De novo assembly and microsatellite marker development of the transcriptome of the endangered Brachymystax lenok tsinlingensis

Wen, Shaoqing; Li, Ping; Wang, Zhen; Li, Jiale; Liu, Haixia; Li, Ning

doi:10.1007/s13258-020-00939-3

Cited by 5 publications

(3 citation statements)

References 25 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As red-crowned cranes are endangered wild animals, we only use random individuals that died of disease for analysis; thus, we could not repeat our experiments to further confirm the obtained results. Most full-length transcripts were found to be enriched in immune-related signaling pathways, as expected in a sick state 30 , 36 , 45 – 47 . Accordingly, the immune expression of the spleen was found to be the highest, suggesting that the spleen is the main immunity organ of the red-crowned cranes beyond all doubt.…”

Section: Resultssupporting

confidence: 60%

Comprehensive transcriptome characterization of Grus japonensis using PacBio SMRT and Illumina sequencing

et al. 2021

Sci Rep

View full text Add to dashboard Cite

The red-crowned crane (Grus japonensis) is an endangered species distributed across southeast Russia, northeast China, Korea, and Japan. Here, we sequenced for the first time the full-length unreferenced transcriptome of red-crowned crane mixed samples using a PacBio Sequel platform. A total of 359,136 circular consensus sequences (CCS) were obtained via clustering to remove redundancy. A total of 303,544 full-length non-chimeric sequences were identified by judging whether CCS contained 5′ and 3′ adapters, and the poly(A) tail. Eight samples were sequenced using Illumina, and PacBio sequencing data were corrected according to the collected Illumina data to obtain more accurate full-length transcripts. A total of 4,100 long non-coding RNAs, 13,115 simple sequences repeat loci and 29 transcription factor families were identified. The expression of lncRNAs and TFs in pancreas was lowest comparing with other tissues. Many enriched immune-related transmission pathways (MHC and IL receptors) were identified in the spleen. This study will contribute to a better understanding of the gene structure and post-transcriptional regulatory network, and provide references for future studies on red-crowned cranes.

show abstract

Section: Resultssupporting

confidence: 60%

Comprehensive transcriptome characterization of Grus japonensis using PacBio SMRT and Illumina sequencing

et al. 2021

Sci Rep

View full text Add to dashboard Cite

show abstract

“…However, they mainly focus on its ecological habits, morphological characteristics, artificial reproduction, etc (Ku and Wen, 1997;Li, 2014;Zhang et al, 2018). Although the sequencing technologies have developed rapidly, different from other endangered animal species (Magalhães et al, 2019;Chen et al, 2020;Grandjean et al, 2020;Wen et al, 2020), there were few researches on genetic information of elongate loach. In this study, we developed a reference transcriptome in elongate loach.…”

Section: De Novo Assembly and Functional Annotation Of Elongate Loachmentioning

confidence: 99%

Transcriptome Sequencing of the Endangered Species Elongate Loach (Leptobotia elongata) From the Yangtze River: De novo Transcriptome Assembly, Annotation, Identification and Validation of EST-SSR Markers

Zhang

Gao

Zhang³

et al. 2021

Front. Mar. Sci.

View full text Add to dashboard Cite

Elongate loach (Leptobotia elongata) is endemic to middle and upper reaches of the Yangtze River in China. Due to overfishing and habitat destruction, this loach has become an endangered species. So far, lack of reliable genetic information and molecular markers has hindered the conservation and utilization of elongate loach resources. Therefore, we here performed an Illumina sequencing and de novo transcriptome assembly in elongate loach, and then developed polymorphic simple sequence repeat markers (SSRs). After assembly, 51,185 unigenes were obtained, with an average length of 1,496 bp. A total of 23,901 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified, distributing in 14,422 unigenes, with a distribution frequency of 28.18%. Out of 16,885 designed EST-SSR primers, 150 primers (3 or 4 base repetition-dominated) were synthesized for polymorphic EST-SSR development. Then, 52 polymorphic EST-SSRs were identified, with polymorphism information contents (PIC) ranging from 0.03 to 0.88 (average 0.54). In conclusion, this was the first report of transcriptome sequencing of elongate loach. Meanwhile, we developed a set of polymorphic EST-SSRs for the loach. This study will provide an important basis, namely genetic information and polymorphic SSRs, for further population genetics and breeding studies of this endangered and economic loach in China.

show abstract

“…Artificial propagation and release is one effective method by which to restore the wild population of B. tsinlingensis Li. However, large-scale artificial propagation of this species has not been successful, partly because of our limited knowledge of the molecular mechanisms governing reproduction in B. tsinlingensis Li. Previous studies in B. tsinlingensis Li mainly focused on behaviours [4], molecular genetic markers [5], feed additives [6], and morphology and the ultrastructure of the sperm [7]. However, research on reproductive development in B. tsinlingensis Li is still lacking, although such research is essential for artificial propagation and further species conservation.…”

Section: Introductionmentioning

confidence: 99%

Comparative Transcriptome Analysis Reveals Sexually Dimorphic Gene Expression in the Gonads of Brachymystax tsinlingensis Li

Huang,

Ye,

Yue

et al. 2023

Animals

View full text Add to dashboard Cite

Brachymystax tsinlingensis Li is an endangered cold-water salmonid fish native to China. This study aimed to identify sex-related genes and biological pathways via gonadal transcriptome sequencing of B. tsinlingensis Li. A total of 167,904 unigenes were identified with an average length of 836 bp and an N50 of 1452 bp, of which 84,977 (50.61%) unigenes were successfully annotated in six major databases. Comparative transcriptome analysis identified 22,864 differentially expressed genes (DEGs), of which 17,231 were up-regulated (male-biased genes, mDEGs) and 5633 were down-regulated (female-biased genes, fDEGs). Several DEGs associated with gonadal development were found through Gene Ontology enrichment analysis, such as ccnb1, zp3, bmp15, dmrt1, and psmc3ip. Signaling pathways related to gonadal development were found to be enriched through analysis using the Kyoto Encyclopedia of Genes and Genomes Pathway database, such as genes involves in base excision repair, the notch signaling pathway, neuroactive ligand-receptor interaction, the VEGF signaling pathway, and the estrogen signaling pathway. In addition, mRNA expression levels of 19 DEGs were determined to validate the reliability of the transcriptomic data by quantitative real-time polymerase chain reaction. These results revealed genes and signaling pathways potentially involved in gonadal development in B. tsinlingensis Li and provided basic molecular data for future research on reproductive regulation and breeding of B. tsinlingensis Li.

show abstract

De novo assembly and microsatellite marker development of the transcriptome of the endangered Brachymystax lenok tsinlingensis

Cited by 5 publications

References 25 publications

Comprehensive transcriptome characterization of Grus japonensis using PacBio SMRT and Illumina sequencing

Comprehensive transcriptome characterization of Grus japonensis using PacBio SMRT and Illumina sequencing

Transcriptome Sequencing of the Endangered Species Elongate Loach (Leptobotia elongata) From the Yangtze River: De novo Transcriptome Assembly, Annotation, Identification and Validation of EST-SSR Markers

Comparative Transcriptome Analysis Reveals Sexually Dimorphic Gene Expression in the Gonads of Brachymystax tsinlingensis Li

Contact Info

Product

Resources

About