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Piégu B, Lefort G, Douet C, Milhes M, Jacques A, Lareyre JJ, Monget P, Fouchécourt S. A first complete catalog of highly expressed genes in eight chicken tissues reveals uncharacterized gene families specific for the chicken testis. Physiol Genomics 2024; 56:445-456. [PMID: 38497118 DOI: 10.1152/physiolgenomics.00151.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/19/2024] Open
Abstract
Based on next-generation sequencing, we established a repertoire of differentially overexpressed genes (DoEGs) in eight adult chicken tissues: the testis, brain, lung, liver, kidney, muscle, heart, and intestine. With 4,499 DoEGs, the testis had the highest number and proportion of DoEGs compared with the seven somatic tissues. The testis DoEG set included the highest proportion of long noncoding RNAs (lncRNAs; 1,851, representing 32% of the lncRNA genes in the whole genome) and the highest proportion of protein-coding genes (2,648, representing 14.7% of the protein-coding genes in the whole genome). The main significantly enriched Gene Ontology terms related to the protein-coding genes were "reproductive process," "tubulin binding," and "microtubule cytoskeleton." Using real-time quantitative reverse transcription-polymerase chain reaction, we confirmed the overexpression of genes that encode proteins already described in chicken sperm [such as calcium binding tyrosine phosphorylation regulated (CABYR), spermatogenesis associated 18 (SPATA18), and CDK5 regulatory subunit associated protein (CDK5RAP2)] but whose testis origin had not been previously confirmed. Moreover, we demonstrated the overexpression of vertebrate orthologs of testis genes not yet described in the adult chicken testis [such as NIMA related kinase 2 (NEK2), adenylate kinase 7 (AK7), and CCNE2]. Using clustering according to primary sequence homology, we found that 1,737 of the 2,648 (67%) testis protein-coding genes were unique genes. This proportion was significantly higher than the somatic tissues except muscle. We clustered the other 911 testis protein-coding genes into 495 families, from which 47 had all paralogs overexpressed in the testis. Among these 47 testis-specific families, eight contained uncharacterized duplicated paralogs without orthologs in other metazoans except birds: these families are thus specific for chickens/birds.NEW & NOTEWORTHY Comparative next-generation sequencing analysis of eight chicken tissues showed that the testis has highest proportion of long noncoding RNA and protein-coding genes of the whole genome. We identified new genes in the chicken testis, including orthologs of known mammalian testicular genes. We also identified 47 gene families in which all the members were overexpressed, if not exclusive, in the testis. Eight families, organized in duplication clusters, were unknown, without orthologs in metazoans except birds, and are thus specific for chickens/birds.
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Affiliation(s)
- Benoît Piégu
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Université de Tours, PRC, Nouzilly, France
| | - Gaëlle Lefort
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Université de Tours, PRC, Nouzilly, France
| | - Cécile Douet
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Université de Tours, PRC, Nouzilly, France
| | - Marine Milhes
- US 1426, GeT-PlaGe, Genotoul, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Castanet-Tolosan, France
| | - Aurore Jacques
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Université de Tours, PRC, Nouzilly, France
| | - Jean-Jacques Lareyre
- UR1037 LPGP, Fish Physiology and Genomics, Campus de Beaulieu, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Rennes, France
| | - Philippe Monget
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Université de Tours, PRC, Nouzilly, France
| | - Sophie Fouchécourt
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Université de Tours, PRC, Nouzilly, France
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Kaku Y, Isono Y, Tanaka H, Kobayashi T, Kanemori Y, Kashiwabara SI. Intronless Pabpc6 encodes a testis-specific, cytoplasmic poly(A)-binding protein but is dispensable for spermatogenesis in the mouse†. Biol Reprod 2024; 110:834-847. [PMID: 38281153 DOI: 10.1093/biolre/ioae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/25/2023] [Accepted: 01/23/2024] [Indexed: 01/30/2024] Open
Abstract
Besides ubiquitous poly(A)-binding protein, cytoplasmic 1 (PABPC1), testis-specific PABPC2/PABPt (in humans, referred to as PABPC3), and female and male germline-specific PABPC1L/ePAB, have been reported in the mouse testis. Recent in silico analysis additionally identified testis-specific Pabpc6 in the mouse. In this study, we characterized PABPC6 and its mutant mice. PABPC6 was initially detectable in the cytoplasm of pachytene spermatocytes, increased in abundance in round spermatids, and decreased in elongating spermatids. PABPC6 was capable of binding to poly(A) tails of various mRNAs and interacting with translation-associated factors, including EIF4G, PAIP1, and PAIP2. Noteworthy was that PABPC6, unlike PABPC1, was barely associated with translationally active polysomes and enriched in chromatoid bodies of round spermatids. Despite these unique characteristics, neither synthesis of testicular proteins nor spermatogenesis was affected in the mutant mice lacking PABPC6, suggesting that PABPC6 is functionally redundant with other co-existing PABPC proteins during spermatogenesis.
