Draft genome of the oriental garden lizard (Calotes versicolor).
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ABSTRACT:
SUBMITTER: Wang Q
PROVIDER: S-EPMC9986473 | biostudies-literature | 2023
REPOSITORIES: biostudies-literature
Publications
Draft genome of the oriental garden lizard (<i>Calotes versicolor</i>).
Wang Qing Q He Fengping F Huang Ru-Yi RY Yang Xueke X Yang Diancheng D Ngatia Jacob Njaramba JN Gong Yanan Y Xu Yanchun Y Huang Song S Liu Hui H
Frontiers in genetics 20230220
Similar Datasets
Project description:The Oriental garden lizard (Calotes versicolor) is one of the few non-gekkonid lizards that are geographically widespread in the tropics. We investigated its population dynamics on Hainan Island and the adjacent mainland of China and Vietnam, focusing on the impact of cyclic upheaval and submergence of land bridges during the Pleistocene. Our Bayesian phylogenetic analysis reveals two mitochondrial lineages, A and B, which are estimated to have coalesced about 0.26 million years ago (95% credibility interval: 0.05-0.61 million years ago). Lineage A contains individuals mainly from central and southern Wuzhi Mountain on Hainan Island, whereas lineage B mainly comprises individuals from other sites on the island plus the adjacent mainland. The estimated coalescence times within lineages A (0.05 million years ago) and B (0.13 million years ago) fall within a period of cyclical land-bridge formation and disappearance in the Pleistocene. A spatial analysis of molecular variance identified two distinct population groupings: I, primarily containing lineage A, and II, mainly consisting of lineage B. However, haplotypes from lineages A and B occur sympatrically, suggesting that gene flow is ongoing. Neither Wuzhi Mountain nor Qiongzhou Strait and Gulf of Tonkin act as barriers to gene flow among C. versicolor populations. Analyses of the data using mismatch distributions and extended Bayesian skyline plots provide evidence of a relatively stable population size through time for Group I, and moderate population expansions and contractions during the end of the Pleistocene for Group II. We conclude that the phylogeographical patterns of C. versicolor are the combined product of Pleistocene sea-level oscillations and nonphysical barriers to gene flow.
| S-EPMC3694074 | biostudies-literature
Project description:Patterns of geographic variation in body size are predicted to evolve as adaptations to local environmental gradients. However, many of these clinal patterns in body size, such as Bergmann's rule, are controversial and require further investigation into ectotherms such as reptiles on a regional scale. To examine the environmental variables (temperature, precipitation, topography and primary productivity) that shaped patterns of geographic variation in body size in the reptile Calotes versicolor, we sampled 180 adult specimens (91 males and 89 females) at 40 locations across the species range in China. The MANOVA results suggest significant sexual size dimorphism in C. versicolor (F23,124 = 11.32, p < .001). Our results showed that C. versicolor failed to fit the Bergmann's rule. We found that the most important predictors of variation in body size of C. versicolor differed for males and females, but mechanisms related to heat balance and water availability hypotheses were involved in both sexes. Temperature seasonality, precipitation of the driest month, precipitation seasonality, and precipitation of the driest quarter were the most important predictors of variation in body size in males, whereas mean precipitation of the warmest quarter, mean temperature of the wettest quarter, precipitation seasonality, and precipitation of the wettest month were most important for body size variation in females. The discrepancy between patterns of association between the sexes suggested that different selection pressures may be acting in males and females.
| S-EPMC5938448 | biostudies-literature
Project description:Vertebrates maintain complex symbiotic relationships with microbiota living within their gastrointestinal tracts which reflects the ecological and evolutionary relationship between hosts and their gut microbiota. However, this understanding is limited in lizards and the spatial heterogeneity and co-occurrence patterns of gut microbiota inside the gastrointestinal tracts of a host and variations of microbial community among samples remain poorly understood. To address this issue and provide a guide for gut microbiota sampling from lizards, we investigated the bacteria in three gut locations of the oriental garden lizard (Calotes versicolor) and the data were analyzed for bacterial composition by 16S ribosomal RNA (16S rRNA) gene amplicon sequencing. We found the relative abundance of the dominant phyla exhibited an increasing trend from the small intestine to the large intestine, and phyla Firmicutes, Bacteroidetes and Proteobacteria were the three primary phyla in the gut microbiota of C. versicolor. There were a higher abundance of genus Bacteroides (Class: Bacteroidia), Coprobacillus and Eubacterium (Class: Erysipelotrichia), Parabacteroides (Family: Porphyromonadaceae) and Ruminococcus (Family: Lachnospiraceae), and Family Odoribacteraceae and Rikenellaceae in the sample from the hindgut. The secondary bile acid biosynthesis, glycosaminoglycan degradation, sphingolipid metabolism and lysosome were significantly higher in the hindgut than that in the small intestine. Taken together our results indicate variations of gut microbiota composition and metabolic pathway in different parts of the oriental garden lizard.
