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Zeng Z, Peng Q, Yang F, Wu J, Guo H, Deng H, Zhao L, Long K, Wang X. Transcriptome analysis of pigeon pituitary gland: expression changes of genes encoding protein and peptide hormones at different breeding stages. Poult Sci 2024; 103:103742. [PMID: 38670056 PMCID: PMC11068619 DOI: 10.1016/j.psj.2024.103742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Unlike other poultry, parent pigeons produce "pigeon milk" in their crops to nurture their squabs, which is mainly controlled by prolactin (PRL). Exception for PRL, the pituitary gland may also release various other peptide and protein hormones. However, whether these hormones change during pigeon crop lactation and their potential physiological functions remain unclear. Here, to identify potential peptide or protein hormone genes that regulate crop lactation, we conducted transcriptome analysis of pigeon pituitary glands at 3 different breeding stages (the ceased stage-nonincubation and non-nurturing stage, the 11th d of the incubation, and the 1st d of the nurturing stage) using RNA sequencing (RNA-Seq). Our analysis identified a total of 15,191 mRNAs and screened out 297 differentially expressed genes (DEG), including PRL, VIP, etc. The expression abundance of PRL mRNA on the 1st d of the nurturing stage was respectively 4.93 and 3.62 folds higher when compared to the ceased stage and the 11th d of the incubation stage. Additionally, the expression abundance of VIP is higher in the 1st d of the nurturing stage than in the ceased stage. Protein-protein interaction (PPI) network and Molecular Complex Detection (MCODE) analysis identified several vital DEGs (e.g., GHRHR, VIP, etc.), being closely linked with hormone and enriched in neuropeptide signaling pathway and response to the hormone. Expression pattern analysis revealed that these DEGs exhibited 4 distinct expression patterns (profile 10, 16, 18, 19). Genes in profile 10 and 19 presented a trend with the highest expression level on 1st d of the nurturing stage, and functional enrichment analysis indicated that these genes are involved in neuropeptide hormone activity, receptor-ligand activity, and the extracellular matrix, etc. Taken together, being consistent with PRL, some genes encoding peptide and protein hormones (e.g., VIP) presented differentially expressed in different breeding stages. It suggests that these hormones may be involved in regulation of the crop lactation process or corresponding behavior in domestic pigeons. The results of this study help to gain new insights into the role of pituitary gland in regulating pigeon lactation.
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Affiliation(s)
- Zhanggui Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Qiyi Peng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Fuxing Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Jie Wu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Hongrui Guo
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P. R. of China
| | - Huidan Deng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P. R. of China
| | - Ling Zhao
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P. R. of China
| | - Keren Long
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, P. R. China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Xun Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, P. R. China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, P. R. China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China.
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Maclary ET, Holt C, Concepcion GT, Sović I, Vickrey AI, Yandell M, Kronenberg Z, Shapiro MD. Assembly and annotation of 2 high-quality columbid reference genomes from sequencing of a Columba livia × Columba guinea F1 hybrid. G3 (Bethesda) 2024; 14:jkad280. [PMID: 38066578 PMCID: PMC10849363 DOI: 10.1093/g3journal/jkad280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023]
Abstract
Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic resources for columbids is essential to further many of these studies. Here, we present high-quality genome assemblies and annotations for 2 columbid species, Columba livia and Columba guinea. We simultaneously assembled C. livia and C. guinea genomes from long-read sequencing of a single F1 hybrid individual. The new C. livia genome assembly (Cliv_3) shows improved completeness and contiguity relative to Cliv_2.1, with an annotation incorporating long-read IsoSeq data for more accurate gene models. Intensive selective breeding of C. livia has given rise to hundreds of breeds with diverse morphological and behavioral characteristics, and Cliv_3 offers improved tools for mapping the genomic architecture of interesting traits. The C. guinea genome assembly is the first for this species and is a new resource for avian comparative genomics. Together, these assemblies and annotations provide improved resources for functional studies of columbids and avian comparative genomics in general.
