Population genetic structure and adaptive differentiation of iron walnut Juglans regia subsp. sigillata in southwestern China

Phylogeography of Morella nana: The Wumeng Mountains as a natural geographical isolation boundary on the Yunnan-Guizhou Plateau

The Yunnan-Guizhou Plateau (YGP) is characterized by the distinctive isolated habitat of the limestone Karst Islands and features the Wumeng Mountains, which divide the YGP into the two Plateaus of Yunnan and Guizhou. This study aimed to assess the effects of geographic isolation and past climate fluctuation on the distribution of flora in the YGP. To achieve this, we carried out the phylogeographical pattern and genetic structure based on chloroplast and nuclear ribosomal DNA sequence in relation to past (Last Glacial Maximum) and present distributions based on ecological niche modeling for Morella nana, an important wild plant resource and endemic to the YGP once considered a vulnerable species. The results suggest that the genetic and chlorotype network structures of M. nana are divided into at least two groups: cpDNA chlorotype H2 (or dominant nrDNA haplotypes h1 and h2), distributed primarily to the east of the Wumeng Mountains, and cpDNA chlorotypes H1 and H3-H10 (or dominant nrDNA haplotype h2 and h3), distributed to the west of the Wumeng Mountains. A deep genetic split was noted within the two groups to reach 25 steps, especially for the cpDNA fragment variation. This east-west divergence reveals the existence of a natural geographical isolation boundary in the form of the Wumeng Mountains, and supports the existence of at least two glacial refuges during the Quaternary glacial period, along with two genetic diversity center, and at least two large geographic protection units for the important species of M. nana. This study indicates that the phylogeographical pattern of M. nana can be attributed to geographic/environmental isolation caused by the Wumeng Mountains and climate fluctuation during the last glacial maximum, and proposes an effective strategy to protecting this important plant resource.

Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions

Cold stress impacts woody tree growth and perennial production, especially when the temperature rapidly changes in late spring. To address this issue, we conducted the genome-wide identification of two important transcription factors (TFs), CBF (C-repeat binding factors) and ICE (inducers of CBF expression), in three walnut (Juglans) genomes. Although the CBF and ICE gene families have been identified in many crops, very little systematic analysis of these genes has been carried out in J. regia and J. sigillata. In this study, we identified a total of 16 CBF and 12 ICE genes in three Juglans genomes using bioinformatics analysis. Both CBF and ICE had conserved domains, motifs, and gene structures, which suggests that these two TFs were evolutionarily conserved. Most ICE genes are located at both ends of the chromosomes. The promoter cis-regulatory elements of CBF and ICE genes are largely involved in light and phytohormone responses. Based on 36 RNA sequencing of leaves from four walnut cultivars ('Zijing', 'Lvling', 'Hongren', and 'Liao1') under three temperature conditions (8 °C, 22 °C, and 5 °C) conditions in late spring, we found that the ICE genes were expressed more highly than CBFs. Both CBF and ICE proteins interacted with cold-related proteins, and many putative miRNAs had interactions with these two TFs. These results determined that CBF1 and ICE1 play important roles in the tolerance of walnut leaves to rapid temperature changes. Our results provide a useful resource on the function of the CBF and ICE genes related to cold tolerance in walnuts.

An overview of remote monitoring methods in biodiversity conservation

Conservation of biodiversity is critical for the coexistence of humans and the sustenance of other living organisms within the ecosystem. Identification and prioritization of specific regions to be conserved are impossible without proper information about the sites. Advanced monitoring agencies like the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) had accredited that the sum total of species that are now threatened with extinction is higher than ever before in the past and are progressing toward extinct at an alarming rate. Besides this, the conceptualized global responses to these crises are still inadequate and entail drastic changes. Therefore, more sophisticated monitoring and conservation techniques are required which can simultaneously cover a larger surface area within a stipulated time frame and gather a large pool of data. Hence, this study is an overview of remote monitoring methods in biodiversity conservation via a survey of evidence-based reviews and related studies, wherein the description of the application of some technology for biodiversity conservation and monitoring is highlighted. Finally, the paper also describes various transformative smart technologies like artificial intelligence (AI) and/or machine learning algorithms for enhanced working efficiency of currently available techniques that will aid remote monitoring methods in biodiversity conservation.

Population-genomic analyses reveal bottlenecks and asymmetric introgression from Persian into iron walnut during domestication

Background

Persian walnut, Juglans regia, occurs naturally from Greece to western China, while its closest relative, the iron walnut, Juglans sigillata, is endemic in southwest China; both species are cultivated for their nuts and wood. Here, we infer their demographic histories and the time and direction of possible hybridization and introgression between them.

Results

We use whole-genome resequencing data, different population-genetic approaches (PSMC and GONE), and isolation-with-migration models (IMa3) on individuals from Europe, Iran, Kazakhstan, Pakistan, and China. IMa3 analyses indicate that the two species diverged from each other by 0.85 million years ago, with unidirectional gene flow from eastern J. regia and its ancestor into J. sigillata, including the shell-thickness gene. Within J. regia, a western group, located from Europe to Iran, and an eastern group with individuals from northern China, experienced dramatically declining population sizes about 80 generations ago (roughly 2400 to 4000 years), followed by an expansion at about 40 generations, while J. sigillata had a constant population size from about 100 to 20 generations ago, followed by a rapid decline.

Conclusions

Both J. regia and J. sigillata appear to have suffered sudden population declines during their domestication, suggesting that the bottleneck scenario of plant domestication may well apply in at least some perennial crop species. Introgression from introduced J. regia appears to have played a role in the domestication of J. sigillata.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-022-02720-z.

Divergence in the Aquilegia ecalcarata complex is correlated with geography and climate oscillations: Evidence from plastid genome data

Quaternary climate oscillations and geographical heterogeneity play important roles in determining species and genetic diversity distribution patterns, but how these factors affect the migration and differentiation of East Asian plants species at the population level remains poorly understood. The Aquilegia ecalcarata complex, a group that originated in the Late Tertiary and is widely distributed throughout East Asia, displays high genetic variation that is suitable for studying elaborate phylogeographic patterns and demographic history related to the impact of Quaternary climate and geography. We used plastid genome data from 322 individuals in 60 populations of the A. ecalcarata complex to thoroughly explore the impact of Quaternary climate oscillations and geography on the phylogeographic patterns and demographic history of the A. ecalcarata complex through a series of phylogenetic, divergence time estimation, and demographic history analyses. The dry, cold climate and frequent climate oscillations that occurred during the early Pleistocene and the Mid-Pleistocene transition led to the differentiation of the A. ecalcarata complex, which was isolated in various areas. Geographically, the A. ecalcarata complex can be divided into Eastern and Western Clades and five subclades, which conform to the divergence of the East Asian flora. Our results clearly show the impact of Quaternary climate and geography on evolutionary history at the population level. These findings promote the understanding of the relationship between plant genetic differentiation and climate and geographical factors of East Asia at the population level.