The complete chloroplast genome sequence of leibnitzia anandria (linnaeus) turczaninow.

Leibnitzia anandria is a perennial herbaceous plant with medicinal properties, and the entire plant can be used in traditional medicine. Leibnitzia anandria was once classified under the genus Gerbera Cass., but was reclassified under Leibnitzia Cass. recently. In this study, using the GeneLab M sequencing technology of the Genemind platform, we have sequenced, assembled, and analyzed the complete chloroplast genome of Leibnitzia anandria for the first time. The genome is 154168 bp in length, consisting of a large single-copy region(LSC, 80166 bp), a small single-copy region(SSC, 18202 bp), and a pair of inverted repeat sequences(IR, 27900 bp). We have predicted and annotated a total of 133 genes, including 88 protein-coding genes, 37 tRNA-coding genes, and 8 rRNA-coding genes. The results of the phylogenetic analysis indicate that Leibnitzia anandria and Leibnitzia nepalensis, as well as the closely related Gerbera plant, clustered into a separate clade, rather than grouping together with the other plants belonging to the tribe Mutisieae. This study provides new information for the phylogeny research of Leibnitzia anandria, contributing to a better understanding of its taxonomy and evolution.

Molecular cloning and evolutionary analysis of GJB6 in mammals.

GJB6 plays a crucial role in hearing. In mammals, bats use ultrasonic echolocation for orientation and locating prey. To investigate the evolution of GJB6 in mammals, we cloned the full-length coding region of GJB6 from 16 species of bats and 4 other mammal species and compared them with orthologous sequences in 11 other mammals. The results show purifying selection on GJB6 in mammals, as well as in the bat lineage, which indicates an important role for GJB6 in mammal hearing. We also found one unique amino acid substitution shared by 16 species of bats and 10 shared by two species of artiodactyls. This positioned the artiodactyls at an abnormal location in the gene tree. In addition, the cytoplasmic loop and carboxy terminus were more variable than other domains in all the mammals. These results demonstrate that GJB6 is basically conserved in mammals but has undergone relatively rapid evolution in particular lineages and domains.

Digital gene expression tag profiling of bat digits provides robust candidates contributing to wing formation.

BACKGROUND: As the only truly flying mammals, bats use their unique wing - consisting of four elongated digits (digits II-V) connected by membranes - to power their flight. In addition to the elongated digits II-V, the forelimb contains one shorter digit (digit I) that is morphologically similar to the hindlimb digits. Here, we capitalized on the morphological variation among the bat forelimb digits to investigate the molecular mechanisms underlying digit elongation and wing formation. Using next generation sequencing technology, we performed digital gene expression tag profiling (DGE-tag profiling) of developing digits in a pooled sample of two Myotis ricketti and validated our sequencing results using real-time quantitative PCR (RT-qPCR) of gene expression in the developing digits of two Hipposideros armiger. RESULTS: Among hundreds of genes exhibiting significant differences in expression between the short and long digits, we highlight 14 genes most related to digit elongation. These genes include two Tbx genes (Tbx3 and Tbx15), five BMP pathway genes (Bmp3, RGMB, Smad1, Smad4 and Nog), four Homeobox genes (Hoxd8, Hoxd9, Hoxa1 and Satb1), and three other genes (Twist1, Tmeff2 and Enpp2) related to digit malformations or cell proliferation. In addition, our results suggest that Tbx4 and Pitx2 contribute to the morphological similarity and five genes (Acta1, Tnnc2, Atp2a1, Hrc and Myoz1) contribute to the functional similarity between the thumb and hindlimb digits. CONCLUSIONS: Results of this study not only implicate many developmental genes as robust candidates underlying digit elongation and wing formation in bats, but also provide a better understanding of the genes involved in autopodial development in general.

A comparative study of prenatal development in Miniopterus schreibersii fuliginosus, Hipposideros armiger and H. pratti.

