Karyotype and LTR-RTs analysis provide insights into oak genomic evolution.

BACKGROUND: Whole-genome duplication and long terminal repeat retrotransposons (LTR-RTs) amplification in organisms are essential factors that affect speciation, local adaptation, and diversification of organisms. Understanding the karyotype projection and LTR-RTs amplification could contribute to untangling evolutionary history. This study compared the karyotype and LTR-RTs evolution in the genomes of eight oaks, a dominant lineage in Northern Hemisphere forests. RESULTS: Karyotype projections showed that chromosomal evolution was relatively conservative in oaks, especially on chromosomes 1 and 7. Modern oak chromosomes formed through multiple fusions, fissions, and rearrangements after an ancestral triplication event. Species-specific chromosomal rearrangements revealed fragments preserved through natural selection and adaptive evolution. A total of 441,449 full-length LTR-RTs were identified from eight oak genomes, and the number of LTR-RTs for oaks from section Cyclobalanopsis was larger than in other sections. Recent amplification of the species-specific LTR-RTs lineages resulted in significant variation in the abundance and composition of LTR-RTs among oaks. The LTR-RTs insertion suppresses gene expression, and the suppressed intensity in gene regions was larger than in promoter regions. Some centromere and rearrangement regions indicated high-density peaks of LTR/Copia and LTR/Gypsy. Different centromeric regional repeat units (32, 78, 79 bp) were detected on different Q. glauca chromosomes. CONCLUSION: Chromosome fusions and arm exchanges contribute to the formation of oak karyotypes. The composition and abundance of LTR-RTs are affected by its recent amplification. LTR-RTs random retrotransposition suppresses gene expression and is enriched in centromere and chromosomal rearrangement regions. This study provides novel insights into the evolutionary history of oak karyotypes and the organization, amplification, and function of LTR-RTs.

Ensemble species distribution modeling and multilocus phylogeography provide insight into the spatial genetic patterns and distribution dynamics of a keystone forest species, Quercus glauca.

BACKGROUND: Forests are essential for maintaining species diversity, stabilizing local and global climate, and providing ecosystem services. Exploring the impact of paleogeographic events and climate change on the genetic structure and distribution dynamics of forest keystone species could help predict responses to future climate change. In this study, we combined an ensemble species distribution model (eSDM) and multilocus phylogeography to investigate the spatial genetic patterns and distribution change of Quercus glauca Thunb, a keystone of East Asian subtropical evergreen broad-leaved forest. RESULTS: A total of 781 samples were collected from 77 populations, largely covering the natural distribution of Q. glauca. The eSDM showed that the suitable habitat experienced a significant expansion after the last glacial maximum (LGM) but will recede in the future under a general climate warming scenario. The distribution centroid will migrate toward the northeast as the climate warms. Using nuclear SSR data, two distinct lineages split between east and west were detected. Within-group genetic differentiation was higher in the West than in the East. Based on the identified 58 haplotypes, no clear phylogeographic structure was found. Populations in the Nanling Mountains, Wuyi Mountains, and the southwest region were found to have high genetic diversity. CONCLUSIONS: A significant negative correlation between habitat stability and heterozygosity might be explained by the mixing of different lineages in the expansion region after LGM and/or hybridization between Q. glauca and closely related species. The Nanling Mountains may be important for organisms as a dispersal corridor in the west-east direction and as a refugium during the glacial period. This study provided new insights into spatial genetic patterns and distribution dynamics of Q. glauca.

High-quality haplotype-resolved genome assembly for ring-cup oak (Quercus glauca) provides insight into oaks demographic dynamics.

Quercus section Cyclobalanopsis represents a dominant woody lineage in East Asian evergreen broadleaved forests. Regardless of its ecological and economic importance, little is known about the genomes of species in this unique oak lineage. Quercus glauca is one of the most widespread tree species in the section Cyclobalanopsis. In this study, a high-quality haplotype-resolved reference genome was assembled for Q. glauca from PacBio HiFi and Hi-C reads. The genome size, contig N50, and scaffold N50 measured 902.88, 7.60, and 69.28 Mb, respectively, for haplotype1, and 913.28, 7.20, and 71.53 Mb, respectively, for haplotype2. A total of 37,457 and 38,311 protein-coding genes were predicted in haplotype1 and haplotype2, respectively. Homologous chromosomes in the Q. glauca genome had excellent gene pair collinearity. The number of R-genes in Q. glauca was similar to most East Asian oaks but less than oak species from Europe and America. Abundant structural variation in the Q. glauca genome could contribute to environmental stress tolerance in Q. glauca. Sections Cyclobalanopsis and Cerris diverged in the Oligocene, in agreement with fossil records for section Cyclobalanopsis, which document its presence in East Asia since the early Miocene. The demographic dynamics of closely related oak species were largely similar. The high-quality reference genome provided here for the most widespread species in section Cyclobalanopsis will serve as an essential genomic resource for evolutionary studies of key oak lineages while also supporting studies of interspecific introgression, local adaptation, and speciation in oaks.

The complete chloroplast genome sequence of Quercus schottkyana, and comparative analysis with related species.

In this study, we sequenced the complete chloroplast genome of Quercus schottkyana. The circular genome is 160,746 bp in size, featuring a typical quadripartite structure comprising one large single-copy region (LSC, 90,136 bp), one small single-copy region (SSC, 18,942 bp), and two copies of inverted repeat regions (IRs, 25,834 bp). The genome contains 131 genes, including 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The overall GC content is 36.90%. The maximum likelihood phylogenetic tree reconstructed using IQ-TREE indicated that Q. schottkyana has a closer relationship with Quercus sichourensis and Quercus acuta.

