Intron sequence diversity of the asian cavity-nesting honey bee, Apis cerana (Hymenoptera: Apidae)

  • cc icon

    The Asian cavity-nesting honeybee, Apis cerana (Hymenoptera: Apidae), has been extensively studied for its biogeography and genetic diversity, but the molecules utilized in past studies were mainly ~90 bp long mitochondrial non-coding sequences, located between tRNALeu and COII. Thus, additional molecular markers may enrich our understanding of the biogeography and genetic diversity of this valuable bee species. In this study, we reviewed the public genome database to find introns of cDNA sequences, with the assumption that these introns may have less evolutionary constraints. The six introns selected were subjected to preliminary tests. Thereafter, two introns, titled White gene and MRJP9 gene, were selected. Sequencing of 552 clones from 184 individual bees showed a total of 222 and 141 sequence types in the White gene and MRJP9 gene introns, respectively. The sequence divergence ranged from 0.6% to 7.9% and from 0.26% to 17.6% in the White gene and the MRJP9 introns, respectively, indicating higher sequence divergence in both introns. Analysis of population genetic diversity for 16 populations originating from Korea, China, Vietnam, and Thailand shows that nucleotide diversity (π) ranges from 0.003117 to 0.025837 and from 0.016541 to 0.052468 in the White gene and MRJP9 introns, respectively. The highest π was found in a Vietnamese population for both intron sequences, whereas the nine Korean populations showed moderate to low sequence divergence. Considering the variability and diversity, these intron sequences can be useful as non-mitochondrial DNA-based molecular markers for future studies of population genetics.


    Asian cavity-nesting honey , Apis cerana , introns , white gene , MRJP9 , sequenced diversity

  • Introduction

    The biogeography and genetic diversity of A. cerana has extensively been studied for its distributional range in the temperate and tropical regions of Asia (De la Rúa et al., 2000; Deowanish et al., 1996; Sihanuntavong et al., 1999; Smith and Hagen, 1996; Smith et al., 2000; Smith et al., 2004; Takahashi et al., 2007; Tan et al., 2007). These studies exclusively used an internal spacer region located between mitochondrial tRNALeu and COII to analyze this species’ genetic diversity (Crozier and Crozier, 1993; Cornuet et al., 1991).

    Nuclear loci require four times more the effective population size than mitochondrial loci (Brown, 1983). Thus, several more folds of nucleotides are required from nuclear DNA to obtain equivalent numbers of variable sites to mitochondrial loci in general (Zink and Barrowclough, 2008). Because of this condition, population genetics studies of A. cerana have focused on mitochondrial DNA. In fact, only a limited number of studies have utilized nuclear locioriginating markers, such as the ribosomal internal transcribed spacer 2 (ITS2) (Kim et al., 2010). Nevertheless, development of nuclear loci might be required to achieve a balance of information to expand our understanding of the population genetics aspects of A. cerana. In particular, recent studies have shown that intron sequences have a distinct rate of evolution, making them potentially useful in resolving relationships over a wide range of taxonomic levels (Yu et al., 2011). However, this method of study requires additional experimental efforts, such as isolation of alleles, PCR optimization, and alignment expertise due to insertion/deletion (indel) (Sang, 2002).

    In this study, we reviewed the genome database to find introns of cDNA sequences for Apis species, including A. cerana. Initially, six introns were selected and primers were designed, and subsequently two introns, each having proper levels of diversity, were selected. These two introns were used to assess the potential of population genetic markers for A. cerana using 552 clones from 184 individuals of A. cerana collected from 16 localities in four countries including Korea.

    Materials and Methods

      >  Sampling

    A total of 184 A. cerana workers collected from 16 localities in four countries (South Korea, China, Vietnam, and Thailand) were used in this study (Table 1). The field-collected bees were preserved in 95% ethanol for molecular experiments.

      >  Molecular experiment

    Total DNA was extracted from one or two legs using the Wizard Genomic DNA Purification Kit, in accordance with the manufacturer’s instructions (Promega, Madison, WI, USA). While reviewing intron sequences of Apis, six cDNAs, which provide the exon–intron structure, were found in the GenBank: the White gene (Kawakita et al., 2008), MRJP9 gene (Peiren et al., 2008), OR2 gene (Unpublished, GenBank accession number FJ666105), 1 inosital 1,4,5-triphosphate receptor gene (Lo et al., 2010), long-wavelength rhodopsin (LWRh) gene (Kawakita et al., 2008), and mitotic checkpoint control protein (Bub3) gene (Kawakita et al., 2008). These cDNAs included one to three introns and two to four exons. Among each of these, one intron having a relatively longer size and/or a proper site for primer design was selected from each gene. Three or four primers from each intron were designed and tested for proper utility (e.g., amplification success). Detailed primer information and origin are provided in Table 2.

