http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2014.989511

MITOGENOME ANNOUNCEMENT

Mitochondrial genome of Hylaeus dilatatus (Hymenoptera: Colletidae) Meihua Tan1,2, Rui Zhang2, Chloe Hardman3, and Xin Zhou2 College of Life Sciences, University of Chinese Academy of Sciences, Shijingshan District, Beijing, China, 2China National GeneBank-Shenzhen, BGI-Shenzhen, Yantian District, Shenzhen, China, and 3School of Agriculture, Policy and Development, University of Reading, Reading, Berkshire, UK

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1

Abstract

Keywords

Bees are one of the most well-known and important type of pollinators in agriculture and natural ecosystems, and maintaining their diversity in nature is essential. In this study, we report the complete mitochondrial genome of Hylaeus dilatatus, the first mitochondrial genome of Colletidae. Its complete mtDNA sequence is 15,475 bp in length, which contains 13 proteincoding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region. The base composition of mtDNA is 44.27% A, 41.52% T, 8.80% C and 5.41% G. The percentage of A + T is 85.79%. The first complete mitogenome of Colletidae family could be used in studies of molecular systematics, conservation genetics, and stock evaluation.

Colletidae, Hylaeus dilatatus, insect pollinator, mitochondrial genome

Pollination services to crops and wild plants are important economically and ecologically. As one of the major groups of insect pollinators, bees can pollinate one or more cultivars of466% of the world’s 1500 crop species and are directly or indirectly essential for an estimated 15–30% of food production (Kremen et al., 2002). Hylaeus dilatatus belongs to Colletidae, a family of solitary bees that have no specific social division system and do not suit artificial breeding, therefore have rarely been studied. As outgroups to social bees, solitary bees including Hylaeus dilatatus will provide important information in ecology research and environment monitoring (Yu et al., 2012; Zhou et al., 2013). Here we sequenced and assembled the complete mitochondrial genome of H. dilatatus (GenBank accession number is KP126800), collected from Hertfordshire County, United Kingdom, on 17 July 2012. Genomic DNA was extracted by TIANprep Midi Plasmid kit (TIANGEN, Beijing, China) and then sequenced using Illumina’s HiSeq2000 platform (Illumina, San Diego, CA) with 200 bp insert size and a pair-end 100 bp sequencing strategy. The sequence reads were first filtered by the programs following Zhou et al. (2013) and then the remaining high-quality reads were assembled using SOAPdenovo-Trans (Xie et al., 2014). The contigs and scaffolds obtained from the assembler were annotated for protein-coding genes (PCGs) using homolog prediction (Zhou et al., 2013), rRNAs by Geneious 6.1.2 (Kearse et al., 2012) and tRNAs according to tRNAscan-SE (Schattner et al., 2005).

History Received 13 November 2014 Accepted 16 November 2014 Published online 28 January 2015

The Hylaeus dilatatus mitogenome, the first mitochondrial genome in Colletidae, is a circular molecule that is 15,475 bp in length and contains 13 PCGs, 22 tRNA genes and 2 rRNA genes (12S rRNA and 16S rRNA) (Table 1). The overall nucleotide base composition of heavy strand is 44.27% A, 41.52% T, 8.80% C, and 5.41% G, and the percentage of A + T is 85.79%, slightly higher than that of the honey bee (84.9%). The arrangement of PCGs and rRNA genes in the mitochondrial genome of Hylaeus dilatatus is in the same order and orientation as the honey bee (Crozier & Crozier, 1993), while the arrangement of tRNA genes varies in all published mitochondrial genomes of Apoidea. Nine PCGs and 13 tRNAs are located on the heavy strand, while the other coding genes are located on the light strand. Thirteen PCGs share the same stop codon, TAA, except the CYTB gene with TAG, without extreme bias in the start codon. Three common start codons of insects are used in 13 PCGs, in which 3 PCGs are with ATA, 4 PCGs are with ATG and 6 PCGs are with ATT. All 22 tRNAs have stem-loops according to tRNAscan-SE. Two rRNA genes locate on light strand, where 16S rRNA is 1309 bp and 12S rRNA is 802 bp. As the first complete mitogenome of Colletidae family of Hymenoptera, this mitogenome will facilitate studies in molecular systematics at species and family level. The sequencing of mtDNA for a solitary bee will greatly contribute to conservation genetics research, environment monitoring and stock evaluation, as the outgroup to social bees.