BACKGROUND: Bats comprise the second largest order of mammals. However, there are far fewer morphological studies of post-implantation embryonic development than early embryonic development in bats. RESULTS: We studied three species of bats (Miniopterus schreibersii fuliginosus, Hipposideros armiger and H. pratti), representing the two suborders Yangochiroptera and Yinpterochiroptera. Using an established embryonic staging system, we identified the embryonic stages for M. schreibersii fuliginosus, H. armiger and H. pratti and described the morphological changes in each species, including the development of the complex and distinctive nose-leaves in H. armiger and H. pratti. Finally, we compared embryonic and fetal morphology of the three species in the present study with five other species for which information is available. CONCLUSION: As a whole, the organogenetic sequence of bat embryos is uniform and the embryos appear homoplastic before Stage 16. Morphological differentiation between species occurs mainly after embryonic Stage 16. Our study provides three new bat species for interspecific comparison of post-implantation embryonic development within the order Chiroptera and detailed data on the development of nose-leaves for bats in the superfamily Rhinolophoidea.

Rhodopsin molecular evolution in mammals inhabiting low light environments.

The ecological radiation of mammals to inhabit a variety of light environments is largely attributed to adaptive changes in their visual systems. Visual capabilities are conferred by anatomical features of the eyes as well as the combination and properties of their constituent light sensitive pigments. To test whether evolutionary switches to different niches characterized by dim-light conditions coincided with molecular adaptation of the rod pigment rhodopsin, we sequenced the rhodopsin gene in twenty-two mammals including several bats and subterranean mole-rats. We compared these to thirty-seven published mammal rhodopsin sequences, from species with divergent visual ecologies, including nocturnal, diurnal and aquatic groups. All taxa possessed an intact functional rhodopsin; however, phylogenetic tree reconstruction recovered a gene tree in which rodents were not monophyletic, and also in which echolocating bats formed a monophyletic group. These conflicts with the species tree appear to stem from accelerated evolution in these groups, both of which inhabit low light environments. Selection tests confirmed divergent selection pressures in the clades of subterranean rodents and bats, as well as in marine mammals that live in turbid conditions. We also found evidence of divergent selection pressures among groups of bats with different sensory modalities based on vision and echolocation. Sliding window analyses suggest most changes occur in transmembrane domains, particularly obvious within the pinnipeds; however, we found no obvious pattern between photopic niche and predicted spectral sensitivity based on known critical amino acids. This study indicates that the independent evolution of rhodopsin vision in ecologically specialised groups of mammals has involved molecular evolution at the sequence level, though such changes might not mediate spectral sensitivity directly.

Adaptive evolution of 5'HoxD genes in the origin and diversification of the cetacean flipper.

The homeobox (Hox) genes Hoxd12 and Hoxd13 control digit patterning and limb formation in tetrapods. Both show strong expression in the limb bud during embryonic development, are highly conserved across vertebrates, and show mutations that are associated with carpal, metacarpal, and phalangeal deformities. The most dramatic evolutionary reorganization of the mammalian limb has occurred in cetaceans (whales, dolphins, and porpoises), in which the hind limbs have been lost and the forelimbs have evolved into paddle-shaped flippers. We reconstructed the phylogeny of digit patterning in mammals and inferred that digit number has changed twice in the evolution of the cetacean forelimb. First, the divergence of the early cetaceans from their even-toed relatives coincided with the reacquisition of the pentadactyl forelimb, whereas the ancestors of tetradactyl baleen whales (Mysticeti) later lost a digit again. To test whether the evolution of the cetacean forelimb is associated with positive selection or relaxation of Hoxd12 and Hoxd13, we sequenced these genes in a wide range of mammals. In Hoxd12, we found evidence of Darwinian selection associated with both episodes of cetacean forelimb reorganization. In Hoxd13, we found a novel expansion of a polyalanine tract in cetaceans compared with other mammals (17/18 residues vs. 14/15 residues, respectively), lengthening of which has previously been shown to be linked to synpolydactyly in humans and mice. Both genes also show much greater sequence variation among cetaceans than across other mammalian lineages. Our results strongly implicate 5'HoxD genes in the modulation of digit number, web forming, and the high morphological diversity of the cetacean manus.