Phylogenomic analyses shed new light on the spatiotemporal evolution of global larches: Implications for the dynamics of boreal forests.

As the Earth warms, understanding the long-term dynamics of forest ecosystems is essential for guiding forest management and biodiversity conservation. Insights from past dynamics may provide valuable lessons for managing today's forests. Here, we investigated the spatiotemporal evolution of global larches to gain further insights into how boreal forests change over time.

Phylotranscriptomic and ecological analyses reveal the evolution and morphological adaptation of Abies.

Coniferous forests are under severe threat of the rapid anthropogenic climate warming. Abies (firs), the fourth-largest conifer genus, is a keystone component of the boreal and temperate dark-coniferous forests and harbors a remarkably large number of relict taxa. However, the uncertainty of the phylogenetic and biogeographic history of Abies significantly impedes our prediction of future dynamics and efficient conservation of firs.

Tracing the geographic origin of endangered plant species using transcriptome-derived SNPs: An example of Cathaya argyrophylla.

Genetic markers have emerged as one of the most promising tools for species identification and geographic traceability in biodiversity conservation and international trade of biological products. However, traditional molecular markers rarely have sufficient resolution at lower taxonomic levels, especially for discriminating closely related forest tree species and their populations. In this study, we developed a panel of RNA-Seq based single nucleotide polymorphism (SNP) markers for tracing the geographic origin of an endangered conifer, Cathaya argyrophylla, which is a paleoendemic restricted to four mountain regions in subtropical China.

Phylotranscriptomics reveals the evolutionary history of subtropical East Asian white pines: further insights into gymnosperm diversification.

Floristic composition within a geographic area is driven by a wide array of factors from local biotic interactions to biogeographical processes. Subtropical East Asia is a key biodiversity hotspot of the world, and harbors the most families of extant gymnosperms and a large number of endemic genera with ancient origins, but rare phylogenetic studies explored whether it served as a diversification center for gymnosperms. Here, we investigated the evolutionary and biogeographical history of subtropical East Asian white pines using an integrative approach that combines phylotranscriptomic and ecological analyses.

Phylogenomic and ecological analyses reveal the spatiotemporal evolution of global pines.

How coniferous forests evolved in the Northern Hemisphere remains largely unknown. Unlike most groups of organisms that generally follow a latitudinal diversity gradient, most conifer species in the Northern Hemisphere are distributed in mountainous areas at middle latitudes. It is of great interest to know whether the midlatitude region has been an evolutionary cradle or museum for conifers and how evolutionary and ecological factors have driven their spatiotemporal evolution.

Cryptic speciation in the Chinese white pine (Pinus armandii): Implications for the high species diversity of conifers in the Hengduan Mountains, a global biodiversity hotspot.

Conifers are the largest and ecologically and economically most important component group of the gymnosperms. Despite their slow rate of molecular evolution, rapid and recent diversification was unexpectedly prevalent in this ancient group in the Hengduan Mountains, a world's biodiversity hotspot and gymnosperm diversity center in Southwest China. In this study, we investigated the underlying mechanisms and disentangled the interactions of geography and ecology in speciation and evolution in Pinus armandii, an important forest tree species endemic to China, by integrating analyses of population transcriptomics, population genetics and ecological niche modeling.

Long-distance dispersal or postglacial contraction? Insights into disjunction between Himalaya-Hengduan Mountains and Taiwan in a cold-adapted herbaceous genus, .

Current disjunct patterns can result from long-distance dispersal or postglacial contraction. We herein investigate the evolutionary history of to elucidate the disjunction between the Himalaya-Hengduan Mountain region (HHM) and Taiwan (TW). Genetic structure of was investigated for 48 populations using sequences from five chloroplast loci and the ribosomal nuclear internal transcribed spacer.

Novel Insights into Tree Biology and Genome Evolution as Revealed Through Genomics.

Reference genome sequences are the key to the discovery of genes and gene families that determine traits of interest. Recent progress in sequencing technologies has enabled a rapid increase in genome sequencing of tree species, allowing the dissection of complex characters of economic importance, such as fruit and wood quality and resistance to biotic and abiotic stresses. Although the number of reference genome sequences for trees lags behind those for other plant species, it is not too early to gain insight into the unique features that distinguish trees from nontree plants.

Revisiting the phosphatidylethanolamine-binding protein (PEBP) gene family reveals cryptic FLOWERING LOCUS T gene homologs in gymnosperms and sheds new light on functional evolution.

