Presence–absence polymorphisms of single-copy genes in the stony coral Acropora digitifera

Abstract

Background: Despite the importance of characterizing genetic variation among coral individuals for understanding phenotypic variation, the correlation between coral genomic diversity and phenotypic expression is still poorly understood. Results: In this study, we detected a high frequency of genes showing presence-absence polymorphisms (PAPs) for single-copy genes in Acropora digitifera. Among 10,455 single-copy genes, 516 (5%) exhibited PAPs, including 32 transposable element (TE)-related genes. Five hundred sixteen genes exhibited a homozygous absence in one (102) or more than one (414) individuals (n = 33), indicating that most of the absent alleles were not rare variants. Among genes showing PAPs (PAP genes), roughly half were expressed in adults and/or larvae, and the PAP status was associated with differential expression among individuals. Although 85% of PAP genes were uncharacterized or had ambiguous annotations, 70% of these genes were specifically distributed in cnidarian lineages in eumetazoa, suggesting that these genes have functional roles related to traits related to cnidarians or the family Acroporidae or the genus Acropora. Indeed, four of these genes encoded toxins that are usually components of venom in cnidarian-specific cnidocytes. At least 17% of A. digitifera PAP genes were also PAPs in A. tenuis, the basal lineage in the genus Acropora, indicating that PAPs were shared among species in Acropora. Conclusions: Expression differences caused by a high frequency of PAP genes may be a novel genomic feature in the genus Acropora; these findings will contribute to improve our understanding of correlation between genetic and phenotypic variation in corals.

Molecular analysis of Taro and Bali cattle using cytochrome oxidase subunit I (COI) in Indonesia

“…The polymorphic sites indicated the differences between individuals within one species (Jaratlerdsiri et al 2014;Viscardi et al 2018;Brodetzki et al 2019;Takahashi-Kariyazono et al 2020). The research on several mitochondrial genes also showed some intra-population variation, and their differences were used as genetic markers (barcode species) (Li et al 2008;Meenakshi et al 2010;Yaacov et al 2012;Wolff et al 2014;Naim et al 2020).…”

Intraspecific de novo gene birth revealed by presence–absence variant genes in Caenorhabditis elegans

“…A type of genetic variants, presence–absence variants (PAVs), is represented by genes present in some genomes but absent in others within the same species ( 14 ). PAV genes might be fast-evolving genes, as they are able to reflect gene birth or death ( 22 ). In addition, PAV genes may contribute to adaptation to changing environments, including pathogen infection, antitumor-agent synthesis or disease resistance in plants as well as immunity in animals ( 15–19 ).…”

Two divergent haplogroups of a sacsin-like gene in Acropora corals

“…Genomic DNA was extracted from three A. digitifera and two A. tenuis individuals from our previous study 18 , 19 . Genomic DNA from single colonies of M. informis and M. aequituberculata were provided by Dr. Masayuki Hatta.…”

“…Four primer sets are capable of amplifying the target sequence when the template genomic DNA does not contain an inversion of the sacsin-like gene, and six primer sets are capable of amplifying the target sequence when the template genomic DNA does not contain an inversion of the sacsin-like gene were used for PCR analysis (Table S3–4 ). To check the quality of genomic DNA, a primer set (34639_F1/34639_R1) 19 was used to amplify elongation factor 1-alpha: LOC107334639 as a positive control. The PCR conditions were as follows: denaturation step for 1 min 30 s at 93 °C, followed by 35 cycles of denaturation for 30 s at 93 °C, annealing for 3 min (PCR#1,2,8 and a positive control) or 8 min (PCR#3–7,9 and 10) at 55 °C, and extension for 10 min at 72 °C.…”