    A 35-cycle amplification (94℃ for 1 min, 50–52℃ for 1 min, and 72℃ for 1 min) process for PCR was conducted after initial denaturation at 94℃ for 5 min and the final extension step continuing for 7 min at 72℃. To confirm successful DNA amplification, electrophoresis was carried out using 0.5× TAE buffer on 0.5% agarose gel. After purification with the PCR purification Kit (Qiagen, Germany), the amplicons were cloned into a pGEM-T Easy vector (Promega, USA). For the cloning process, XL1-Blue competent cells (Stratagene, USA) were transformed with the ligated DNA, and the resultant plasmid DNA was isolated using a Wizard Plus SV Minipreps DNA Purification System (Promega, USA). Two or three clones with limited sampling were sequenced for preliminary experiments and the obtained sequences were analyzed for their variability. Eventually, the White gene and the MRJP9 gene introns were selected and these introns were subjected to full individual screening, analyzing three clones per individual. DNA sequencing was conducted using the ABI PRISM® BigDye® Terminator ver. 3.1 Cycle Sequencing Kit with an ABI 3100 Genetic Analyzer (PE Applied Biosystems, USA). All products were sequenced from both strands.

      >  Sequence analysis

    Sequence delimitation was conducted by comparing newly acquired sequences to the GenBank-registered corresponding cDNA using MAFFT ver. 6 (Table 2; Katoh et al., 2002). When one or more nucleotide base or insertion/deletion (indel) position differed to the obtained sequences, the sequences were considered different sequence types.

      >  Variability estimate

    In order to estimate the variability of the intron sequences, population diversity estimates, such as sequence diversity and nucleotide diversity, both of which are reflective of genetic diversity within a population, were determined using Arlequin ver. 3.5 (Excoffier and Lischer, 2010). The maximum sequence divergence within each locality was estimated via extraction of the within-locality estimates of unrooted pairwise distances from PAUP ver. 4.0b (Swofford, 2002).

    Results and Discussion

      >  Selection of two introns

    As a preliminary experiment, sequencing was performed only for limited individuals: 53 clones from the intron of the White gene, 18 from MRJP9 gene, 24 from OR2 gene, 31 from 1 inosital 1,4,5-triphosphate receptor gene, 27 from LWRh gene, and 29 from Bub3 gene. Six introns provided multiple numbers of sequence types (8–20), but the introns of the Bub3 gene and the LWRh gene provided one and two sequence types, respectively (Table 3). When diversity of sequence types was considered, the intron of one inosital 1,4,5-triphosphate receptor gene showed the lowest as eight (25.8%), excluding the introns of Bub3 gene and LWRh gene. Furthermore, this intron was shorter in original length at 92–94 bp and this may be problematic, considering the potential of variable sites in a given length. The intron of OR2 gene provided the second highest diversity of sequence type (45.83%) and the highest sequence divergence (0.79–7.14%), but the original sequence length of the intron is only the third (118–126 bp), after the introns of the White gene and the MRJP9 gene (158–160 bp and 310–313 bp, respectively). Thus, these were excluded from subsequent full individual screening, and finally, the introns of the White gene and the MRJP9 gene were selected for full investigation to evaluate their potential as nuclear population genetic markers.

