Spatio-temporal expression patterns of glycine-rich beta proteins and cysteine-rich beta proteins in setae development of Gekko japonicus.

BACKGROUND: Setae on the pad lamellae of the Japanese gecko Gekko japonicus (Schlegel, 1836), a vital epidermal derivative, are primarily composed of cornified beta-proteins (CBPs) and play a pivotal role in adhesion and climbing. The amino acid composition of CBPs might be a determining factor influencing their functional properties. However, the molecular mechanisms governed by CBP genes with diverse amino acid compositions in setae development remain unexplored. RESULTS: Based on RNA-seq analyses, this study confirmed that all G. japonicus CBPs (GjCBPs) are involved in setae formation. Cysteine-rich CBPs encoding genes (ge-cprp-17 to ge-cprp-26) and glycine-rich CBPs encoding genes (ge-gprp-17 to ge-gprp-22) were haphazardly selected, with quantitative real-time PCR revealing their expression patterns in embryonic pad lamellae and dorsal epidermis. It is inferred that glycine-rich CBPs are integral to the formation of both dorsal scales and lamellar setae, cysteine-rich CBPs are primarily associated with setae development. Additionally, fluorescence in situ hybridization revealed spatiotemporal differences in the expression of a glycine-rich CBP encoding gene (ge-gprp-19) and a cysteine-rich CBP encoding gene (ge-cprp-17) during dorsal scales and/or lamellar development. CONCLUSIONS: All 66 CBPs are involved in the formation of setae. Glycine-rich CBPs hold a significant role in the development of dorsal scales and lamellar setae, whereas most cysteine-rich CBPs appear to be essential components of G. japonicus setae. Even GjCBPs with similar amino acid compositions may play diverse functions. The clear spatio-temporal expression differences between the glycine-rich and cysteine-rich CBP encoding genes during epidermal scale and/or setae formation were observed. Embryonic developmental stages 39 to 42 emerged as crucial phases for setae development. These findings lay the groundwork for deeper investigation into the function of GjCBPs in the development of G. japonicus setae.

Insights into the adaptive evolution of chromosome and essential traits through chromosome-level genome assembly of Gekko japonicus.

Gekko japonicus possesses flexible climbing and detoxification abilities under insectivorous habits. Still, the evolutionary mechanisms behind these traits remain unclarified. This study presents a chromosome-level G. japonicus genome, revealing that its evolutionary breakpoint regions were enriched with specific repetitive elements and defense response genes. Gene families unique to G. japonicus and positively selected genes are mainly enriched in immune, sensory, and nervous pathways. Expansion of bitter taste receptor type 2 primarily in insectivorous species could be associated with toxin clearance. Detox cytochrome P450 in G. japonicus has undergone more birth and death processes than biosynthesis-type P450 genes. Proline, cysteine, glycine, and serine in corneous beta proteins of G. japonicus might influence flexibility and setae adhesiveness. Certain thermosensitive transient receptor potential channels under relaxed purifying selection or positive selection in G. japonicus might enhance adaptation to climate change. This genome assembly offers insights into the adaptive evolution of gekkotans.

The identification, adaptive evolutionary analyses and mRNA expression levels of homeobox (hox) genes in the Chinese mitten crab Eriocheir sinensis.

BACKGROUND: Arthropods are the largest group in the animal kingdom and are morphologically characterized by heterorhythmic segments. Brachyuran decapod crustaceans undergo brachyurization metamorphosis in the early developmental process, characterized by a reduced abdomen that is folded beneath the cephalothorax and inserted between the pereiopods or in a special cavity. As the main cause of major alterations in the evolution of animal body plans, Hox genes encode transcription factors and are involved in bilaterian anterior-posterior axis patterning. RESULTS: We found eight Hox genes (labial, proboscipedia, Deformed, zerknüllt, Sex combs reduced, Antennapedia, Ultrabithorax, fushi tarazu, abdominal-A and Abdominal-B) in Eriocheir sinensis. The phylogenetic topology of 13 arthropod Hox genes was closely related to traditional taxonomic groupings. Genome collinearity analysis was performed using genomic data and chromosomal location data of E. sinensis and Portunus trituratus. We found that their chromosomes were highly collinear, and there was a corresponding collinear relationship between the three Hox genes (lab, ftz and Abd-B). The mRNA expression levels of Scr and Antp fluctuated significantly in different developmental stages of E. sinensis, especially in the brachyurization stages. Evolutionary analysis indicated the presence of positively selected sites in Ubx. CONCLUSIONS: In this study, we used genome-wide analysis to identify and analyze all members of the Hox genes in E. sinensis. Our data will contribute to a better understanding of Hox genes in E. sinensis and provide useful molecular evolutionary information for further investigation on their roles in the brachyurization of crabs.