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Affiliation(s)
- Yuko Kaku
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yuka Isono
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hideto Tanaka
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Tomohiro Kobayashi
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshinori Kanemori
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Shin-Ichi Kashiwabara
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Yin Z, Ding G, Xue Y, Yu X, Dong J, Huang J, Ma J, He F. A postmeiotically bifurcated roadmap of honeybee spermatogenesis marked by phylogenetically restricted genes. PLoS Genet 2023; 19:e1011081. [PMID: 38048317 PMCID: PMC10721206 DOI: 10.1371/journal.pgen.1011081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/14/2023] [Accepted: 11/22/2023] [Indexed: 12/06/2023] Open
Abstract
Haploid males of hymenopteran species produce gametes through an abortive meiosis I followed by meiosis II that can either be symmetric or asymmetric in different species. Thus, one spermatocyte could give rise to two spermatids with either equal or unequal amounts of cytoplasm. It is currently unknown what molecular features accompany these postmeiotic sperm cells especially in species with asymmetric meiosis II such as bees. Here we present testis single-cell RNA sequencing datasets from the honeybee (Apis mellifera) drones of 3 and 14 days after emergence (3d and 14d). We show that, while 3d testes exhibit active, ongoing spermatogenesis, 14d testes only have late-stage spermatids. We identify a postmeiotic bifurcation in the transcriptional roadmap during spermatogenesis, with cells progressing toward the annotated spermatids (SPT) and small spermatids (sSPT), respectively. Despite an overall similarity in their transcriptomic profiles, sSPTs express the fewest genes and the least RNA content among all the sperm cell types. Intriguingly, sSPTs exhibit a relatively high expression level for Hymenoptera-restricted genes and a high mutation load, suggesting that the special meiosis II during spermatogenesis in the honeybee is accompanied by phylogenetically young gene activities.
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Affiliation(s)
- Zhiyong Yin
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Guiling Ding
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingdi Xue
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xianghui Yu
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jie Dong
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiaxing Huang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Ma
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang, China
| | - Feng He
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang, China
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Barros CP, Derks MFL, Mohr J, Wood BJ, Crooijmans RPMA, Megens HJ, Bink MCAM, Groenen MAM. A new haplotype-resolved turkey genome to enable turkey genetics and genomics research. Gigascience 2022; 12:giad051. [PMID: 37489751 PMCID: PMC10360393 DOI: 10.1093/gigascience/giad051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 12/12/2022] [Accepted: 06/27/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND The domesticated turkey (Meleagris gallopavo) is a species of significant agricultural importance and is the second largest contributor, behind broiler chickens, to world poultry meat production. The previous genome is of draft quality and partly based on the chicken (Gallus gallus) genome. A high-quality reference genome of M. gallopavo is essential for turkey genomics and genetics research and the breeding industry. RESULTS By adopting the trio-binning approach, we were able to assemble a high-quality chromosome-level F1 assembly and 2 parental haplotype assemblies, leveraging long-read technologies and genome-wide chromatin interaction data (Hi-C). From a total of 40 chromosomes (2n = 80), we captured 35 chromosomes in a single scaffold, showing much improved genome completeness and continuity compared to the old assembly build. The 3 assemblies are of higher quality than the previous draft quality assembly and comparable to the chicken assemblies (GRCg7) shown by the largest contig N50 (26.6 Mb) and comparable BUSCO gene set completeness scores (96-97%). Comparative analyses confirm a previously identified large inversion of around 19 Mbp on the Z chromosome not found in other Galliformes. Structural variation between the parent haplotypes was identified, which poses potential new target genes for breeding. CONCLUSIONS We contribute a new high-quality turkey genome at the chromosome level, benefiting turkey genetics and other avian genomics research as well as the turkey breeding industry.