      >  Sequence analysis of the two introns

    The sequence analyses of 552 clones from 184 individual bees provided a total of 222 sequence types, ranging in size from 157 to 163 bp for the White gene intron and 141 sequence types, ranging in size from 307 to 357 bp for the MRJP9 intron (Table 4). The G/C content was ~27.8% (72.2% in A/T content) in the White gene intron and 19.5% (80.5% in A/T content) in the MRJP9 intron, indicating that the two introns are highly biased for A/T nucleotides. The sequence divergence of the two introns was 0.6%–7.9% in the White gene intron and 0.26%–17.6% in the MRJP9 intron, indicating moderate to substantial divergence. Previously, Lee et al. (2015) reported the sequence divergence of two mitochondrial non-coding sequences (NC1 and NC2) from the same individual bees as 3.093% (three positions) to 1.031% (one position) and 2.597% to 0.433%, respectively. The NC2 has been proven to be useful for genetic diversity and biogeographic study for worldwide A. cerana populations (Smith and Hagen, 1996; Smith et al., 2000; Smith et al., 2004; Warrit et al., 2006; Takahashi et al., 2007). The NC1 was newly developed in Lee et al. (2015) and also showed near equal variability to NC2. Further, these non-coding sequences each provided ten in NC2 and nine haplotypes in NC1 from the 184 individual bees (Lee et al., 2015). Compared to the above result, in this study, the sequence divergence of the two introns are much larger in terms of number of sequence type and sequence divergence. Thus, these intron sequences might be useful as non-mitochondrial DNA-based molecular markers for future population studies.

      >  Genetic diversity

    In order to understand the population genetic diversity of A. cerana in populations, several diversity estimations were made (Tables 5 and 6). In the case of the White gene intron, the nucleotide diversity (π) ranged from 0.003117 (locality 3, Hongcheon-gun) to 0.025837 (locality 15, Vin Phuc, Vietnam), showing at least an eight-fold difference between them (Table 6). For the MRJP9 intron, diversity ranged from 0.016541 (locality, 4, Namwon-si) to 0.052468 (locality 15, Vin Phuc, Vietnam), showing at least a three-fold difference (Table 6). Thus, the MRJP9 intron showed two to five fold greater diversity than that of the White gene intron.

    Among the 16 populations, the highest π was found in Vin Phuc, Vietnam (locality 15) in both intron sequences. The second highest estimate were found in Chanthaburi population, Thailand (locality 16) as 0.010435 in the White gene intron and Beijing, China (locality 14) as 0.027619 in the MRJP9 intron. On the other hand, the nine Korean populations ranged from 0.003117 to 0.007170 and 0.015984 to 0.022876 in the White gene intron and MRJP9 gene intron, respectively. This indicates that the Korean populations are relatively low in diversity of the two intron sequences, although their locality of seven (Cheongyanggun) ranked the fifth in the MRJP9 intron and eighth in the White gene intron. In fact, Lee et al. (2015), based on NC2, has also shown that the India, Indonesia, Malaysia, Philippines, and Burma populations were several-fold higher in genetic diversity than the Korean populations, indicating the presence of small effective populations in Korea. Similar to π estimates, haplotype diversity (H) also was the highest in Vin Phuc, Vietnam (locality 15) for both intron sequences. The H of the nine Korean populations ranged from 0.4190 to 0.7059 in the White gene intron and 0.7905 to 0.9673 in the MRJP9 gene intron. These estimates are not high; however, they are better than those of π found in several Korean localities showing more improved ranks in the H than those of π. Nevertheless, it is obvious that the Korean populations have an overall low diversity.

    In summary, we selected two intron sequences from the public genome database and sequenced 552 clones from 184 individuals of A. cerana collected from 16 localities in four countries. The high variability and diversity of the intron sequences show their high potential for use as non-mitochondrial DNA-based molecular markers for future population genetics studies.