Expression analysis of alpha keratins and corneous beta-protein genes during embryonic development of Gekko japonicus.

Epidermal appendages of birds and reptiles, including claws, feathers, scales, and setae, are primarily composed of alpha keratins (KRTs) and corneous beta-proteins (CBPs). A comprehensive and systematic knowledge of KRTs and CBPs in Schlegel's Japanese gecko (Gekko japonicus) is still lacking. In this study, 22 candidate Gecko japonicus keratin (GjKRT) family genes (12 type I genes, 10 type II genes) were identified in the G. japonicus genome. The majority of GjKRT genes across various subgroups had undergone a prolonged and highly conservative evolutionary process. Through a combination of morphological observation, RNA-seq analysis, and qRT-PCR assay, it was possible to discern the dynamic alterations in the expression of GjKRTs and Gecko japonicus corneous beta-proteins genes (GjCBPs). These findings strongly indicate that GjKRTs gradually accumulate to constitute an α-layer, which is subsequently succeeded by the formation of the corneous beta layer containing GjCBPs at late stages (40-42) of embryonic development. The epidermal appendages in G. japonicus may result from the joint accumulation of KRTs and CBPs, with stages 40-42 being critical for their development. These findings provide novel insights into KRTs and CBPs of G. japonicus and offer a foundation for investigating the functions of GjKRT and GjCBP gene families. Furthermore, this knowledge contributes to unraveling the molecular mechanisms underlying the formation of epidermal appendages in G. japonicus.

Comparative transcriptome, digital gene expression and proteome profiling analyses provide insights into the brachyurization from the megalopa to the first juvenile in Eriocheir sinensis.

Eriocheir sinensis larva normally experiences 11 stages. The reduced abdomen folded beneath the thorax is the most prominent characteristic of morphological alteration from megalopa to juvenile crab. Up to date, the molecular mechanisms of brachyurization remain a mystery. Here, transcriptome library, digital gene expression (DGE) libraries and proteome libraries at two developmental stages [the megalopa stage of E. sinensis (stage M) and the first stage of juvenile crab (stage J1)] of the Chinese mitten crab larva were constructed for RNA sequencing and iTRAQ approaches followed by bioinformatics analysis, respectively. In total, 1106 genes and 871 proteins were differentially expressed between the stage M and stage J1. Moreover, several important pathways were identified, including biosynthesis of secondary metabolites, metabolic pathways, focal adhesion, and some disease pathways. Besides, muscle contraction, oxidative phosphorylation, calcium signaling, PI3K-Akt, DNA replication pathway, and integrin signaling pathway also had important functions in brachyurization process. Furthermore, the components, actin, actin-related protein, collagens, filamin-A/B, laminin, integrins, paxillin, and fibronectin had up-regulated expression levels in M stage compared to J1 stage.

Phylogenetic Analysis and Genetic Structure of Schlegel's Japanese Gecko (Gekko japonicus) from China Based on Mitochondrial DNA Sequences.

Gekko japonicus, i.e., Schlegel's Japanese Gecko, is an important species which is widely distributed in East Asia. However, the information about population genetics of this species from China remains unclear. To address this issue, we used sequences from a fragment of the mitochondrial protein-coding gene cytochrome c oxidase I to estimate genetic diversity, genetic structure, and historical demography of G. japonicus populations from China. Phylogenetic analysis indicated that G. japonicus had a close relationship with Gekko wenxianensis. A total of 14 haplotypes were obtained, of which haplotype 1 was the most common and widely distributed. The genetic diversity of G. japonicus was comparatively low across different geographic populations. The populations of G. japonicus were divided into four groups which exhibited low levels of genetic differentiation, and expressed an unclear pattern of population structuring. In addition, potential population expansion of G. japonicus has occurred as well. Overall, these results demonstrate that the populations of G. japonicus reveal low genetic diversity in China, which is attributed to the founder and bottleneck events among populations. Our results will provide meaningful information on the population genetics of G. japonicus and will provide some insights into the study of origin of populations.