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Affiliation(s)
- Carolina P Barros
- Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Martijn F L Derks
- Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Jeff Mohr
- Hybrid Turkeys, 650 Riverbend Drive Suite C, Kitchener, ON N2K 3S2, Canada
| | - Benjamin J Wood
- Hybrid Turkeys, 650 Riverbend Drive Suite C, Kitchener, ON N2K 3S2, Canada
- School of Veterinary Science, University of Queensland, Gatton, QLD 4343, Australia
| | | | - Hendrik-Jan Megens
- Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Marco C A M Bink
- Hendrix Genetics Research, Technology & Services, Boxmeer, AC 5830, The Netherlands
| | - Martien A M Groenen
- Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
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CLPP Depletion Causes Diplotene Arrest; Underlying Testis Mitochondrial Dysfunction Occurs with Accumulation of Perrault Proteins ERAL1, PEO1, and HARS2. Cells 2022; 12:cells12010052. [PMID: 36611846 PMCID: PMC9818230 DOI: 10.3390/cells12010052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Human Perrault syndrome (PRLTS) is autosomal, recessively inherited, and characterized by ovarian insufficiency with hearing loss. Among the genetic causes are mutations of matrix peptidase CLPP, which trigger additional azoospermia. Here, we analyzed the impact of CLPP deficiency on male mouse meiosis stages. Histology, immunocytology, different OMICS and biochemical approaches, and RT-qPCR were employed in CLPP-null mouse testis. Meiotic chromosome pairing and synapsis proceeded normally. However, the foci number of the crossover marker MLH1 was slightly reduced, and foci persisted in diplotene, most likely due to premature desynapsis, associated with an accumulation of the DNA damage marker γH2AX. No meiotic M-phase cells were detected. Proteome profiles identified strong deficits of proteins involved in male meiotic prophase (HSPA2, SHCBP1L, DMRT7, and HSF5), versus an accumulation of AURKAIP1. Histone H3 cleavage, mtDNA extrusion, and cGAMP increase suggested innate immunity activation. However, the deletion of downstream STING/IFNAR failed to alleviate pathology. As markers of underlying mitochondrial pathology, we observed an accumulation of PRLTS proteins ERAL1, PEO1, and HARS2. We propose that the loss of CLPP leads to the extrusion of mitochondrial nucleotide-binding proteins to cytosol and nucleus, affecting late meiotic prophase progression, and causing cell death prior to M-phase entry. This phenotype is more severe than in mito-mice or mutator-mice.