| S-EPMC8388656 | biostudies-literature
Project description:SbfI RAD-tag Sequencing of Calotes versicolor
| PRJNA408283 | ENA
Project description:BackgroundTransition from a lizard-like to a snake-like body form is one of the most important transformations in reptilian evolution. The increasing number of sequenced reptilian genomes is enabling a deeper understanding of vertebrate evolution, although the genetic basis of the loss of limbs in reptiles remains enigmatic. Here we report genome sequencing, assembly, and annotation for the Asian glass lizard Ophisaurus gracilis, a limbless lizard species with an elongated snake-like body form. Addition of this species to the genome repository will provide an excellent resource for studying the genetic basis of limb loss and trunk elongation.FindingsO. gracilis genome sequencing using the Illumina HiSeq2000 platform resulted in 274.20 Gbp of raw data that was filtered and assembled to a final size of 1.78 Gbp, comprising 6,717 scaffolds with N50 = 1.27 Mbp. Based on the k-mer estimated genome size of 1.71 Gbp, the assembly appears to be nearly 100% complete. A total of 19,513 protein-coding genes were predicted, and 884.06 Mbp of repeat sequences (approximately half of the genome) were annotated. The draft genome of O. gracilis has similar characteristics to both lizard and snake genomes.ConclusionsWe report the first genome of a lizard from the family Anguidae, O. gracilis. This supplements currently available genetic and genomic resources for amniote vertebrates, representing a major increase in comparative genome data available for squamate reptiles in particular.
| S-EPMC4391233 | biostudies-literature
Project description:Calotes versicolor isolate:BHU-M1 Genome sequencing and assembly
| PRJNA408142 | ENA
Project description:The whole mitogenome can prove useful tools for phylogenetic reconstruction and efficiently recover with reasonable taxon sampling. Calotes emma is widely distributed and arboreal in habits. However, studies of C. emma are still very limited, including population genetics and evolutionary biology. In this study, we reported the complete mitochondrial genome of the C. emma by next-generation sequencing for future more researches on systematics and evolution of C. emma from the perspective of mitochondrial DNA. The length of mitogenome was 17,688 bp, including 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 tRNA genes and a control region. The phylogenetic tree recovered the monophyly of the Calotes and revealed that newly sequenced C. emma well supported as the sister taxon to C. mystaceus by very high posterior probabilities (1.0). The complete mitochondrial genome of C.emma in this study will be helpful for understanding the phylogenetic systematics and relationships, and molecular evolution of Calotes in Agamidae.
| S-EPMC8725836 | biostudies-literature
Project description:Oriental melon (Cucumis melo L. var. makuwa) is one of the most important cultivated cucurbits, and is grown widely in Northeast Asian countries. With increasing interest in its biological properties and economic importance, oriental melon has become an attractive model crop for studying various horticultural traits. A previous genome sequence of the melon was constructed from a homozygous double-haploid line. Thus, individual reference genomes are required to perform functional studies and further breeding applications. Here, we report draft genome sequences of two oriental melons, Chang Bougi and SW3. The assembled 344 Mb genome of Chang Bougi was obtained with scaffold N50 1.0 Mb, and 36,235 genes were annotated. The 354 Mb genome of SW3 was assembled with scaffold N50 1.6 Mb, and has 38,173 genes. These newly constructed genomes will enable studies of fruit development, disease resistance, and breeding applications in the oriental melon.
| S-EPMC6805853 | biostudies-literature
Project description:1. The egg-shell of the oriental garden cricket, Gryllus mitratus, contained at least two different types of structural protein in an approximate ratio of 5:1. The major fraction was extracted in a solvent containing dithiothreitol, EDTA and 8m-urea, and was purified to apparent homogeneity as judged by free-boundary electrophoresis and ultracentrifugation. This was designated SH-fraction and its S-carboxymethyl derivative (CM-fraction) was also prepared. The minor fraction, insoluble in the solvent, was designated insoluble residue. 2. The major fraction was a phosphoprotein, rich in serine (29.8mol% of the total amino acids) and phosphate (nearly equimolar to serine), and O-phosphoserine was identified in its partial acid hydrolysate. The content of cystine was rather low (0.9mol%) in spite of the importance of this amino acid residue in the native form of the protein. The insoluble residue contained only a small amount of phosphorus, and its amino acid composition was clearly different from the major fraction. 3. CM-fraction, a fibrous protein with an average molecular weight of 57500, behaved as a typical polyanion owing to the high content of phosphate. SH-fraction and CM-fraction were precipitable from their aqueous solutions by the addition of bivalent metal cations, and the precipitation of CM-fraction by Ca(2+) and Mg(2+) was studied in detail. 4. When SH-fraction was exposed to air, intermolecular disulphide linkages were formed, yielding a net-like gel that changed its volume with changes in Ca(2+), Mg(2+) and Na(+). 5. The possible role of this protein fraction in maintaining the integrity of the egg-shell, and a comparison of its composition and properties with other egg-shell proteins and other phosphoproteins, are discussed.
| S-EPMC1178084 | biostudies-other