Expression of specific corneous beta proteins in the developing digits of the Japanese gecko (Gekko japonicus) reveals their role in the growth of adhesive setae.

Geckos possess strong adhesion ability, even can climb on smooth surface. Previous studies have shown that the setae of geckos play a crucial role in their ability to climb on vertical walls. But the biological molecular mechanism of their adhesion ability remains unclear. In the present study, the expression patterns of corneous beta proteins (CBPs) genes related to claws, scales, and feathers development (named as ge-gprp-9, ge-gprp-10, ge-gprp-11, ge-gprp-12, ge-gprp-13, ge-gprp-14, ge-gprp-15, and ge-gprp-16 respectively) in the developing pad lamellae of different embryonic stages (stage 34, stage 36, stage 39, and stage 42) of the Japanese gecko Gekko japonicus were detected using fluorescence quantitative PCR approach. The results showed that there were significant up-regulated expression of CBPs mRNA at embryonic stage 39 with the embryonic continuous maturation and the highest expression level was detected at embryonic stage 39 or stage 42. Moreover, the expression levels of four CBPs genes ge-gprp-9, ge-gprp-10, ge-gprp-11, and ge-gprp-12 in the embryonic and adult development of gecko were detected by fluorescence in situ hybridization technique. The results from in situ hybridization detection revealed that the positive signals of these CBPs genes expression were the same in the developing pad lamellae of G. japonicus. The positive signals of eight CBPs genes were mainly found in the setae tissue, oberhautchen, and ß layer, which suggests these CBPs genes are involved in the growth of setae.

Myosin Va from Eriocheir sinensis: cDNA cloning, expression and involvement in growth and development.

Myosin Va, a member of the myosin superfamily, has been widely identified associated with processes of cellular motility, which include neurotransmitter release and synaptic plasticity during neurodevelopment. However, the function of myosin Va in the growth and development of crustaceans has not yet been reported. In this study, a full-length cDNA of myosin Va (named as EsMyoVa) was cloned from the Chinese mitten crab, Eriocheir sinensis, and the expression patterns were detected in different tissues and larval developmental stages. The full-length cDNA of EsMyoVa was 6037 bp in length. Real time quantitative reverse transcription PCR (qRT-PCR) analysis showed that EsMyoVa transcript has a wide tissue distribution pattern and is expressed in zoeae, megalopa, juvenile crab stages and adults. In order to further study the function of this gene, we used RNAi technology in the muscle, hepatopancreas, gill, and gonad. After double-stranded RNA (dsRNA) injection, the expression level of EsMyoVa was significantly decreased in all tissues in both sexes and the gene knockdown effects of dsRNA persisted for at least 6 days. Subsequently, the role of EsMyoVa was revealed by silencing the transcript through one month injections of Myosin Va dsRNA. Crabs with reduced levels of EsMyoVa transcripts displayed a dramatic slowing in growth rate and considerably higher mortality compared to control groups, which indicated that this gene had important role of regulating growth and development.

Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater.

Cetaceans (whales, dolphins, and porpoises) are a group of mammals adapted to various aquatic habitats, from oceans to freshwater rivers. We report the sequencing, de novo assembly and analysis of a finless porpoise genome, and the re-sequencing of an additional 48 finless porpoise individuals. We use these data to reconstruct the demographic history of finless porpoises from their origin to the occupation into the Yangtze River. Analyses of selection between marine and freshwater porpoises identify genes associated with renal water homeostasis and urea cycle, such as urea transporter 2 and angiotensin I-converting enzyme 2, which are likely adaptations associated with the difference in osmotic stress between ocean and rivers. Our results strongly suggest that the critically endangered Yangtze finless porpoises are reproductively isolated from other porpoise populations and harbor unique genetic adaptations, supporting that they should be considered a unique incipient species.

Genetic basis of brain size evolution in cetaceans: insights from adaptive evolution of seven primary microcephaly (MCPH) genes.

