- Result: By comparative genomic analysis, we found massive expansions of nAChR genes in molluscs and some other lophotrochozoans. - The expansion is particularly pronounced in stationary bivalve molluscs with simple nervous systems, with the number of nAChR genes ranging from 99 to 217 in five bivalves, compared with 10 to 29 in five ecdysozoans and vertebrates. - The expanded molluscan nAChR genes tend to be intronless and in tandem arrays due to retroposition followed by tandem duplication. - The expanded molluscan nAChR genes are highly diverse in sequence, domain structure, temporal and spatial expression profiles, implying diversified functions. - Some molluscan nAChR genes are expressed in early development before the development of the nervous system, while others are involved in immune and stress responses.. - Conclusion: The massive expansion and diversification of nAChR genes in bivalve molluscs may be a. - farreri, two nAChR genes were detected in all organs including adductor muscle, mantle, gill, hep- atopancreas, kidney and gonad, and their expression increased after LPS and TNF-a stimulation, indicating a role in immunomodulation [8]. - Our analysis of available genomic and transcriptomic data revealed a massive expansion and diversification of nAChR genes in molluscs and some other lophotrochozoans, possibly in adaptation to stationary life under variable environments.. - Homology-based annotation with InterProScan, KEGG, Nr and manual corrections identified a surprisingly large number of nAChR genes in various species. - Compared with model species from Ecdysozoa and Deuterostomia, a massive expansion of nAChR genes was found in molluscs (Fig. - The expansion was particularly pro- nounced in stationary bivalve molluscs with simple ner- vous systems, with the number of nAChR genes ranging from 99 to 217 in five bivalves, compared with 10 to 29 in five ecdysozoans and vertebrates. - A significant expan- sion of nAChR genes was also observed in Annelida (52–129), another branch of Lophotrochozoa.. - Evolution of nAChR gene families. - During evolution, the number of gene families decreased in all lineages, while the number of nAChR genes increased in molluscs and annelids. - In molluscs, the number of gene families decreased to 9–14, but the number of typical nAChR genes expanded to 205 in P. - Most of the expansion and contraction of nAChR genes are lineage-specific as exemplified by Family 3832.. - This family has 316 nAChR genes in the nine extant species analyzed, which can be traced back to 11 ortho- logs in the MRCA of bilaterians (Fig. - Massive intronless nAChR genes in molluscs. - Exon-intron structure analysis revealed large numbers of intronless nAChR genes in molluscs. - The number of intronless nAChR genes in molluscs ranged from 11 to 120, while intronless nAChRs were not observed in H.. - Further, many nAChR genes from molluscs (9–43) had only one or two introns, com- pared to an average of 6.8 introns per gene in humans (Additional file 1: Figure S1). - gigas of the 132 nAChRs were intronless, and nAChRs contained only 1–2 introns. - martensii of the 217 nAChRs were intronless, and 43 nAChRs (19.8%) had only 1–2 introns (Fig. - Phylogenetic analysis of 307 nAChR genes from C.. - Furthermore, intron-rich nAChR genes (>. - Detailed analysis of one cluster showed that some of the intron positions are conserved in the intron-rich nAChRs, while intron positions in the one-intron only nAChRs were novel, probably represent- ing newly gained introns after retroposition (Fig. - 1 Expansion of nAChR genes in molluscs. - a Number of nAChR genes in different species. - Within the same cluster, intron-rich and intron-poor nAChR genes differed in temporal and spatial expression profiles, indicative of divergence in regulatory elements and possibly function. - marten- sii, some intron-poor nAChRs expressed during embry- onic development before trochophore stage and the development of the nervous system, while intron-rich nAChRs expressed at D- and late larval stages (Fig. - Overall, expression analysis of all nAChR genes from C. - Tandem duplication of nAChR genes. - Of the 132 nAChR genes in C. - martensii of the 217 nAChR genes are present in tandem ar- rays: 18 two-gene pairs, 11 three-gene arrays, 2–3 arrays of 4–6 genes, one array of seven genes and two arrays of 12 genes. - Thus, in addition to retroposition, tandem duplication is also a major con- tributor to the massive expansion of nAChR genes in molluscs.. - 2 Evolution of nAChR gene families. - a Phylogenetic tree of 644 nAChR genes with the typical LBD-NTM domain structure (without other functional domains) from nine species. - The number of nAChR families is in green, and the number of nAChR genes is in red. - b Phylogenetic tree of Family 3832 with the number of nAChR genes in red. - The two arrays originated in the common ancestor of the two bi- valves as indicated by sequence homology and similar- ities in gene structure (Fig. - The massive expansion has resulted in high sequence di- versity of the expanded nAChR genes. - The sequences of the Cys- loop from C. - Analysis of the developmental transcriptomes of P. - martensii indicated that 4 nAChR genes were highly expressed in fertilized eggs, 32 nAChRs were highly expressed at D-stage, along with some nAChRs highly and specifically expressed at other devel- opmental stages (Fig. - gigas, 10 nAChRs were highly expressed before or during the trochophore stage and before the development of the nervous system, and 21 nAChRs were only expressed after spat stage. - 3 Massive intronless nAChR genes in molluscs. - a Number of nAChR genes with >. - sapiens, showing lineage-specific expansion and close relationship between nAChR genes with no or 1 – 2 introns. - Analysis of organ transcriptomes revealed that the expression of many nAChR genes are organ-specific, which may reflect diversification in spatial regulation or functional compartmentalization. - Synthesis of the ACh in organs and during development Choline O-acetyltransferase (ChAT), a transferase en- zyme responsible for the synthesis