De novo transcriptome analysis and antimicrobial peptides screening in skin of Paa boulengeri

Jiang, Yi; Fan, Wenqiao; Xu, Jingming

doi:10.1007/s13258-017-0532-9

Cited by 4 publications

(6 citation statements)

References 65 publications

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“…For high-throughput short read sequencing, assembly with high-quality will provide benefit for the post transcriptomic analysis like annotation, gene identification and comparative genomics. According to most of published de novo transcriptome assembly, the quality of assembly is principally evaluated by the length distribution of transcripts [40]. In the present study, more than half of the de novo assembled unigenes were greater than 500 bp in length and the mean length of unigenes reached 1093 bp (Table 1, Fig 1).…”

Section: Discussionmentioning

confidence: 48%

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De novo transcriptomic characterization of Betta splendens for identifying sex-biased genes potentially involved in aggressive behavior modulation and EST-SSR maker development

Yang

Wang

et al. 2018

Preprint

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Betta splendens is not only a commercially important labyrinth fish but also a nice research model for understanding the biological underpinnings of aggressive behavior. However, the shortage of basic genetic resource severely inhibits investigations on the molecular mechanism in sexual dimorphism of aggressive behavior typicality, which are essential for further behavior-related studies. There is a lack of knowledge regarding the functional genes involved in aggression expression. The scarce marker resource also impedes research progress of population genetics and genomics. In order to enrich genetic data and sequence resources, transcriptomic analysis was conducted for mature B. splendens using a multiple-tissues mixing strategy. A total of 105,505,486 clean reads were obtained and by de novo assembly, 69,836 unigenes were generated. Of which, 35,751 unigenes were annotated in at least one of queried databases. The differential expression analysis resulted in 17,683 transcripts differentially expressed between males and females. Plentiful sex-biased genes involved in aggression exhibition were identified via a screening from Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways, such as htr, drd, gabr, cyp11a1, cyp17a1, hsd17b3, dax1, sf-1, hsd17b7, gsdf1 and fem1c. These putative genes would make good starting points for profound mechanical exploration on aggressive behavioral regulation. Moreover, 12,751 simple sequence repeats were detected from 9,617 unigenes for marker development. Nineteen of the 100 randomly selected primer pairs were demonstrated to be polymorphic. The large amount of transcript sequences will considerably increase available genomic information for gene mining and function analysis, and contribute valuable microsatellite marker resources to in-depth studies on molecular genetics and genomics in the future.

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Section: Discussionmentioning

confidence: 48%

“…In contrast with other de novo assembly softwares e.g. Newbler [42], iAssembler [43] and CLC Genomics Workbench [44], the most satisfying assembler Trinity could provide a unified solution for good-quality transcriptome reconstruction in species without a reference genome [26, 40].…”

Section: Discussionmentioning

confidence: 99%

De novo transcriptomic characterization of Betta splendens for identifying sex-biased genes potentially involved in aggressive behavior modulation and EST-SSR maker development

Yang

Wang

et al. 2018

Preprint

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“…For high-throughput short-read sequencing, high-quality assembly facilitates post-transcriptional annotation, gene identification, comparative genomics and other analyses. Compared with other de novo assembly tools for NGS technologies (e.g., Newbler [ 27 ], iAssembler [ 28 ] and CLC Genomics Workbench [ 29 ]), Trinity gives more satisfactory results, as it can provide a unified and better solution for the reconstruction of transcriptomes without requiring a reference genome [ 15 , 30 ]. According to most of published transcriptome sequencing data, the quality of de novo assembly is primarily assessed by the length distribution of transcripts [ 30 ].…”

Section: Discussionmentioning

confidence: 99%

De Novo Transcriptomic Characterization Enables Novel Microsatellite Identification and Marker Development in Betta splendens