BACKGROUND: Cetacean brain size expansion is an enigmatic event in mammalian evolution, yet its genetic basis remains poorly explored. Here, all exons of the seven primary microcephaly (MCPH) genes that play key roles in size regulation during brain development were investigated in representative cetacean lineages. RESULTS: Sequences of MCPH2-7 genes were intact in cetaceans but frameshift mutations and stop codons was identified in MCPH1. Extensive positive selection was identified in four of six intact MCPH genes: WDR62, CDK5RAP2, CEP152, and ASPM. Specially, positive selection at CDK5RAP2 and ASPM were examined along lineages of odontocetes with increased encephalization quotients (EQ) and mysticetes with reduced EQ but at WDR62 only found along odontocete lineages. Interestingly, a positive association between evolutionary rate (ω) and EQ was identified for CDK5RAP2 and ASPM. Furthermore, we tested the binding affinities between Calmodulin (CaM) and ASPM IQ motif in cetaceans because only CaM combined with IQ, can ASPM perform the function in determining brain size. Preliminary function assay showed binding affinities between CaM and IQ motif of the odontocetes with increased EQ was stronger than for the mysticetes with decreased EQ. In addition, evolution rate of ASPM and CDK5RAP2 were significantly related to mean group size (as one measure of social complexity). CONCLUSIONS: Our study investigated the genetic basis of cetacean brain size evolution. Significant positive selection was examined along lineages with both increased and decreased EQ at CDK5RAP2 and ASPM, which is well matched with cetacean complex brain size evolution. Evolutionary rate of CDK5RAP2 and ASPM were significantly related to EQ, suggesting that these two genes may have contributed to EQ expansion in cetaceans. This suggestion was further indicated by our preliminary function test that ASPM might be mainly linked to evolutionary increases in EQ. Most strikingly, our results suggested that cetaceans evolved large brains to manage complex social systems, consisting with the 'social brain hypothesis', as evolutionary rate of ASPM and CDK5RAP2 were significantly related to mean group size.

Evolution of Digestive Enzymes and RNASE1 Provides Insights into Dietary Switch of Cetaceans.

Although cetaceans (whales, porpoises, and dolphins) have multi-chambered stomachs, feeding habits of modern cetaceans have dramatically changed from herbivorous to carnivorous. However, the genetic basis underlying this dietary switch remains unexplored. Here, we present the first systematic investigation of 10 digestive enzymes genes (i.e., CYP7A1, CTRC, LIPC, LIPF, PNLIP, PGC, PRSS1, SI, SLC5A1, and TMPRSS15) of representative cetaceans, and the evolutionary trajectory of RNASE1 in cetartiodactylans. Positive selections were detected with proteinases (i.e., CTRC, PRSS1, and TMPRSS15) and lipases (i.e., CYP7A1, LIPF, and PNLIP) suggesting that cetaceans have evolved an enhanced digestion capacity for proteins and lipids, the major nutritional components of their prey (fishes and invertebrates). In addition, it was found that RNASE1 gene duplicated after the cetartiodactylan speciation and two independent gene duplication events took place in Camelidae and Ruminantia. Positive selection was detected with RNASE1 of Camelidae and Bovidae, suggesting enhanced digestive efficiency in the ruminants. Remarkably, even though the ancestors of cetaceans were terrestrial artiodactyls that are herbivorous, modern cetaceans lost the pancreatic RNASE1 copy with digestive function, which is in accordance with the dietary change from herbivorous to carnivorous. In sum, this is the first study that provides new insights into the evolutionary mechanism of dietary switch in cetaceans.

A new species of Hemiphyllodactylus Bleeker, 1860 (Squamata: Gekkonidae) from Guizhou, China.

A new species of the genus Hemiphyllodactylus is described from Huishui County, Guizhou Province, Southwest China. Hemiphyllodactylus huishuiensis sp. nov. is distinguished from all other congeners by having the unique combination of the following characters: a maximum SVL of 51.2 mm; 8 or 10 chin scales; enlarged postmental scales; 3 circumnasal scales; 2 or 3 scales between the supranasals; 9-11 supralabials; 9-11 infralabials; 13-15 dorsal scales; 7-9 ventral scales; a lamellar hand formula of 3-4-4-4 or 4-4/5-5-4; a lamellar foot formula of 4-4/5-5-4/5; 3 subdigital lamellae on the first finger and first toe; a continuous precloacal and femoral pore series of less than 20; one cloacal spur in both males and females; no enlarged subcaudal scales; dark dorsal transverse blotches; dark postorbital stripe; a brown postsacral mark bearing anteriorly projecting arms; and unpigmented caecum and gonads. The new species also occurs in Ziyun County, Guizhou Province, China.