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Affiliation(s)
- Emily T Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Carson Holt
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Ivan Sović
- Pacific Biosciences, Menlo Park, CA 94025, USA
- Digital BioLogic d.o.o, Ivanić-Grad 10310, Croatia
| | - Anna I Vickrey
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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Fu Y, Song Y, Jiang D, Pan J, Li W, Zhang X, Chen W, Tian Y, Shen X, Huang Y. Comprehensive Transcriptomic and Metabolomic Analysis Revealed the Functional Differences in Pigeon Lactation between Male and Female during the Reproductive Cycle. Animals (Basel) 2023; 14:75. [PMID: 38200806 PMCID: PMC10778231 DOI: 10.3390/ani14010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Lactation is a unique reproductive behavior in pigeons, with the crop serving as the organ responsible for secreting pigeon milk. Both male and female pigeons can produce crop milk and rear their offspring through a division of labor. Since the time of the secretion of pigeon crop milk is different in the process of feeding the young, whether the metabolism and formation of pigeon milk use the same mechanism is a very interesting scientific question. However, the metabolic dynamics and underlying genetic mechanisms involved in the formation of pigeon crop milk remain unclear, particularly during the incubation-feeding reproductive cycle. In this study, we integrated lactation-associated metabolism and transcriptome data from the crop tissues of both male and female pigeons during the brooding and feeding stages. We mapped the changes in metabolites related to milk formation in the crop tissues during these stages. Through metabolome profiling, we identified 1413 metabolites among 18 crop tissues. During the breeding cycles, the concentrations of estrone, L-ergothioneine, and L-histidine exhibited the most dynamic changes in females. In contrast, estrone, L-anserine, 1-methylhistidine, homovanillate, oxidized glutathione, and reducing glutathione showed the most dynamic changes in males. Gender-specific differences were observed in the metabolome, with several metabolites significantly differing between males and females, many of which were correlated with cytokine binding, immunity, and cytochrome P450 activity. Using this dataset, we constructed complex regulatory networks, enabling us to identify important metabolites and key genes involved in regulating the formation of pigeon milk in male and female pigeons, respectively. Additionally, we investigated gender-associated differences in the crop metabolites of pigeons. Our study revealed differences in the modulation of pigeon crop milk metabolism between males and females and shed light on the potential functions of male and female pigeon milk in the growth, development, and immunity of young pigeons, an area that has not been previously explored. In conclusion, our results provide new insights into the metabolic regulation of pigeon crop milk formation during the brooding and breeding stages. Furthermore, our findings lay the foundation for the accurate development of artificial pigeon milk.
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Affiliation(s)
- Yuting Fu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
| | - Yan Song
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
| | - Danli Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
| | - Jianqiu Pan
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
| | - Wanyan Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
| | - Xumeng Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
| | - Wenbin Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yunbo Tian
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
| | - Xu Shen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
| | - Yunmao Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
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Maclary ET, Holt C, Concepcion GT, Sović I, Vickrey AI, Yandell M, Kronenberg Z, Shapiro MD. Assembly and annotation of two high-quality columbid reference genomes from sequencing of a Columba livia x Columba guinea F 1 hybrid. bioRxiv 2023:2023.10.11.561892. [PMID: 37873124 PMCID: PMC10592783 DOI: 10.1101/2023.10.11.561892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic resources for colubids is essential to further many of these studies. Here, we present high-quality genome assemblies and annotations for two columbid species, Columba livia and C. guinea. We simultaneously assembled C. livia and C. guinea genomes from long-read sequencing of a single F1 hybrid individual. The new C. livia genome assembly (Cliv_3) shows improved completeness and contiguity relative to Cliv_2.1, with an annotation incorporating long-read IsoSeq data for more accurate gene models. Intensive selective breeding of C. livia has given rise to hundreds of breeds with diverse morphological and behavioral characteristics, and Cliv_3 offers improved tools for mapping the genomic architecture of interesting traits. The C. guinea genome assembly is the first for this species and is a new resource for avian comparative genomics. Together, these assemblies and annotations provide improved resources for functional studies of columbids and avian comparative genomics in general.
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Affiliation(s)
- Emily T. Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Carson Holt
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | | | - Ivan Sović
- Pacific Biosciences, Menlo Park, CA, USA
- Digital BioLogic d.o.o, Ivanić-Grad, Croatia
| | - Anna I. Vickrey
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | | | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
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