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Yin Y, Mu W, Yu X, Wang Z, Xu K, Wu X, Cai Y, Zhang M, Lu G, Chan WY, Ma J, Huang T, Liu H. LRRC46 Accumulates at the Midpiece of Sperm Flagella and Is Essential for Spermiogenesis and Male Fertility in Mouse. Int J Mol Sci 2022; 23:8525. [PMID: 35955660 PMCID: PMC9369233 DOI: 10.3390/ijms23158525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
The sperm flagellum is essential for male fertility. Multiple morphological abnormalities of the sperm flagella (MMAF) is a severe form of asthenoteratozoospermia. MMAF phenotypes are understood to result from pathogenic variants of genes from multiple families including AKAP, DANI, DNAH, RSPH, CCDC, CFAP, TTC, and LRRC, among others. The Leucine-rich repeat protein (LRRC) family includes two members reported to cause MMAF phenotypes: Lrrc6 and Lrrc50. Despite vigorous research towards understanding the pathogenesis of MMAF-related diseases, many genes remain unknown underlying the flagellum biogenesis. Here, we found that Leucine-rich repeat containing 46 (LRRC46) is specifically expressed in the testes of adult mice, and show that LRRC46 is essential for sperm flagellum biogenesis. Both scanning electron microscopy (SEM) and Papanicolaou staining (PS) presents that the knockout of Lrrc46 in mice resulted in typical MMAF phenotypes, including sperm with short, coiled, and irregular flagella. The male KO mice had reduced total sperm counts, impaired sperm motility, and were completely infertile. No reproductive phenotypes were detected in Lrrc46-/- female mice. Immunofluorescence (IF) assays showed that LRRC46 was present throughout the entire flagella of control sperm, albeit with evident concentration at the mid-piece. Transmission electron microscopy (TEM) demonstrated striking flagellar defects with axonemal and mitochondrial sheath malformations. About the important part of the Materials and Methods, SEM and PS were used to observe the typical MMAF-related irregular flagella morphological phenotypes, TEM was used to further inspect the sperm flagellum defects in ultrastructure, and IF was chosen to confirm the location of protein. Our study suggests that LRRC46 is an essential protein for sperm flagellum biogenesis, and its mutations might be associated with MMAF that causes male infertility. Thus, our study provides insights for understanding developmental processes underlying sperm flagellum formation and contribute to further observe the pathogenic genes that cause male infertility.
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Affiliation(s)
- Yingying Yin
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China; (Y.Y.); (W.M.); (X.Y.); (Z.W.); (K.X.); (X.W.); (Y.C.); (M.Z.); (J.M.)
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
| | - Wenyu Mu
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China; (Y.Y.); (W.M.); (X.Y.); (Z.W.); (K.X.); (X.W.); (Y.C.); (M.Z.); (J.M.)
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
| | - Xiaochen Yu
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China; (Y.Y.); (W.M.); (X.Y.); (Z.W.); (K.X.); (X.W.); (Y.C.); (M.Z.); (J.M.)
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
| | - Ziqi Wang
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China; (Y.Y.); (W.M.); (X.Y.); (Z.W.); (K.X.); (X.W.); (Y.C.); (M.Z.); (J.M.)
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
| | - Ke Xu
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China; (Y.Y.); (W.M.); (X.Y.); (Z.W.); (K.X.); (X.W.); (Y.C.); (M.Z.); (J.M.)
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
| | - Xinyue Wu
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China; (Y.Y.); (W.M.); (X.Y.); (Z.W.); (K.X.); (X.W.); (Y.C.); (M.Z.); (J.M.)
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
| | - Yuling Cai
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China; (Y.Y.); (W.M.); (X.Y.); (Z.W.); (K.X.); (X.W.); (Y.C.); (M.Z.); (J.M.)
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
| | - Mingyu Zhang
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China; (Y.Y.); (W.M.); (X.Y.); (Z.W.); (K.X.); (X.W.); (Y.C.); (M.Z.); (J.M.)
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
| | - Gang Lu
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China; (G.L.); (W.-Y.C.)
| | - Wai-Yee Chan
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China; (G.L.); (W.-Y.C.)
| | - Jinlong Ma
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China; (Y.Y.); (W.M.); (X.Y.); (Z.W.); (K.X.); (X.W.); (Y.C.); (M.Z.); (J.M.)
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China; (G.L.); (W.-Y.C.)
| | - Tao Huang
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China; (Y.Y.); (W.M.); (X.Y.); (Z.W.); (K.X.); (X.W.); (Y.C.); (M.Z.); (J.M.)