Chen

Wang

et al. 2021

Life

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The wild populations of the commercially valuable ornamental fish species, Betta splendens, and its germplasm resources have long been threatened by habitat degradation and contamination with artificially bred fish. Because of the lack of effective marker resources, population genetics research projects are severely hampered. To generate genetic data for developing polymorphic simple sequence repeat (SSR) markers and identifying functional genes, transcriptomic analysis was performed. Illumina paired-end sequencing yielded 105,505,486 clean reads, which were then de novo assembled into 69,836 unigenes. Of these, 35,751 were annotated in the non-redundant, EuKaryotic Orthologous Group, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology databases. A total of 12,751 SSR loci were identified from the transcripts and 7970 primer pairs were designed. One hundred primer pairs were randomly selected for PCR validation and 53 successfully generated target amplification products. Further validation demonstrated that 36% (n = 19) of the 53 amplified loci were polymorphic. These data could not only enrich the genetic information for the identification of functional genes but also effectively facilitate the development of SSR markers. Such knowledge would accelerate further studies on the genetic variation and evolution, comparative genomics, linkage mapping and molecular breeding in B. splendens.

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“…For high-throughput short read sequencing, high-quality assembly will provide benefit for post transcriptomic analysis like annotation, gene identification and comparative genomics. According to many past studies, the quality of assembly is evaluated mainly by the length distribution of contigs or transcripts (Jiang, Fan, & Xu, 2017). In this experiment, more than half of the de novo assembled unigenes were >500 bp in length and the mean length of unigenes reached 1282 bp (Table 1; Figure 1a).…”

Section: Sequencing and Assemblymentioning

confidence: 93%

“…In contrast with other de novo assembly softwares e.g. CLC Genomics Workbench (Malachowicz, Wenne, & Burzynski, 2017), iAssembler (Chen et al, 2013) and Newbler , the most satisfying assembler Trinity could provide a unified solution for good-quality transcriptome reconstruction in species without a reference genome (Grabherr et al, 2011;Jiang et al, 2017). A longer assembled sequence can provide more adequate information for further gene investigation and identification of molecular markers.…”

Section: Sequencing and Assemblymentioning

confidence: 99%

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Yang¹,

Lin²,

Li³

et al. 2019

Turk. J. Fish. Aquat. Sci.

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Amphiprion ocellaris is suggested to be an excellent research model for understanding socially controlled sex change of sequential hermaphrodite teleosts. However, there is a lack of knowledge regarding the genes involved in reproduction regulation in sex transition process. In order to enrich genetic data and sequence resources, Illumina HiSeq transcriptome sequencing was conducted for fully mature A. ocellaris using a multiple tissues mixing strategy. A total of 109,408,556 raw reads were obtained and 81,395 unigenes were generated by Trinity de novo assembly. Of which, 60,457 unigenes were annotated in at least one of the queried NR, COG, Swiss-Prot, KEGG and NT databases. After screening from reproduction-related Gene Ontology (GO) terms and pathways, plentiful candidate genes involved in reproductive process were identified, such as gnrh1, fsh, mtnr1a, avt, dmrt1, sox9a, amh, dax1, sf-1, foxl2 and cyp19a1. These candidates could make good starting points for profound mechanical analysis on the reproductive regulation during sex change. Moreover, 18,037 potential simple sequence repeats (SSRs) were detected in 14,212 unigenes for marker development. This transcript dataset will greatly increase available resources for gene mining and function analysis, and could contribute valuable information to in-depth studies on reproductive biology, genetics and genomics in the future.

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De novo transcriptome analysis and antimicrobial peptides screening in skin of Paa boulengeri

Cited by 4 publications

References 65 publications

De novo transcriptomic characterization of Betta splendens for identifying sex-biased genes potentially involved in aggressive behavior modulation and EST-SSR maker development

De novo transcriptomic characterization of Betta splendens for identifying sex-biased genes potentially involved in aggressive behavior modulation and EST-SSR maker development

De Novo Transcriptomic Characterization Enables Novel Microsatellite Identification and Marker Development in Betta splendens

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