Evolutionary Genetics of Hypoxia Tolerance in Cetaceans during Diving.

Hypoxia was a major challenge faced by cetaceans during the course of secondary aquatic adaptation. Although physiological traits of hypoxia tolerance in cetaceans have been well characterized, the underlying molecular mechanisms remain unknown. We investigated the sequences of 17 hypoxia-tolerance-related genes in representative cetaceans to provide a comprehensive insight into the genetic basis of hypoxia tolerance in these animals. Genes involved in carrying and transporting oxygen in the blood and muscle (hemoglobin-α and ß, myoglobin), and genes involved in the regulation of vasoconstriction (endothelin-1, -2, and -3; endothelin receptor type A and B; adrenergic receptor α-1D; and arginine vasopressin) appear to have undergone adaptive evolution, evidence for positive selection on their particular sites, and radical physiochemical property changes of selected condons. Interestingly, "long-diving" cetaceans had relatively higher ω (dN/dS) values than "short-diving" cetaceans for the hemoglobin ß gene, indicating divergent selective pressure presented in cetacean lineages with different diving abilities. Additionally, parallel positive selection or amino acid changes (ADRA1D: P50A, A53G,AVPR1B: I/V270T) among animals exposed to different hypoxia habitats reflect functional convergence or similar genetic mechanisms of hypoxia tolerance. In summary, positive selection, divergent selective pressures, and parallel evolution at the molecular level provided some new insights into the genetic adaptation of hypoxia tolerance.

The mitochondrial genome of the gold-dust day gecko, Phelsuma laticauda (Sauria, Gekkota, Gekkonidae).

We sequenced the nearly complete mitochondrial genome of the gold-dust day gecko, Phelsuma laticauda, which is native to northern Madagascar. The mitogenome is 15,416 bp in size, consisting of 37 genes coding for 13 proteins, 22 tRNAs, and 2 rRNAs. Due to the unsuccessful sequencing of the control region, the length is relatively shorter than that of other gekkonids. The gene organization conforms to the vertebrate consesus gene arrangement.

'Obesity' is healthy for cetaceans? Evidence from pervasive positive selection in genes related to triacylglycerol metabolism.

Cetaceans are a group of secondarily adapted marine mammals with an enigmatic history of transition from terrestrial to fully aquatic habitat and subsequent adaptive radiation in waters around the world. Numerous physiological and morphological cetacean characteristics have been acquired in response to this drastic habitat transition; for example, the thickened blubber is one of the most striking changes that increases their buoyancy, supports locomotion, and provides thermal insulation. However, the genetic basis underlying the blubber thickening in cetaceans remains poorly explored. Here, 88 candidate genes associated with triacylglycerol metabolism were investigated in representative cetaceans and other mammals to test whether the thickened blubber matched adaptive evolution of triacylglycerol metabolism-related genes. Positive selection was detected in 41 of the 88 candidate genes, and functional characterization of these genes indicated that these are involved mainly in triacylglycerol synthesis and lipolysis processes. In addition, some essential regulatory genes underwent significant positive selection in cetacean-specific lineages, whereas no selection signal was detected in the counterpart terrestrial mammals. The extensive occurrence of positive selection in triacylglycerol metabolism-related genes is suggestive of their essential role in secondary adaptation to an aquatic life, and further implying that 'obesity' might be an indicator of good health for cetaceans.

A new species of Hemiphyllodactylus Bleeker, 1860 (Squamata: Gekkonidae) from western Yunnan, China.

