The Woody Planet: From Past Triumph to Manmade Decline

Adaptive divergence and genetic vulnerability of relict species under climate change: a case study of Pterocarya macroptera

BACKGROUND AND AIMS

Understanding adaptive genetic variation and whether it can keep pace with predicted future climate change is critical in assessing the genetic vulnerability of species and developing conservation management strategies. The lack of information on adaptive genetic variation in relict species carrying abundant genetic resources hinders the assessment of genetic vulnerability. Using a landscape genomics approach, this study aimed to determine how adaptive genetic variation shapes population divergence and to predict the adaptive potential of Pterocarya macroptera (a vulnerable relict species in China) under future climate scenarios.

METHODS

We applied restriction site-associated DNA sequencing (RAD-seq) to obtain 8244 single-nucleotide polymorphisms (SNPs) from 160 individuals across 28 populations. We examined the pattern of genetic diversity and divergence, and then identified outliers by genetic differentiation (FST) and genotype-environment association (GEA) methods. We further dissected the effect of geographical/environmental gradients on genetic variation. Finally, we predicted genetic vulnerability and adaptive risk under future climate scenarios.

KEY RESULTS

We identified three genetic lineages within P. macroptera: the Qinling-Daba-Tianmu Mountains (QDT), Western Sichuan (WS) and Northwest Yunnan (NWY) lineages, which showed significant signals of isolation by distance (IBD) and isolation by environment (IBE). IBD and IBE explained 3.7-5.7 and 8.6-12.8 % of the genetic structure, respectively. The identified GEA SNP-related genes were involved in chemical defence and gene regulation and may exhibit higher genetic variation to adapt to the environment. Gradient forest analysis revealed that the genetic variation was mainly shaped by temperature-related variables, indicating its adaptation to local thermal environments. A limited adaptive potential was suggested by the high levels of genetic vulnerability in marginal populations.

CONCLUSIONS

Environmental gradient mainly shaped the population differentiation of P. macroptera. Marginal populations may be at high risk of extinction, and thus proactive management measures, such as assisted gene flow, are required to ensure the survival of these populations.

Dynamic evolution of the plastome in the Elm family (Ulmaceae)

This study compared the plastomes of Ulmaceae allowing analyses of the dynamic evolution, including genome structure, codon usage bias, repeat sequences, molecular mutation rates, and phylogenetic inferences. Ulmaceae is a small family in the order Rosales. This family consists of seven genera, including Ulmus, Zelkova, Planera, Hemiptelea, Phyllostylon, Ampelocera, and Holoptelea. Ulmaceae is an interesting lineage from plant biogeographic, systematic, evolutionary, and paleobotanic perspectives. It is also a good model to investigate the evolution of the plastomes in woody plants. In this study, we sequenced and assembled the complete plastomes of the six Ulmaceae genera to compare genomic structures and reveal the molecular evolutionary patterns. The size of the quadripartite plastomes ranged from 158,290 bp to 161,886 bp. The genomes contained 131 genes, including 87 coding genes, 36 tRNA, and 8 rRNA. The gene number, gene content, and genomic structure were highly consistent among the Ulmaceae genera. Nine variable regions including ndhA intron, ndhF-rpl32, ycf1, psbK-trnS, rps16-trnQ, trnT-trnL, trnT-psbD, trnS-trnG, and rpl32-trnL, were identified in Ulmaceae plastomes according to the nucleotide diversity values. Condon usage was biased among the genes and showed consistent trends in the seven genera. Molecular evolution analyses revealed that most of the genes and all gene groups were under widespread purifying selection. Twelve genes (ccsA, matK, psbH, psbK, rbcL, rpl22, rpl32, rpoA, rps12, rps15, rps16, and ycf2) were under positive selection. Phylogenetic analyses supported that Ulmaceae should be divided into two main clades, such as the temperate clade, including Ulmus, Zelkova, Planera, and Hemiptelea and the tropical clade, including Phyllostylon, Ampelocera and Holoptelea. This study reports the structure and evolutionary characteristics of the Elm family. These new genomic data will benefit assessments of genomic evolution and provide information to elucidate the phylogenetic relationships among Ulmaceae species.

Bioinformatics approaches and applications in plant biotechnology

BACKGROUND

In recent years, major advance in molecular biology and genomic technologies have led to an exponential growth in biological information. As the deluge of genomic information, there is a parallel growth in the demands of tools in the storage and management of data, and the development of software for analysis, visualization, modelling, and prediction of large data set.

MAIN BODY

Particularly in plant biotechnology, the amount of information has multiplied exponentially with a large number of databases available from many individual plant species. Efficient bioinformatics tools and methodologies are also developed to allow rapid genome sequence and the study of plant genome in the 'omics' approach. This review focuses on the various bioinformatic applications in plant biotechnology, and their advantages in improving the outcome in agriculture. The challenges or limitations faced in plant biotechnology in the aspect of bioinformatics approach that explained the low progression in plant genomics than in animal genomics are also reviewed and assessed.