  • 1. Cornuet JM, Garnery L, Solignac M (1991) Putative origin and function of the intergenic region between COI and COII of Apis mellifera L. [mitochondrial DNA. Genetics] Vol.128 P.393-403 google
  • 2. Crozier RH, Crozier YC (1993) The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization. [Genetics] Vol.133 P.97-117 google
  • 3. Deowanish S, Nakamura J, Matsuka M, Kimura K (1996) mtDNA variation among subspecies of Apis cerana using restriction fragment length polymorphism. [Apidologie] Vol.27 P.407-413 google doi
  • 4. De la Rua P, Simon UE, Tilde AC, Moritz RFA, Fuchs S (2000) MtDNA variation in Apis cerana populations from the Philippines. [Heredity] Vol.84 P.124-130 google
  • 5. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. [Mol Ecol Resour] Vol.10 P.564-567 google doi
  • 6. Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. [Nucleic Acids Res] Vol.30 P.3059-3066 google doi
  • 7. Kawakita A, Ascher JS, Sota T, Kato M, Roubik DW (2008) Phylogenetic analysis of the corbiculate bee tribes based on 12 nuclear protein-coding genes (Hymenoptera: Apoidea: Apidae). [Apidologie] Vol.39 P.163-175 google doi
  • 8. Kim HK, Lee MY, Lee ML, Choi YS, Hong IP, Kim MS, Lee KG, Jin BR (2010) Genetic diversity of the Apis cerana in Korea by mitochondrial DNA and ITS ribosomal DNA sequence. [J Apic] Vol.25 P.9-16 google
  • 9. Lee JY, Wang AR, Choi YS, Thapa R, Kwon HW, Kim I (2015) Mitochondrial DNA variations in Korean Apis cerana (Hymenoptera: Apidae) and development of another potential marker. google
  • 10. Lo N, Gloag RS, Anderson DL, Oldroyd BP (2010) A molecular phylogeny of the genus Apis suggests that the Giant Honey Bee of the Philippines, A. breviligula Maa, and the Plains Honey Bee of southern India, A. indica Fabricius, are valid species. [Syst Entomol] Vol.35 P.226-233 google doi
  • 11. Peiren N, de Graaf DC, Vanrobaeys F, Danneels EL, Devreese B, Van Beeumen J, Jacobs FJ (2008) Proteomic analysis of the honey bee worker venom gland focusing on the mechanisms of protection against tissue damage. [Toxicon] Vol.52 P.72-83 google doi
  • 12. Sang T (2002) Utility of low-copy nuclear gene sequences in plant phylogenetics. [Crit Rev Biochem Mol Biol] Vol.37 P.121-147 google doi
  • 13. Sihanuntavong D, Sittipraneed S, Klinbunga S (1999) Mitochondrial DNA diversity and population structure of the honey bee, Apis cerana, in Thailand. [J Apic Res] Vol.38 P.211-219 google
  • 14. Smith DR, Hagen RH (1996) The biogeography of Apis cerana as revealed by mitochondrial DNA sequence data. [J Kans Entomol Soc] Vol.69 P.249-310 google
  • 15. Smith DR, Villafuerte L, Otis G, Palmer MR (2000) Biogeography of Apis cerana F. and A. nigrocincta Smith: Insights from mtDNA studies. [Apidologie] Vol.31 P.265-279 google doi
  • 16. Smith DR, Warrit N, Hepburn HR (2004) Apis cerana from Myanmar (Burma): unusual distribution of mitochondrial lineages [Apidologie] Vol.35 P.637-644 google doi
  • 17. Swofford DL (2002) PAUP*. Phylogenetic Analysis Using Parsimony (*and other method) software ver. 4.10, Sinauer Associates. google
  • 18. Takahashi J, Yoshida T, Takagi T, Akimoto S, Wood KS, Deowanish S, Hepburn R, Nakamura S, Matsuka M (2007) Geographic variation in the Japanese islands of Apis cerana japonica and in A. cerana populations bordering its geographic range [Apidologie] Vol.38 P.335-340 google doi
  • 19. Tan K, Warrit N, Smith DR (2007) Mitochondrial DNA diversity of Chinese Apis cerana. [Apidologie] Vol.38 P.238-246 google doi
  • 20. Warrit N, Smith DR, Lekprayoon C (2006) Genetic subpopulations of Varroa mites and their Apis cerana hosts in Thailand. [Apidologie] Vol.37 P.19-30 google doi
  • 21. Yu L, Luan PT, Jin W, Ryder OA, Chemnick LG, Davis HA, Zhang YP (2011) Phylogenetic utility of nuclear introns in interfamilial relationships of Caniformia (order Carnivora). [Syst Biol] Vol.60 P.175-187 google doi
  • 22. Zink RM, Barrowclough GF (2008) Mitochondrial DNA under siege in avian phylogeography. [Mol Ecol] Vol.17 P.2107-2121 google doi
  • [Table 1.] A list of trapping localities, sample numbers and GenBank accession numbers
    A list of trapping localities, sample numbers and GenBank accession numbers
  • [Table 2.] List of primer sequences used to amplify and sequence the introns of Apis cerana
    List of primer sequences used to amplify and sequence the introns of Apis cerana
  • [Table 3.] Preliminary information of intron sequenced
    Preliminary information of intron sequenced
  • [Table 4.] Characteristic of intron sequences
    Characteristic of intron sequences
  • [Table 5.] Within-locality diversity estimates of Apis cerana from White gene intron
    Within-locality diversity estimates of Apis cerana from White gene intron
  • [Table 6.] Within-locality diversity estimates of Apis cerana from MRJP9 gene intron
    Within-locality diversity estimates of Apis cerana from MRJP9 gene intron