Ancient allopatry and ecological divergence act together to promote plant diversity in mountainous regions: evidence from comparative phylogeography of two genera in the Sino-Himalayan region.

BACKGROUND: How geographical isolation and ecological divergence act together to promote plant diversity in mountainous regions remains largely unknown. In this study, we chose two genera comprising a small number of species distributed in the Sino-Himalayan region, Megacodon (Gentianaceae) and Beesia (Ranunculaceae), which both exhibit a fragmented distribution pattern and are found across a wide range of elevations. By summarizing their common patterns of speciation and/or divergence processes, we aim to understand how environmental changes accelerated lineage diversification in the Sino-Himalayan region through ancient allopatry and ecological divergence. RESULTS: Using ddRAD-seq, chloroplast genome sequences, and specific molecular markers, we studied the phylogenetic relationships, population structure, and historical biogeography of Beesia and Megacodon. Both genera began to diverge from the late Miocene onwards, with ancient allopatry at lower elevations formed narrow-range species or relict populations. Mantel tests between genetic distance and climatic, elevational, or geographic distance revealed an isolation-by-distance pattern in Beesia and Megacodon stylophorus. Megacodon showed two clades occupying entirely different altitudinal ranges, whereas Beesia calthifolia exhibited a genetic divergence pattern along an elevation gradient. Furthermore, we conducted morphological measurements on Beesia calthifolia and found that different elevational groups had distinct leaf shapes. CONCLUSIONS: The regional disjunctions of plant groups in the Sino-Himalayan region are drastic and closely related to several biogeographic boundaries. As a consequence of major geological and climate change, ecological divergence when different elevations are colonized often happens simultaneously within plant groups. Although habitat fragmentation and parapatric ecological divergence each spur speciation to different extents, a combined effect of these two factors is a common phenomenon in the Sino-Himalayan region.

Rapid Genome Evolution and Adaptation of Thlaspi arvense Mediated by Recurrent RNA-Based and Tandem Gene Duplications.

Retrotransposons are the most abundant group of transposable elements (TEs) in plants, providing an extraordinarily versatile source of genetic variation. Thlaspi arvense, a close relative of the model plant Arabidopsis thaliana with worldwide distribution, thrives from sea level to above 4,000 m elevation in the Qinghai-Tibet Plateau (QTP), China. Its strong adaptability renders it an ideal model system for studying plant adaptation in extreme environments. However, how the retrotransposons affect the T. arvense genome evolution and adaptation is largely unknown. We report a high-quality chromosome-scale genome assembly of T. arvense with a scaffold N50 of 59.10 Mb. Long terminal repeat retrotransposons (LTR-RTs) account for 56.94% of the genome assembly, and the Gypsy superfamily is the most abundant TEs. The amplification of LTR-RTs in the last six million years primarily contributed to the genome size expansion in T. arvense. We identified 351 retrogenes and 303 genes flanked by LTRs, respectively. A comparative analysis showed that orthogroups containing those retrogenes and genes flanked by LTRs have a higher percentage of significantly expanded orthogroups (SEOs), and these SEOs possess more recent tandem duplicated genes. All present results indicate that RNA-based gene duplication (retroduplication) accelerated the subsequent tandem duplication of homologous genes resulting in family expansions, and these expanded gene families were implicated in plant growth, development, and stress responses, which were one of the pivotal factors for T. arvense's adaptation to the harsh environment in the QTP regions. In conclusion, the high-quality assembly of the T. arvense genome provides insights into the retroduplication mediated mechanism of plant adaptation to extreme environments.

New insights into the evolutionary history of Megacodon: Evidence from a newly discovered species.

Megacodon is an ideal genus to study speciation and ecological adaptation in the Sino-Himalayan region. The genus contains two species distributed at different elevations and in two separate areas. However, studies of this genus have long been impeded by a lack of fieldwork on one of its species, Megacodon venosus. In this study, we collected specimens of two Megacodon species and found an extraordinary new species of Megacodon in Lushui county of north-west Yunnan province, which we have since named Megacodon lushuiensis. We propose new species based on both morphological and molecular evidence. The finding of this new species emphasized the importance of ecological divergence in the divergence of Megacodon stylophorus and its parapatric low-elevation Megacodon species. To identify genetic determinants that underlie adaptations to different elevations, we characterized transcriptomes of the new species M. lushuiensis, which is distributed at low elevations, and M. stylophorus, which is distributed at high elevations. Comparative transcriptome analysis identified 8926 orthogroups containing single-copy genes, and 370 orthogroups containing significantly positively selected genes. The set of positively selected genes was enriched into 25 Gene Ontology terms, including "response to water deprivation", "response to osmotic stress", and "cellular response to external stimulus". Our results provide new insights into how ecological adaptation and speciation occurred in Megacodon and highlight the role of heterogeneous habitats in the speciation of plants in the Sino-Himalayan region.

Functional Conservation and Divergence of Soybean GmSTOP1 Members in Proton and Aluminum Tolerance.

Proton (H+) and aluminum (Al) rhizotoxicity are two major factors limiting crop production in acid soils. Orthologs of the zinc-finger transcription factor, Sensitive To Proton Rhizotoxicity1 (STOP1), have been found to play an essential role in the tolerance to both stresses by regulating the transcription of multiple H+ and Al tolerant genes. In the present study, color three GmSTOP1 homologs were identified in the soybean genome. All three GmSTOP1 exhibited similar properties as reflected by the harboring of four potential zinc finger domains, localizing in the nucleus, and having transactivation activity. Expression profiling showed that H+ stress slightly modulated transcription of all three GmSTOP1s, while Al significantly up-regulated GmSTOP1-1 and GmSTOP1-3 in root apexes and GmSTOP1-3 in basal root regions. Furthermore, complementation assays in an Arabidopsis Atstop1 mutant line overexpressing these GmSTOP1s demonstrated that all three GmSTOP1s largely reverse the H+ sensitivity of the Atstop1 mutant and restore the expression of genes involved in H+ tolerance. In contrast, only GmSTOP1-1 and GmSTOP1-3 could partially recover Al tolerance in the Atstop1 mutant. These results suggest that the function of three GmSTOP1s is evolutionarily conserved in H+ tolerance, but not in Al tolerance.

Characterization of the soybean GmALMT family genes and the function of GmALMT5 in response to phosphate starvation.

A potential mechanism to enhance utilization of sparingly soluble forms of phosphorus (P) is the root secretion of malate, which is mainly mediated by the ALMT gene family in plants. In this study, a total of 34 GmALMT genes were identified in the soybean genome. Expression patterns diverged considerably among GmALMTs in response to phosphate (Pi) starvation in leaves, roots and flowers, with expression altered by P availability in 26 of the 34 GmALMTs. One root-specific GmALMT whose expression was significantly enhanced by Pi-starvation, GmALMT5, was studied in more detail to determine its possible role in soybean P nutrition. Analysis of GmALMT5 tissue expression patterns, subcellular localization, and malate exudation from transgenic soybean hairy roots overexpressing GmALMT5, demonstrated that GmALMT5 is a plasma membrane protein that mediates malate efflux from roots. Furthermore, both growth and P content of transgenic Arabidopsis overexpressing GmALMT5 were significantly increased when sparingly soluble Ca-P was used as the external P source. Taken together, these results indicate that members of the soybean GmALMT gene family exhibit diverse responses to Pi starvation. One member of this family, GmALMT5, might contribute to soybean P efficiency by enhancing utilization of sparingly soluble P sources under P limited conditions.