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
| | - Hongbin Liu
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China; (Y.Y.); (W.M.); (X.Y.); (Z.W.); (K.X.); (X.W.); (Y.C.); (M.Z.); (J.M.)
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China; (G.L.); (W.-Y.C.)
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Fouchécourt S, Fillon V, Marrauld C, Callot C, Ronsin S, Picolo F, Douet C, Piégu B, Monget P. Expanding duplication of the testis PHD Finger Protein 7 (PHF7) gene in the chicken genome. Genomics 2022; 114:110411. [PMID: 35716824 DOI: 10.1016/j.ygeno.2022.110411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/06/2022] [Accepted: 06/10/2022] [Indexed: 11/04/2022]
Abstract
Gene duplications increase genetic and phenotypic diversity and occur in complex genomic regions that are still difficult to sequence and assemble. PHD Finger Protein 7 (PHF7) acts during spermiogenesis for histone-to-histone protamine exchange and is a determinant of male fertility in Drosophila and the mouse. We aimed to explore and characterise in the chicken genome the expanding family of the numerous orthologues of the unique mouse Phf7 gene (highly expressed in the testis), observing the fact that this information is unclear and/or variable according to the versions of databases. We validated nine primer pairs by in silico PCR for their use in screening the chicken bacterial artificial chromosome (BAC) library to produce BAC-derived probes to detect and localise PHF7-like loci by fluorescence in situ hybridisation (FISH). We selected nine BAC that highlighted nine chromosomal regions for a total of 10 distinct PHF7-like loci on five Gallus gallus chromosomes: Chr1 (three loci), Chr2 (two loci), Chr12 (one locus), Chr19 (one locus) and ChrZ (three loci). We sequenced the corresponding BAC by using high-performance PacBio technology. After assembly, we performed annotation with the FGENESH program: there were a total of 116 peptides, including 39 PHF7-like proteins identified by BLASTP. These proteins share a common exon-intron core structure of 8-11 exons. Phylogeny revealed that the duplications occurred first between chromosomal regions and then inside each region. There are other duplicated genes in the identified BAC sequences, suggesting that these genomic regions exhibit a high rate of tandem duplication. We showed that the PHF7 gene, which is highly expressed in the rooster testis, is a highly duplicated gene family in the chicken genome, and this phenomenon probably concerns other bird species.
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Affiliation(s)
| | - Valérie Fillon
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet Tolosan, France
| | - Christelle Marrauld
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet Tolosan, France
| | - Caroline Callot
- CNRGV - Plant Genomic Center, INRAE, F-31326, Castanet Tolosan, France
| | - Sarah Ronsin
- CNRS, IFCE, INRAE, Université de Tours, PRC, F-37380, Nouzilly, France
| | - Floriane Picolo
- CNRS, IFCE, INRAE, Université de Tours, PRC, F-37380, Nouzilly, France
| | - Cécile Douet
- CNRS, IFCE, INRAE, Université de Tours, PRC, F-37380, Nouzilly, France
| | - Benoit Piégu
- CNRS, IFCE, INRAE, Université de Tours, PRC, F-37380, Nouzilly, France
| | - Philippe Monget
- CNRS, IFCE, INRAE, Université de Tours, PRC, F-37380, Nouzilly, France
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8
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A comparative genomic approach using mouse and fruit fly data to discover genes involved in testis function in hymenopterans with a focus on Nasonia vitripennis. BMC Ecol Evol 2021; 21:90. [PMID: 34011283 PMCID: PMC8132408 DOI: 10.1186/s12862-021-01825-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 05/12/2021] [Indexed: 11/18/2022] Open
Abstract
Background Spermatogenesis appears to be a relatively well-conserved process even among distantly related animal taxa such as invertebrates and vertebrates. Although Hymenopterans share many characteristics with other organisms, their complex haplodiploid reproduction system is still relatively unknown. However, they serve as a complementary insect model to Drosophila for studying functional male fertility. In this study, we used a comparative method combining taxonomic, phenotypic data and gene expression to identify candidate genes that could play a significant role in spermatogenesis in hymenopterans. Results Of the 546 mouse genes predominantly or exclusively expressed in the mouse testes, 36% had at least one ortholog in the fruit fly. Of these genes, 68% had at least one ortholog in one of the six hymenopteran species we examined. Based on their gene expression profiles in fruit fly testes, 71 of these genes were hypothesized to play a marked role in testis function. Forty-three of these 71 genes had an ortholog in at least one of the six hymenopteran species examined, and their enriched GO terms were related to the G2/M transition or to cilium organization, assembly, or movement. Second, of the 379 genes putatively involved in male fertility in Drosophila, 224 had at least one ortholog in each of the six Hymenoptera species. Finally, we showed that 199 of these genes were expressed in early pupal testis in Nasonia vitripennis; 86 exhibited a high level of expression, and 54 displayed modulated expression during meiosis. Conclusions In this study combining phylogenetic and experimental approaches, we highlighted genes that may have a major role in gametogenesis in hymenopterans; an essential prerequisite for further research on functional importance of these genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01825-6.
