Genome-wide characterization of the TGF-ß gene family and their expression in different tissues during tail regeneration in the Schlegel's Japanese gecko Gekko japonicus.

The transforming growth factor-ß (TGF-ß) gene family is unique to animals and is involved in various important processes including tissue regeneration. Here, we identified 52 TGF-ß family genes based on genome sequences of the gecko (Gekko japonicus), compared TGF-ß genes between G. japonicus and other four reptilian species, and evaluated the expression of 14 randomly selected genes in muscle, kidney, liver, heart, and brain during tail regeneration to investigate whether their expression was tissue-dependent. We detected 23 conserved domains, 13 in the TGF-ß ligand subfamily, and 10 in the receptor subfamily. The pattern of higher genetic variation in the ligand subfamily than in the receptor subfamily in vertebrates might result from the precise localization of agonists and antagonists in the cell surface and intracellular compartment. TGF-ß genes were unevenly distributed across 15 chromosomes in G. japonicus, presumably resulting from gene losses and gains during evolution. Genes in the TGF-ß receptor subfamily (ACVR2A, ACVR2B, ACVR1, BMPR1A, ACVRL1, BMPR2 and TGFBR1) played a vital role in the TGF-ß signal pathway. The expression of all 14 randomly selected TGF-ß genes was tissue-specific. Our study supports the speculation that some TGF-ß family genes are involved in the early stages of tail regeneration.

Genomic insights into local adaptation in the Asiatic toad Bufo gargarizans, and its genomic offset to climate warming.

Genomic signatures of local adaptation have been identified in many species but remain sparsely studied in amphibians. Here, we explored genome-wide divergence within the Asiatic toad, Bufo gargarizans, to study local adaptation and genomic offset (i.e., the mismatch between current and future genotype-environment relationships) under climate warming scenarios. We obtained high-quality SNP data for 94 Asiatic toads from 21 populations in China to study spatial patterns of genomic variation, local adaptation, and genomic offset to warming in this wide-ranging species. Population structure and genetic diversity analysis based on high-quality SNPs revealed three clusters of B. gargarizans in the western, central-eastern, and northeastern portions of the species' range in China. Populations generally dispersed along two migration routes, one from the west to the central-east and one from the central-east to the northeast. Both genetic diversity and pairwise F ST were climatically correlated, and pairwise F ST was also correlated with geographic distance. Spatial genomic patterns in B. gargarizans were determined by the local environment and geographic distance. Global warming will increase the extirpation risk of B. gargarizans.

Gut microbiota differs between two cold-climate lizards distributed in thermally different regions.

BACKGROUND: The metabolic cold-climate adaption hypothesis predicts that animals from cold environments have relatively high metabolic rates compared with their warm-climate counterparts. However, studies testing this hypothesis are sparse. Here, we compared gut microbes between two cold-climate lizard species of the genus Phrynocephalus to see if gut microbiota could help lizards adapt to cold environments by promoting metabolism. We conducted a 2 species (P. erythrurus and P. przewalskii) × 2 temperatures (24 and 30 °C) factorial design experiment, whereby we kept lizards of two Phrynocephalus species at 24 and 30 °C for 25 d and then collected their fecal samples to analyze and compare the microbiota based on 16S rRNA gene sequencing technology. RESULTS: The gut microbiota was mainly composed of bacteria of the phyla Proteobacteria, Firmicutes, Bacteroidetes, and Verrucomicrobia in both species (Proteobacteria > Firmicutes > Verrucomicrobiota in P. erythrurus, and Bacteroidetes > Proteobacteria > Firmicutes in P. przewalskii). Further analysis revealed that the gut microbiota promoted thermal adaptation in both lizard species, but with differences in the relative abundance of the contributory bacteria between the two species. An analysis based on the Kyoto Encyclopedia of Genes and Genomes revealed that the gut microbiota played important roles in metabolism, genetic information processing, cellular processes, and environmental information processing in both species. Furthermore, genes related to metabolism were more abundant in P. erythrurus at 24 °C than in other species ⋅ temperature combinations. CONCLUSION: Our study provides evidence that gut microbiota promotes thermal adaptation in both species but more evidently in P. erythrurus using colder habitats than P. przewalskii all year round, thus confirming the role of gut microbiota in cold-climate adaptation in lizards.

Loss and Natural Variations of Blast Fungal Avirulence Genes Breakdown Rice Resistance Genes in the Sichuan Basin of China.

Magnaporthe oryzae is the causative agent of rice blast, a devastating disease in rice worldwide. Based on the gene-for-gene paradigm, resistance (R) proteins can recognize their cognate avirulence (AVR) effectors to activate effector-triggered immunity. AVR genes have been demonstrated to evolve rapidly, leading to breakdown of the cognate resistance genes. Therefore, understanding the variation of AVR genes is essential to the deployment of resistant cultivars harboring the cognate R genes. In this study, we analyzed the nucleotide sequence polymorphisms of eight known AVR genes, namely, AVR-Pita1, AVR-Pii, AVR-Pia, AVR-Pik, AVR-Pizt, AVR-Pi9, AVR-Pib, and AVR-Pi54 in a total of 383 isolates from 13 prefectures in the Sichuan Basin. We detected the presence of AVR-Pik, AVR-Pi54, AVR-Pizt, AVR-Pi9, and AVR-Pib in the isolates of all the prefectures, but not AVR-Pita1, AVR-Pii, and AVR-Pia in at least seven prefectures, indicating loss of the three AVRs. We also detected insertions of Pot3, Mg-SINE, and indels in AVR-Pib, solo-LTR of Inago2 in AVR-Pizt, and gene duplications in AVR-Pik. Consistently, the isolates that did not harboring AVR-Pia were virulent to IRBLa-A, the monogenic line containing Pia, and the isolates with variants of AVR-Pib and AVR-Pizt were virulent to IRBLb-B and IRBLzt-t, the monogenic lines harboring Pib and Piz-t, respectively, indicating breakdown of resistance by the loss and variations of the avirulence genes. Therefore, the use of blast resistance genes should be alarmed by the loss and nature variations of avirulence genes in the blast fungal population in the Sichuan Basin.