrophic vanilloids retained some crucial genes. Vanilloideae were located between Apostasioideae and Cypripedioideae in the maximum likelihood tree.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Ecology
Patrick S. Fahey, Rachael M. Fowler, Todd G. B. McLay, Frank Udovicic, David J. Cantrill, Michael J. Bayly
Summary: This study examined the genetic relationships between populations of the mallee eucalypt, Eucalyptus behriana, in southeastern Australia, revealing the greatest genetic divergence between populations on either side of the Lower Murray Basin. It was found that the western populations fragmented earlier than the eastern ones, likely tied to climatic changes associated with glacial-interglacial cycles. The results suggest that environmental processes played a significant role in driving the fragmentation of the species' distribution.
ECOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Rachael M. Fowler, Daniel J. Murphy, Todd G. B. McLay, Bevan J. Buirchell, Robert J. Chinnock, Michael J. Bayly
Summary: This study conducted phylogenetic analysis of genera in tribe Myoporeae using nuclear ribosomal cistron data, revealing Eremophila as a paraphyletic group with other genera nested within it. The suggestion to synonymize Calamphoreus and Diocirea under Eremophila was proposed as an immediate step, while additional phylogenetic data are needed to clarify the relationships of Bontia, Glycocystis, and Myoporum before further taxonomic changes are proposed.
Article
Ecology
Megan E. Rixon, Michael J. Bayly, Todd G. B. McLay, Teresa Lebel
Summary: This study has revealed the hidden diversity and interactions of gall midges, their associated microfungal symbionts, and parasitoid wasps in temperate saltmarsh ecosystems. It also highlights the importance of investigating all trophic levels simultaneously in these complex interactions.
ARTHROPOD-PLANT INTERACTIONS
(2021)
Article
Plant Sciences
Todd G. B. McLay, Joanne L. Birch, Bee F. Gunn, Weixuan Ning, Jennifer A. Tate, Lars Nauheimer, Elizabeth M. Joyce, Lalita Simpson, Alexander N. Schmidt-Lebuhn, William J. Baker, Felix Forest, Chris J. Jackson
Summary: Expanding the Angiosperms353 target file to create the 'mega353' target file, with sequences from 566 transcriptomes, resulted in increased on-target reads by 32%, improved locus recovery, and increased total length of concatenated loci.
APPLICATIONS IN PLANT SCIENCES
(2021)
Article
Plant Sciences
Todd G. B. McLay, Jennifer A. Tate, Chrissen E. C. Gemmill, Avi S. Holzapfel, V. Vaughan Symonds
Summary: Despite a rich history of botanical research, little is known about the distribution of genetic variation within New Zealand plant species. This study investigated the population genetic structure of the endemic root holoparasite, Dactylanthus taylorii, and revealed a hierarchical pattern of genetic diversity, with evidence for three broad geographic regional groupings and further subdivisions within each group. The genetic structure provides important information for the management of D. taylorii and our understanding of New Zealand biogeography.
NEW ZEALAND JOURNAL OF BOTANY
(2022)
Article
Multidisciplinary Sciences
Todd G. B. McLay, Daniel J. Murphy, Gareth D. Holmes, Sarah Mathews, Gillian K. Brown, David J. Cantrill, Frank Udovicic, Theodore R. Allnutt, Chris J. Jackson
Summary: Acacia is the largest and most widespread genus of plants in the Australian flora. This study generated a genome assembly for Acacia pycnantha and predicted its gene functions. The genome assembly and annotation will be a valuable resource for studying Acacia's evolution, conservation, breeding, invasiveness, physiology, and for comparative studies of legumes.
Editorial Material
Plant Sciences
Russell L. Barrett, Margaret M. Hanes, Todd G. B. McLay
Article
Plant Sciences
Harvey K. Orel, Todd G. B. McLay, Will C. Neal, Paul I. Forster, Michael J. Bayly
Summary: This study investigated the relationships within the 'Eriostemon group' of sclerophyllous Rutaceae in Australia. The researchers used complete plastome sequence data for 60 species and a supermatrix including sequences of four plastome spacer regions for 22 additional species. The results revealed four major clades branching from a polytomy, with discussions on the evolutionary inferences of each lineage. However, the polytomy could not be resolved due to insufficient data or rapid radiation.
AUSTRALIAN SYSTEMATIC BOTANY
(2023)
Article
Plant Sciences
Chris Jackson, Todd McLay, Alexander N. N. Schmidt-Lebuhn
Summary: The HybPiper pipeline is widely used for target capture data assembly in phylogenomic analysis. The identification of paralogs is crucial for accurate evolutionary relationship inference. This study containerized and expanded the functionality of HybPiper and a pipeline for ortholog group inference, providing novel options for target capture sequence data treatment. The results are important for the phylogenetic community.
APPLICATIONS IN PLANT SCIENCES
(2023)
Article
Plant Sciences
Harvey K. Orel, Todd G. B. Mclay, Lydia K. Guja, Marco F. Duretto, Michael J. Bayly
Summary: This study examined the genetic relationships and diversity of three closely related species and two related species in New South Wales, Australia. The results confirm the current taxonomic status and suggest the existence of a potential new species. The genetic diversity of the endangered species is similar to that of more widespread species. Additionally, the study identified several genotypes of the endangered species that are not represented in ex situ collections and provided suggestions for their inclusion in future collections.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
Article
Plant Sciences
Todd McLay, Gareth D. Holmes, Paul I. Forster, Susan E. Hoebee, Denise R. Fernando
AUSTRALIAN SYSTEMATIC BOTANY
(2018)