of ACh, was not expressed in the gill but highly expressed in the labial palp (Fig. - gigas imply that ACh is produced in labial palp and trans- ported to the gill where most of the nAChR genes are expressed.. - 4 Intron position and expression of one cluster of nAChR genes. - Our analysis of a comprehensive set of genomic and transcriptomic data revealed massive expansion and diversity of nAChR genes in molluscs as well as some annelids, compared with ecdysozoans and deutero- stomes. - Prior to this study, only 14 nAChR genes have been reported and characterized in molluscs [7, 8]. - The finding of large numbers of nAChR genes in molluscs is surprising and provides an opportunity to study the evo- lution of this important class of receptors. - The largest expansion of nAChR genes is found in bivalve molluscs with simple nervous systems, 138 in scallop M. - A phylogenetic analysis of nAChRs from vertebrates and ecdysozoans revealed two gene duplication events before the diver- gence of the two lineages [36]. - During subsequent evolution and divergence, the number of gene families declined in all lineages, and the number of nAChR genes greatly expanded in bivalve molluscs but reduced in ecdysozoans and deutero- stomes. - Cephalo- pods and gastropods with more advanced nervous sys- tems and enhanced mobility have fewer nAChR genes than stationary bivalves. - platifrons that lives in a more stable deep-sea environment has 99 nAChR genes. - Thus, the massive expansion and diversification of nAChRs in bivalve molluscs could be an important part of the adaptation to stationary life under variable environments in compensation for simple nervous Table 2 Tandem duplication of nAChR genes in C. - Thus, the exceptionally high expression of nAChR genes in the gill may be an adaptation for rapid response to dynamic environmental conditions. - Our analysis indicates that both retroposition and tan- dem duplication have contributed to the massive expan- sion of nAChR genes in bivalve molluscs, as indicated by high proportion of intronless or intron-poor genes and tandem arrays. - Intronless nAChR genes are only found in molluscs, not in ecdysozoans and vertebrates, and they are homologous to the intron containing nAChR genes from molluscs, indicating that these intronless nAChR are derived from intron-rich nAChRs by retroposition in molluscs and not from. - The massive expansion of nAChR genes in bivalve mol- luscs, through both retroposition and tandem duplication, has led to extensive diversity in sequence, domain struc- ture and expression profile, which may support functional diversity and adaptation. - As such, high sequence diversity of the LBD may have broadened the ligand specificity of the ex- panded molluscan nAChRs.. - mAChRs are members of the G protein-coupled recep- tors (GPCRs), which are widely distributed in multiple organs and critical to the maintenance of central and peripheral cholinergic neurotransmission [48]. - 5 Stepwise and lineage-specific tandem duplication of nAChR genes in C. - a Arrangement of nAChR genes in two tandemly duplicated arrays from C. - b Phylogenetic relationship and corresponding gene structure of tandemly duplicated nAChR genes. - In conclusion, massive expansion and diversity of nAChR genes are observed in molluscs and annelids especially in stationary bivalve molluscs with simple nervous systems.. - Some of the expanded nAChR genes are expressed during early development, while others are involved in immune and stress responses. - 6 Diversity in temporal and spatial expression of nAChR genes in molluscs. - b expression patterns of nAChR genes in different tissues in C. - This study reveals unprecedented diversity of nAChRs and provides insights into the evolution of the cholinergic signaling pathways. - 7 Expression of ChAT, AChE and four nAChR genes in different organs and during early development in C. - e – h High and specific expression of four nAChR genes before trochophore stage. - elegans and Ciona intestinalis were extracted from the NCBI gene database (https://www.ncbi.nlm.nih.gov/gene/?term=gene) anno- tated as nAChR genes. - A total of 644 nAChR genes that had the canonical LBD-NTM domain structure (without other functional domains) were used for nAChR gene family analysis.. - Phylogenetic analysis of the above nine species were conducted using MrBayes [50]. - After filtering, 182 nAChR genes from P. - Exon-intron structure analysis of nAChR genes. - gigas nAChR genes were obtained from published genome data [28, 29].. - Structure information for nAChR genes of other species were downloaded from NCBI database. - The exon and intron structure of nAChR genes were drew using the Gene Struc- ture Display Server (GSDS, http://gsds.cbi.pku.edu.cn/) [53].. - Expression profile of nAChR genes. - The transcriptome data from different organs, at differ- ent stages and under challenge by pathogens and differ- ent environmental conditions were collected from the published research and analyzed to ex- tract expression profile of nAChR genes. - Extron-intron structure of nAChR genes from H. - Multi-alignment of Cys-loop of nAChR genes from C. - Multi-alignment of alpha nAChR genes from H. - Sequence diversity at and around ACh binding sites in 33 nAChR genes of C. - Expression of six nAChR genes in gills of C. - Expression of nAChR genes in gills of C.. - Expression of nAChR genes (RPKM >. - The nicotinic acetylcholine receptor gene family of the silkworm, Bombyx mori. - Identification and functional expression of a family of nicotinic acetylcholine receptor subunits in the central nervous system of the mollusc Lymnaea stagnalis. - The nicotinic acetylcholine receptor: the founding father of the pentameric ligand-gated ion channel superfamily. - State of the art on insect nicotinic acetylcholine receptor function in learning and memory. - The human CHRNA7 and CHRFAM7A genes: A review of the genetics, regulation, and function. - Molecular evolution of the nicotinic acetylcholine receptor: an example of multigene family in excitable cells
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