Angiosperms and gymnosperms are two major groups of extant seed plants. It has been suggested that gymnosperms lack FLOWERING LOCUS T (FT), a key integrator at the core of flowering pathways in angiosperms. Taking advantage of newly released gymnosperm genomes, we revisited the evolutionary history of the plant phosphatidylethanolamine-binding protein (PEBP) gene family through phylogenetic reconstruction.

Phylogeography of Pinus armandii and its relatives: heterogeneous contributions of geography and climate changes to the genetic differentiation and diversification of Chinese white pines.

Geographic barriers and Quaternary climate changes are two major forces driving the evolution, speciation, and genetic structuring of extant organisms. In this study, we used Pinus armandii and eleven other Asian white pines (subsection Strobus, subgenus Pinus) to explore the influences of geographic factors and Pleistocene climatic oscillations on species in South China, a region known to be centers of plant endemism and biodiversity hotspots. Range-wide patterns of genetic variation were investigated using chloroplast and mitochondrial DNA markers, with extensive sampling throughout the entire range of P.

Molecular phylogeny and biogeography of Pseudotsuga (Pinaceae): insights into the floristic relationship between Taiwan and its adjacent areas.

Climatic oscillations and geological events play major roles in shaping species diversity and the distribution of plants. The mechanisms underlying the high level of plant species diversity in eastern Asia are hotly debated. In this study, five cpDNA regions, two mtDNA fragments and one nuclear gene (LEAFY) were employed to investigate species diversification and the historical biogeography of Pseudotsuga (Pinaceae), a genus with a typical eastern Asia and western North America disjunct distribution.

Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae).

The mitochondrial genomes of seed plants are unusually large and vary in size by at least an order of magnitude. Much of this variation occurs within a single family, the Cucurbitaceae, whose genomes range from an estimated 390 to 2,900 kb in size. We sequenced the mitochondrial genomes of Citrullus lanatus (watermelon: 379,236 nt) and Cucurbita pepo (zucchini: 982,833 nt)--the two smallest characterized cucurbit mitochondrial genomes--and determined their RNA editing content.

Molecular phylogeny and biogeography of Picea (Pinaceae): implications for phylogeographical studies using cytoplasmic haplotypes.

The center of diversity is not necessarily the place of origin, as has been established by many plant molecular phylogenies. Picea is a complicated but very important genus in coniferous forests of the Northern Hemisphere, with a high species diversity in Asia. Its phylogeny and biogeography were investigated here using sequence analysis of the paternally inherited chloroplast trnC-trnD and trnT-trnF regions and the maternally inherited mitochondrial nad5 intron 1.

Recolonization and radiation in Larix (Pinaceae): evidence from nuclear ribosomal DNA paralogues.

Gene paralogy frequently causes the conflict between gene tree and species tree, but sometimes the coexistence of a few paralogous copies could provide more markers for tracing the phylogeographical process of some organisms. In the present study, nrDNA ITS paralogues were cloned from all but one species of Larix, an Eocene genus having two sections, Larix and Multiserialis, with a huge circumboreal distribution and an Eastern Asia-Western North America disjunction, respectively. A total of 96 distinct clones, excluding five putative pseudogenes or recombinants, were obtained and used in the gene genealogy analysis.

Evolution of 4-coumarate:coenzyme A ligase (4CL) gene and divergence of Larix (Pinaceae).

The evolutionary dynamics of the 4CL gene encoding 4-coumarate:coenzyme A ligase was investigated in the genus Larix (Pinaceae) by comparing copy number, GC content and codon usage, sequence divergence, and phylogenetic analysis. All 4CL clones of Larix formed a strongly supported monophyletic group, in which two robust clades (4clA and 4clB) derived from an ancient gene duplication event in the common ancestor of Larix were identified. Further gene duplication in the 4clA clade gave rise to two subclades 4clA(1) and 4clA(2).

Marked intragenomic heterogeneity and geographical differentiation of nrDNA ITS in Larix potaninii (Pinaceae).

Nuclear ribosomal DNA (nrDNA) of gymnosperms, especially Pinaceae, is characterized by slow concerted evolution and exhibits substantial ITS-region length variation (975-3663 bp), in sharp contrast to the narrow range (565-700 bp) in angiosperms. Here we examined intra- and intergenomic heterogeneity of the nrDNA internal transcribed spacer (ITS) region in four varieties of Larix potaninii, a species from the mountainous areas of western China. Two clones with more than a 100-bp deletion in ITS1 were detected in L.