The complete chloroplast genome sequence of Quercus chungii (Fagaceae).

Quercus chungii F.P.Metcalf, a rare oak with endemic to southern China, belongs to the compound trichome base (CTB) lineage in the Cyclobalanopsis section. The complete chloroplast genome of the species was assembled and annotated in this study. The circular genome was 160,731 bp in size, presenting a typical quadripartite structure including one large single-copy region (LSC, 90,140 bp), one small single-copy region (SSC, 18,911 bp), and two copies of inverted repeat regions (IRs, 25,840 bp). It encoded a total of 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The maximum-likelihood (ML) phylogenetic tree reconstructed by IQ-TREE indicated that Q. chungii was more closely related to Q. myrsinifolia and Q. sichourensis.

Land bridges in the Pleistocene contributed to flora assembly on the continental islands of South China: Insights from the evolutionary history of Quercus championii.

The South China Mainland (SCM) and its adjacent continental islands are a global biodiversity hotspot. However, how and when plants dispersed between SCM and Hainan/Taiwan Islands remains largely unknown. In this study, we used restriction site-associated DNA sequencing (RAD-seq) to identify the demographic dynamics and local adaptation of Quercus championii, a dominant forests tree distributed in SCM and Hainan/Taiwan Islands. Through phylogenetic reconstruction, principal components analysis (PCA) and structure analysis, we identified four distinct Q. championii lineages that correspond to its geographical distribution. The genetic structure of Hainan Island population was distinct, possibly reflecting an introgression. We conducted an approximate Bayesian computation analyses and found that Q. championii originated from Southwest China-Northern Vietnam, then dispersed to Southeast China as the climate warmed. During the Pleistocene glacial period, land bridges arose between SCM and Hainan/Taiwan Islands, and the land bridges likely facilitated species dispersal from SCM to these islands. We found a strong correlation between genetic variation and isothermality through a gradient forest analysis and identified precipitation seasonality as a key driver to the local adaptation of Q. championii. Finally, we analyzed putative adaptation loci and identified genes regulating vegetative and reproductive organ development as important for the adaptation of Q. championii to heterogeneous environments. We provide new insights into the evolutionary history and local adaptation of biotas in Southern China and adjacent islands.

[Effect of Cr(VI) stress on growth of three herbaceous plants and their Cr uptake].

In order to elucidate the toxic mechanisms of Trifolium repens, Festuca arundinacea and Medicago sativa under chromium [Cr (VI)] stress, provide a theoretic foundation for phytoremediation of Cr-contaminated soil, pot experiment was conducted to investigate the effects of Cr(VI) on plant growth, physiological characteristics, Cr accumulation and distribution in three herbaceous plants. Soil sample was treated by adding K2Cr2O7 with the Cr(VI) concentration of 0, 100, 200, 300 and 400 mg x kg(-1), respectively. The results indicated that the average tolerance indices of T. repens, F. arundinacea and M. sativa were 62.5, 48.3 and 36.33, respectively. Compared with control group, contents of chlorophyll, the activity of superoxide dismutase(SOD) and peroxidase (POD) were 57.14%, 51.51%, 35.76% and 63.27%, 52.96%, 41.36% in T. repens, and F. arundinacea, respectively, but M. sativa died in 400 mg x kg(-1) Cr(VI) treatment. The plant height, root length, dry mass of roots and shoots decreased under Cr(VI) stress in three herbaceous plants, and M. sativa > F. arundinacea > T. repens, however, the content of malonyldialdehyde (MDA) increased compared to the control, and the variation range of M. sativa was the highest, while T. repens was the smallest among them. The tolerance of Cr( VI) was T. repens > F. arundinacea > M. sativa. Cr mainly distributed in cell wall and then in the cytoplasm, and less distributed in the mitochondrion and chloroplast in leaves of three herbaceous plants, whereas the content of chlorophyll, MDA, the activity of SOD and POD correlated well with Cr accumulation in the mitochondrion and chloroplast. Cr concentration in the subcellular of leaves increased with the adding Cr(VI) concentration,and M. sativa > F. arundinacea > T. repens. In comparison with T. repens, F. arundinacea, Cr concentration in the leaves of M. sativa was the maximal, i.e. 51.44 mg x kg(-1), and the proportions in the mitochondrion (18.04%) and chloroplast (19.09%) were also higher in 300 mg x kg(-1) Cr(VI). The average accumulation factors of shoots/roots were 1.22/1.54, 1.16/1.44 and 1.26/1.62, while the average translocation factors were 0.78, 0.78 and 0.74 in T. repens, F. arundinacea and M. sativa, respectively. The results suggest that T. repens and F. arundinacea are promising for the phytoremediation of Cr-contaminated soil.

[Investigation on the integrative course of genetics and genomics].

Genomics is an important subdiscipline of genetics, and it forms a complete research system based on novel theories and techniques. Incorporating genomics in undergraduate curriculum is a response to the need of the development of genetics. The teaching of genomics has significant advantages on developing scientific thinking, enhances bioethics accomplishment, and professional interests in undergraduate students. The integration of genomics into genetics is in accordance with the principles of subject development and education. Related textbooks for undergraduate education are currently available in China, and it is feasible to set up a genetics and genomics integrative course by modifying teaching contents of the genetics course, selecting appropriate teaching approaches, and optimal application of the computer-assisted instruction.