CONCLUSION

There is a critical need for effective bioinformatic tools, which are able to provide longer reads with unbiased coverage in order to overcome the complexity of the plant's genome. The advancement in bioinformatics is not only beneficial to the field of plant biotechnology and agriculture sectors, but will also contribute enormously to the future of humanity.

Complete Chloroplast Genome of an Endangered Species Quercus litseoides, and Its Comparative, Evolutionary, and Phylogenetic Study with Other Quercus Section Cyclobalanopsis Species

Quercus litseoides, an endangered montane cloud forest species, is endemic to southern China. To understand the genomic features, phylogenetic relationships, and molecular evolution of Q. litseoides, the complete chloroplast (cp) genome was analyzed and compared in Quercus section Cyclobalanopsis. The cp genome of Q. litseoides was 160,782 bp in length, with an overall guanine and cytosine (GC) content of 36.9%. It contained 131 genes, including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. A total of 165 simple sequence repeats (SSRs) and 48 long sequence repeats with A/T bias were identified in the Q. litseoides cp genome, which were mainly distributed in the large single copy region (LSC) and intergenic spacer regions. The Q. litseoides cp genome was similar in size, gene composition, and linearity of the structural region to those of Quercus species. The non-coding regions were more divergent than the coding regions, and the LSC region and small single copy region (SSC) were more divergent than the inverted repeat regions (IRs). Among the 13 divergent regions, 11 were in the LSC region, and only two were in the SSC region. Moreover, the coding sequence (CDS) of the six protein-coding genes (rps12, matK, atpF, rpoC2, rpoC1, and ndhK) were subjected to positive selection pressure when pairwise comparison of 16 species of Quercus section Cyclobalanopsis. A close relationship between Q. litseoides and Quercus edithiae was found in the phylogenetic analysis of cp genomes. Our study provided highly effective molecular markers for subsequent phylogenetic analysis, species identification, and biogeographic analysis of Quercus.

Global Estimation and Mapping of the Conservation Status of Tree Species Using Artificial Intelligence

Trees are fundamental for Earth's biodiversity as primary producers and ecosystem engineers and are responsible for many of nature's contributions to people. Yet, many tree species at present are threatened with extinction by human activities. Accurate identification of threatened tree species is necessary to quantify the current biodiversity crisis and to prioritize conservation efforts. However, the most comprehensive dataset of tree species extinction risk-the Red List of the International Union for the Conservation of Nature (IUCN RL)-lacks assessments for a substantial number of known tree species. The RL is based on a time-consuming expert-based assessment process, which hampers the inclusion of less-known species and the continued updating of extinction risk assessments. In this study, we used a computational pipeline to approximate RL extinction risk assessments for more than 21,000 tree species (leading to an overall assessment of 89% of all known tree species) using a supervised learning approach trained based on available IUCN RL assessments. We harvested the occurrence data for tree species worldwide from online databases, which we used with other publicly available data to design features characterizing the species' geographic range, biome and climatic affinities, and exposure to human footprint. We trained deep neural network models to predict their conservation status, based on these features. We estimated 43% of the assessed tree species to be threatened with extinction and found taxonomic and geographic heterogeneities in the distribution of threatened species. The results are consistent with the recent estimates by the Global Tree Assessment initiative, indicating that our approach provides robust and time-efficient approximations of species' IUCN RL extinction risk assessments.

Biogeographic Overview of Ulmaceae: Diversity, Distribution, Ecological Preferences, and Conservation Status

The elm family (Ulmaceae) is a woody plant group with important scientific, societal, and economic value. We aim to present the first biogeographic synthesis investigating the global diversity, distribution, ecological preferences, and the conservation status of Ulmaceae. A literature review was performed to explore the available data for all extant species. Our study made it possible to map the actual global distribution of Ulmaceae with high precision, and to elucidate the centers of diversity, located mainly in China and in the southeastern USA. A detailed comparative analysis of the macroclimatic niche for each species was produced, which shows the general biogeographic pattern of the family and pinpoints the outlier species. The results corroborate recent molecular analyses and support the division of Ulmaceae into two taxonomically, biogeographically, and ecologically well-differentiated groups: the so-called temperate clade with 4 genera and 43 species and the tropical clade with 3 genera and 13 species. The elm family is often described as a typical temperate plant group, however the diversity peak of all Ulmaceae is located in the subtropical zone, and a non-negligible part of the family is exclusively distributed in the tropics. We also noticed that a high proportion of Ulmaceae is linked to humid macro- or microhabitats. Finally, we highlighted that nearly 25% of all Ulmaceae are threatened. Fieldwork, conservation efforts, and research activities are still necessary for this family, particularly for the tropical members and the most endangered species.