A new species of the genus Hemiphyllodactylus is described from mountainous area of Changning County, Yunnan Province, China. Hemiphyllodactylus changningensis sp. nov. is distinguished from all other congeners by morphology and a significant genetic divergence of greater than 17% (ND2 gene). The new species from Changning is characterized by the following features: a maximum SVL of 40.1 mm in males and 43.8 mm in females; 11-15 dorsal scale rows; 6-8 ventral scale rows; a forefoot lamellar formula of 3-3/4-3/4-3; a hindfoot lamellar formula of 3-4-4-4 or 3-3-3-3; precloacal and femoral pore series continuous; cloacal spurs present in both sexes; dark dorsal transverse blotches; dark postorbital stripe; a brown postsacral mark bearing anteriorly projecting arms; and unpigmented caecum and gonads. The new species occurs also in Longyang District of Baoshan City, Yunnan Province, China.

The world's second largest population of humpback dolphins in the waters of Zhanjiang deserves the highest conservation priority.

Chinese white dolphins (Sousa chinensis) inhabiting shallow coastal waters are vulnerable to impacts from human activities in the near shore waters. This study examined the population of Chinese white dolphins occurring off the coast of Zhanjiang in the northern South China Sea. A total of 492 Chinese white dolphins were identified, 176 of which were photographed on more than one occasion. The Zhanjiang Chinese white dolphin population is isolated from populations of conspecifics along the Guangdong coast. It is composed of approximately 1485 individuals (95% CI = 1371-1629; SE = 63.8), with estimates of mean representative range and core area of 168.51 and 44.26 km(2), respectively. The high site fidelity and long-term residence of Chinese white dolphins in the study area are well established. A review of all available data indicates that based on what is currently known, the Zhanjiang Chinese white dolphin population is the second largest of the species and genus in the world. However, the recent industrial boom along the Zhanjiang coast has increased concerns regarding the conservation of the Zhanjiang Chinese white dolphin population. We recommend the designation of a national nature reserve as a most urgent measure for protecting Chinese white dolphins in Zhanjiang waters.

The loss of taste genes in cetaceans.

BACKGROUND: Five basic taste modalities, sour, sweet, bitter, salt and umami, can be distinguished by humans and are fundamental for physical and ecological adaptations in mammals. Molecular genetic studies of the receptor genes for these tastes have been conducted in terrestrial mammals; however, little is known about the evolution and adaptation of these genes in marine mammals. RESULTS: Here, all five basic taste modalities, sour, sweet, bitter, salt and umami, were investigated in cetaceans. The sequence characteristics and evolutionary analyses of taste receptor genes suggested that nearly all cetaceans may have lost all taste modalities except for that of salt. CONCLUSIONS: This is the first study to comprehensively examine the five basic taste modalities in cetaceans with extensive taxa sampling. Our results suggest that cetaceans have lost four of the basic taste modalities including sour, sweet, umami, and most of the ability to sense bitter tastes. The integrity of the candidate salt taste receptor genes in all the cetaceans examined may be because of their function in Na(+) reabsorption, which is key to osmoregulation and aquatic adaptation.

Complete mitochondrial genome of the Tioman Island rock gecko, Cnemaspis limi (Sauria, Gekkota, Gekkonidae).

We sequenced the complete mitochondrial genome of the Tioman Island rock gecko, Cnemaspis limi, which is known as an endemic species to Malaysia. The complete mitogenome is 16,680 bp in size, consisting of 37 genes coding for 13 proteins, 22 transfer RNAs, two ribosomal RNAs and one control region. The A + T content of the overall base composition of H-strand is 53.09% (T: 23.20%, C: 32.48%, A: 29.89% and G: 14.43%). The major non-coding region (control region) is 1254 bp in length with the A + T content of 55.09% and four replicates of a 76-bp repeat within this region.

Complete mitochondrial genome of the San Lucan gecko, Phyllodactylus unctus (Sauria, Gekkota, Phyllodactylidae), in comparison with Tarentola mauritanica.

We sequenced the complete mitochondrial genome of the San Lucan gecko, Phyllodactylus unctus, which is endemic to Mexico. The complete mitochondrial genome was 16,881 bp in size, consisting of 37 genes coding for 13 proteins, 2 rRNAs, 22 tRNAs and 1 control region. Its gene arrangement pattern was identical with most vertebrates. We compared the mitochondrial genome of P. unctus with that of the Moorish gecko, Tarentola mauritanica, which is the only other sequenced species from Phyllodactylidae. Nucleotide sequence divergence (p distance) between two mitochondrial genomes was 31.32%. The detailed comparison between the mitochondrial genomes of two species was done.