Development of SNVs and indels markers mined out of the first multi-organ transcriptomes from Hypancistrus zebra (Loricariidae), an endangered Amazonian catfish

Magalhães, Maithê Gaspar Pontes; Moreira, Daniel A.; Furtado, Carolina; Parente, Thiago Estevam

doi:10.1016/j.ygeno.2019.06.013

Cited by 3 publications

(4 citation statements)

References 31 publications

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“…This was consistent with the findings in Acipenser dabryanus (Chen et al, 2020). However, dinucleotide-repeat SSR was the main type in other fishes (Magalhães et al, 2019).…”

Section: Identification and Classification Of Est-ssrssupporting

confidence: 92%

“…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%

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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.

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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.

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“…This was consistent with the findings in Acipenser dabryanus (Chen et al, 2020). However, dinucleotide-repeat SSR was the main type in other fishes (Magalhães et al, 2019).…”

Section: Identification and Classification Of Est-ssrssupporting

confidence: 92%

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.

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“…On the other hand, the BUSCO analysis showed that most of the Actinopterygian single-copy orthologs (61%) were found completely in our assembly and 30.2% of the 3,640 orthologs were classified as missing from our assembly. This seems to be a relatively good level of completeness, when comparing with other assemblies reported for this class of organisms, especially if we consider that BUSCO recovery tends to be higher when multiple tissues and different stages are used to generate the assemblies, and our assembly was made from a single tissue of a single specimen 50,51 . Furthermore, only 8.8% of the orthologs were recovered partially, indicating a low level of incomplete transcripts.…”

Section: Discussionmentioning

confidence: 82%

“…To evaluate the quality and completeness of our transcriptome assembly we used the N50 reference-free metric and the reference-based BUSCO metric, which give us an idea of how good our assembly is in terms of continuity and coverage of the contigs respectively. The N50 measure showed that 50% of total sequence length is contained in sequences equal or greater than 2,019 bp, which is not a short length for the transcripts in our transcriptome assembly 47,49,50 . On the other hand, the BUSCO analysis showed that most of the Actinopterygian single-copy orthologs (61%) were found completely in our assembly and 30.2% of the 3,640 orthologs were classified as missing from our assembly.…”

Section: Discussionmentioning

confidence: 93%

De novo assembly and characterization of the liver transcriptome of Mugil incilis (lisa) using next generation sequencing

Bertel-Sevilla

Alzate

Olívero-Verbel

2020

Sci Rep

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Mugil incilis (lisa) is an important commercial fish species in many countries, living along the coasts of the western Atlantic ocean. it has been used as a model organism for environmental monitoring and ecotoxicological investigations. nevertheless, available genomic and transcriptomic information for this organism is extremely deficient. The aim of this study was to characterize M. incilis hepatic transcriptome using Illumina paired-end sequencing. A total of 32,082,124 RNA-Seq read pairs were generated utilizing the HiSeq platform and subsequently cleaned and assembled into 93,912 contigs (N50 = 2,019 bp). The analysis of species distribution revealed that M. incilis contigs had the highest number of hits to Stegastes partitus (13.4%). Using a sequence similarity search against the public databases GO and KEGG, a total of 7,301 and 16,967 contigs were annotated, respectively. KeGG database showed genes related to environmental information, metabolism and organismal system pathways were highly annotated. complete or partial coding DnA sequences for several candidate genes associated with stress responses/detoxification of xenobiotics, as well as housekeeping genes, were employed to design primers that were successfully tested and validated by RT-qPCR. This study presents the first transcriptome resources for Mugil incilis and provides basic information for the development of genomic tools, such as the identification of RNA markers, useful to analyze environmental impacts on this fish Caribbean species.

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Comparative transcriptome sequencing analysis of the narrow-clawed crayfish Pontastacus leptodactylus (Eschscholtz, 1823) and discovery of candidate sex-related genes

Nazari

Khoshkholgh

Baeza

2022

Aquaculture Reports

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Development of SNVs and indels markers mined out of the first multi-organ transcriptomes from Hypancistrus zebra (Loricariidae), an endangered Amazonian catfish

Cited by 3 publications

References 31 publications

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

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

De novo assembly and characterization of the liver transcriptome of Mugil incilis (lisa) using next generation sequencing

Comparative transcriptome sequencing analysis of the narrow-clawed crayfish Pontastacus leptodactylus (Eschscholtz, 1823) and discovery of candidate sex-related genes

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