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Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo
BACKGROUND: Water buffalo (Bubalus bubalis) are divided into river buffalo and swamp buffalo subspecies and are essential livestock for agriculture and the local economy. Studies on buffalo reproduction have primarily focused on optimal fertility and embryonic mortality. There is currently limited k...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894430/ https://www.ncbi.nlm.nih.gov/pubmed/31824777 http://dx.doi.org/10.7717/peerj.8185 |
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author | Pang, Chun-Ying Bai, Ming-Zhou Zhang, Chi Chen, Junhui Lu, Xing-Rong Deng, Ting-Xian Ma, Xiao-Ya Duan, An-Qin Liang, Sha-sha Huang, Yun-Qi Xiu, Zhihui Liang, Xian-Wei |
author_facet | Pang, Chun-Ying Bai, Ming-Zhou Zhang, Chi Chen, Junhui Lu, Xing-Rong Deng, Ting-Xian Ma, Xiao-Ya Duan, An-Qin Liang, Sha-sha Huang, Yun-Qi Xiu, Zhihui Liang, Xian-Wei |
author_sort | Pang, Chun-Ying |
collection | PubMed |
description | BACKGROUND: Water buffalo (Bubalus bubalis) are divided into river buffalo and swamp buffalo subspecies and are essential livestock for agriculture and the local economy. Studies on buffalo reproduction have primarily focused on optimal fertility and embryonic mortality. There is currently limited knowledge on buffalo embryonic development, especially during the preimplantation period. Assembly of the river buffalo genome offers a reference for omics studies and facilitates transcriptomic analysis of preimplantation embryo development (PED). METHODS: We revealed transcriptomic profile of four stages (2-cell, 8-cell, Morula and Blastocyst) of PED via RNA-seq (Illumina HiSeq4000). Each stage comprised three biological replicates. The data were analyzed according to the basic RNA-seq analysis process. Ingenuity analysis of cell lineage control, especially transcription factor (TF) regulatory networks, was also performed. RESULTS: A total of 21,519 expressed genes and 67,298 transcripts were predicted from approximately 81.94 Gb of raw data. Analysis of transcriptome-wide expression, gene coexpression networks, and differentially expressed genes (DEGs) allowed for the characterization of gene-specific expression levels and relationships for each stage. The expression patterns of TFs, such as POU5F1, TEAD4, CDX4 and GATAs, were elucidated across diverse time series; most TF expression levels were increased during the blastocyst stage, during which time cell differentiation is initiated. All of these TFs were involved in the composition of the regulatory networks that precisely specify cell fate. These findings offer a deeper understanding of PED at the transcriptional level in the river buffalo. |
format | Online Article Text |
id | pubmed-6894430 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-68944302019-12-10 Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo Pang, Chun-Ying Bai, Ming-Zhou Zhang, Chi Chen, Junhui Lu, Xing-Rong Deng, Ting-Xian Ma, Xiao-Ya Duan, An-Qin Liang, Sha-sha Huang, Yun-Qi Xiu, Zhihui Liang, Xian-Wei PeerJ Agricultural Science BACKGROUND: Water buffalo (Bubalus bubalis) are divided into river buffalo and swamp buffalo subspecies and are essential livestock for agriculture and the local economy. Studies on buffalo reproduction have primarily focused on optimal fertility and embryonic mortality. There is currently limited knowledge on buffalo embryonic development, especially during the preimplantation period. Assembly of the river buffalo genome offers a reference for omics studies and facilitates transcriptomic analysis of preimplantation embryo development (PED). METHODS: We revealed transcriptomic profile of four stages (2-cell, 8-cell, Morula and Blastocyst) of PED via RNA-seq (Illumina HiSeq4000). Each stage comprised three biological replicates. The data were analyzed according to the basic RNA-seq analysis process. Ingenuity analysis of cell lineage control, especially transcription factor (TF) regulatory networks, was also performed. RESULTS: A total of 21,519 expressed genes and 67,298 transcripts were predicted from approximately 81.94 Gb of raw data. Analysis of transcriptome-wide expression, gene coexpression networks, and differentially expressed genes (DEGs) allowed for the characterization of gene-specific expression levels and relationships for each stage. The expression patterns of TFs, such as POU5F1, TEAD4, CDX4 and GATAs, were elucidated across diverse time series; most TF expression levels were increased during the blastocyst stage, during which time cell differentiation is initiated. All of these TFs were involved in the composition of the regulatory networks that precisely specify cell fate. These findings offer a deeper understanding of PED at the transcriptional level in the river buffalo. PeerJ Inc. 2019-12-02 /pmc/articles/PMC6894430/ /pubmed/31824777 http://dx.doi.org/10.7717/peerj.8185 Text en ©2019 Pang et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Agricultural Science Pang, Chun-Ying Bai, Ming-Zhou Zhang, Chi Chen, Junhui Lu, Xing-Rong Deng, Ting-Xian Ma, Xiao-Ya Duan, An-Qin Liang, Sha-sha Huang, Yun-Qi Xiu, Zhihui Liang, Xian-Wei Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo |
title | Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo |
title_full | Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo |
title_fullStr | Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo |
title_full_unstemmed | Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo |
title_short | Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo |
title_sort | global transcriptome analysis of different stages of preimplantation embryo development in river buffalo |
topic | Agricultural Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894430/ https://www.ncbi.nlm.nih.gov/pubmed/31824777 http://dx.doi.org/10.7717/peerj.8185 |
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