A reference gene set construction using RNA-seq of multiple tissues of Chinese giant salamander, Andrias davidianus

Geng, Xiaofang; Li, Wanshun; Shang, Haitao; Gou, Qiang; Zhang, Fuchun; Zang, Xiayan; Zeng, Benhua; Jiang, Li; Wāng, Ying; Ma, Junjun; Guo, Jiuxin; Jian, Jianbo; Chen, Bing; Qiao, Zhengxue; Zhou, Minghui; Wei, Hong; Fang, Xiaodong; Xu, Chi

doi:10.1093/gigascience/gix006

Cited by 20 publications

(20 citation statements)

References 16 publications

(14 reference statements)

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“…We obtained higher total and mean data per specimen than reported in Anolis carolinensis, Lupinus angustifolius , or Pistacia vera. Due to the large genome of A. davidianus (~50Gb) analyzed by flow cytometry [30], the sequence coverage in this study averaged 0.29 x per salamander. The results were available to explore the sex-specific marker to identify the genetic sex of A. davidianus, especially the larvae and sex reversed individuals in the non-model species.…”

Section: Discussionmentioning

confidence: 99%

“…However, due to the environmental degradation and human harvesting, the wild population has sharply decreased, and it is now classified as an endangered species. A.davidianus possesses 30 pairs of chromosomes with 19 pairs of microchromosomes [18] and a genome of ∼50 GB, making assembly a challenge [30]. Therefore, RAD-seq is a useful method to explore a sex-specific marker in A. davidianus .…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide RAD sequencing to identify a sex-specific marker in Chinese giant salamander Andrias davidianus

Chang

Wang

et al. 2019

BMC Genomics

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Background Chinese giant salamander Andrias davidianus is an endangered species. The success of artificial breeding provides a useful way to protect this species. However, the method to identify the sex and mechanism of sex determination were unclear which hinder the improvement of the artificial breeding. Detection of a sex specific marker provides an effective approach to identify genetic sex and investigate the sex determination mechanism. Results We used restriction-site-associated DNA (RAD) sequencing to isolate a sex-specific genetic marker in A. davidianus to expand knowledge of the sex determination mechanism. Four male and four female specimens were subjected to RAD sequencing, which generated 934,072,989 reads containing approximately 134.4 Gb of sequences. The first round of comparison of the assembled sequence against the opposite sex raw reads revealed 19,097 female and 17,994 male unmatched sequences. Subsequently, 19,097 female sequences were subjected to a BLAST search against male genomic data, which revealed 308 sequences unmapped to the male genome. One hundred of these were randomly selected and validated by PCR in five male and five female specimens, and four putative sex-specific sequences were produced. Further validation was performed by PCR in another 24 females and 24 males, and all female individuals exhibited the expected specific bands, while the males did not. To apply the sex-specific marker, three specimens reversed from genetic female to physiological male were found in a group exposed to elevated temperature, and 13 individuals reversed from genetic male to physiological female were obtained in a 17β-estradiol exposed group. Conclusion This is the first report of a sex-specific marker in A. davidianus and may have potential for elucidation of its sex determination mechanism and, hence, its conservation . Electronic supplementary material The online version of this article (10.1186/s12864-019-5771-5) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-wide RAD sequencing to identify a sex-specific marker in Chinese giant salamander Andrias davidianus

Chang

Wang

et al. 2019

BMC Genomics

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“…The Chinese giant salamander ( Andrias davidianus ) is a species that has been classified as a class II critically endangered species on the national list of protected animals in China. The Chinese giant salamander is often called a living fossil and is considered a valuable model species for phylogenetic and evolutionary studies (Geng et al ). Giant salamanders are susceptible to bacterial infections (Meng, Zeng, Yang, & Xiao, ).…”

Section: Introductionmentioning

confidence: 99%

Age‐related changes in the gut microbiota of the Chinese giant salamander (Andrias davidianus)

et al. 2018

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The composition of the intestinal microbial community may vary across developmental stages. In this study, we explored how this microbial community shifted along the intestinal tract of the Chinese giant salamander ( Andrias davidianus ) at various ages. Next‐generation sequencing was used to sequence the bacterial 16S rRNA gene from different kind of samples, including the stomach, duodenum, ileum, and rectum. The highest mean relative abundance of the bacterial community in the gastrointestinal tract shifted in relation to age: within the first year, Bacteroidetes (47.76%) dominated the gut microbiome, whereas Proteobacteria was the most dominant at age 2 (32.88%) and age 3 (30.78%), and finally, Firmicutes was the most dominant at age 4 (34.70%). The overall richness of the gut bacterial community also generally increased from age 2 to 4. Hierarchical cluster analysis revealed that the gut microbiome at age 2 had greater variability than that at either age 3 or 4, likely representing a shift in diet from yolk or redworms as a juvenile to shrimp or crab as an adult. As these salamanders develop, their gastrointestinal tracts increase in complexity, and this compartmentalization may also facilitate an increase in microbial gut diversity.

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“…A limitation of our study was that just a single biological sample was used in the RNA‐seq. Also, it has been reported that the RNA‐seq was carried out only from a single biological sample in several researches (Geng et al, ; Liu et al, ; Gardner et al, ; Singh et al, ). In the present study, on the basis of RNA‐seq data, secondary and tertiary methods of analyses were used to validate the observed differences.…”

Section: Discussionmentioning

confidence: 99%

Endochondral ossification in hindlimbs during bufo gargarizans metamorphosis: A model of studying skeletal development in vertebrates

Gao

Zhang

Wang

2018

Developmental Dynamics

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Background Endochondral ossification, the process by which most of the skeleton is formed, is accurately regulated by many specific groups of molecules and extracellular matrix components. The molecular mechanisms of endochondral ossification have been extensively investigated in mammals. However, there are few studies about it in amphibians. Results Ossification of femur and tibiofibula was observed at Gs 40, and tarsals and metatarsals were ossified at Gs 42. Most of the skeletons in hindlimbs were completely ossified except for articular cartilages at Gs 46. Thirty-two genes related to endochondral ossification were found in the differentially expressed genes (DEGs) library of hindlimbs, and nine of these genes were validated by qRT-PCR during metamorphosis. Sox9 was expressed in the columnar, prehypertrophic, and upper hypertrophic zones, and the expression of Ihh was observed in prehypertrophic chondrocyte zone in hindlimbs of B. gargarizans. Conclusions The ossification of hindlimbs increased gradually, and the ossification sequence was from proximal to distal in B. gargarizans during metamorphosis. Thirty-two genes found in the DEGs library were related to the regulation of endochondral ossification of hindlimbs in amphibians. The present study will provide a valuable genomic resource for the future study of endochondral ossification in amphibian. Developmental Dynamics 247:1121-1134, 2018. © 2018 Wiley Periodicals, Inc.

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A reference gene set construction using RNA-seq of multiple tissues of Chinese giant salamander, Andrias davidianus

Cited by 20 publications

References 16 publications

Genome-wide RAD sequencing to identify a sex-specific marker in Chinese giant salamander Andrias davidianus

Genome-wide RAD sequencing to identify a sex-specific marker in Chinese giant salamander Andrias davidianus

Age‐related changes in the gut microbiota of the Chinese giant salamander (Andrias davidianus)

Endochondral ossification in hindlimbs during bufo gargarizans metamorphosis: A model of studying skeletal development in vertebrates

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