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Greither T, Schumacher J, Dejung M, Behre HM, Zischler H, Butter F, Herlyn H. Fertility Relevance Probability Analysis Shortlists Genetic Markers for Male Fertility Impairment. Cytogenet Genome Res 2020; 160:506-522. [PMID: 33238277 DOI: 10.1159/000511117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/26/2020] [Indexed: 12/27/2022] Open
Abstract
Impairment of male fertility is one of the major public health issues worldwide. Nevertheless, genetic causes of male sub- and infertility can often only be suspected due to the lack of reliable and easy-to-use routine tests. Yet, the development of a marker panel is complicated by the large quantity of potentially predictive markers. Actually, hundreds or even thousands of genes could have fertility relevance. Thus, a systematic method enabling a selection of the most predictive markers out of the many candidates is required. As a criterion for marker selection, we derived a gene-specific score, which we refer to as fertility relevance probability (FRP). For this purpose, we first categorized 2,753 testis-expressed genes as either candidate markers or non-candidates, according to phenotypes in male knockout mice. In a parallel approach, 2,502 genes were classified as candidate markers or non-candidates based on phenotypes in men. Subsequently, we conducted logistic regression analyses with evolutionary rates of genes (dN/dS), transcription levels in testis relative to other organs, and connectivity of the encoded proteins in a protein-protein interaction network as covariates. In confirmation of the procedure, FRP values showed the expected pattern, thus being overall higher in genes with known relevance for fertility than in their counterparts without corresponding evidence. In addition, higher FRP values corresponded with an increased dysregulation of protein abundance in spermatozoa of 37 men with normal and 38 men with impaired fertility. Present analyses resulted in a ranking of genes according to their probable predictive power as candidate markers for male fertility impairment. Thus, AKAP4, TNP1, DAZL, BRDT, DMRT1, SPO11, ZPBP, HORMAD1, and SMC1B are prime candidates toward a marker panel for male fertility impairment. Additional candidate markers are DDX4, SHCBP1L, CCDC155, ODF1, DMRTB1, ASZ1, BOLL, FKBP6, SLC25A31, PRSS21, and RNF17. FRP inference additionally provides clues for potential new markers, thereunder TEX37 and POU4F2. The results of our logistic regression analyses are freely available at the PreFer Genes website (https://prefer-genes.uni-mainz.de/).
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Affiliation(s)
- Thomas Greither
- Center for Reproductive Medicine and Andrology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Julia Schumacher
- Anthropology, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Mario Dejung
- Quantitative Proteomics, Institute of Molecular Biology (IMB) Mainz, Mainz, Germany
| | - Hermann M Behre
- Center for Reproductive Medicine and Andrology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Hans Zischler
- Anthropology, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Falk Butter
- Quantitative Proteomics, Institute of Molecular Biology (IMB) Mainz, Mainz, Germany
| | - Holger Herlyn
- Anthropology, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany,
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