Correspondence: Xin Zhou, China National GeneBank-Shenzhen, BGI-Shenzhen, Beishan Road, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China. Tel: +86-0755-25273620. Fax: +86-0755-25273620. E-mail: [email protected]

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M. Tan et al.

Mitochondrial DNA, Early Online: 1–2

Table 1. The mitochondrial genome order of H. dilatatus.

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Position

Codon

Gene name

From

To

Length (bp)

Strand

tRNA-Ile tRNA-Met tRNA-Gln ND2 tRNA-Cys tRNA-Tyr tRNA-Trp COX1 tRNA-Leu COX2 tRNA-Asp tRNA-Lys ATP8 ATP6 COX3 tRNA-Gly ND3 tRNA-Arg tRNA-Ala tRNA-Asn tRNA-Ser tRNA-Glu tRNA-Phe ND5 tRNA-His ND4 ND4L tRNA-Thr tRNA-Pro ND6 CYTB tRNA-Ser ND1 tRNA-Leu 16S rRNA 12S rRNA tRNA-Val

1 246 315 453 1432 1499 1565 1649 3207 3271 3950 4021 4091 4240 4917 5720 5777 6164 6233 6301 6363 6420 6487 6551 8225 8296 9633 9949 10,045 10,137 10,622 11,757 11,815 12,769 12,827 14,174 14,962

67 309 378 1433 1495 1564 1628 3211 3270 3951 4017 4090 4252 4917 5708 5785 6139 6230 6301 6363 6419 6498 6550 8227 8289 9633 9890 10,010 10,107 10,619 11,758 11,821 12,711 12,835 14,135 14,975 15,023

67 64 64 981 64 66 64 1563 64 681 68 70 162 678 792 66 363 67 69 63 57 79 64 1677 65 1338 258 62 63 483 1137 65 897 67 1309 802 62

H H L H L L H H H H H H H H H H H L H H H H L L L L L H L H H H L L L L L

Acknowledgements We would like to thank Professor Douglas W. Yu of Kunming Institute of Zoology for his effort in coordinating the sampling and relevant project.

Declaration of interest The authors report no conflict of interest and are responsible for the content and writing of the paper. This work was supported by the National High Technology Research and Development Program of China – 863 Program, Chinese 863 Program (No. 2012AA021600, 2012AA021601) and the National Key Technology R&D Program (2012BAK11B06).

References Crozier RH, Crozier YC. (1993). The mitochondrial genome of the honeybee Apis mellifera: Complete sequence and genome organization. Genetics 133:97–117.

Start

Stop

ATA

TAA

Gene overlap (bp)

2 ATA

TAA

ATT

TAA

5 2 ATT ATG ATG

TAA TAA TAA

13 1

ATA

TAA

9 1 1 12

ATT

TAA

ATG ATT

TAA TAA

ATT ATG

TAA TAG

ATT

TAA

3 1

2 7 9 14

Kearse M, Moir R, Wilson A, Stones HS, Cheung M, Sturrock S, Buxton S, et al. (2012). Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–9. Kremen C, Williams NM, Thorp RW. (2002). Crop pollination from native bees at risk from agricultural intensification. Proc Natl Acad Sci 99:16812–16. Schattner P, Brooks AN, Lowe TM. (2005). The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33:686–9. Xie YL, Wu GX, Tang JB, Luo RB, Patterson J, Liu SL, Huang WH, et al. (2014). SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads. Bioinformatics 30:1660–6. Yu DW, Ji YQ, Emerson BC, Wang XY, Ye CX, Yang CY, Ding ZL. (2012). Biodiversity soup: Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods Ecol Evol 3:613–23. Zhou X, Li YY, Liu SL, Yang Q, Su X, Zhou LL, Tang M, et al. (2013). Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. Gigascience 2:4.

Mitochondrial genome of Hylaeus dilatatus (Hymenoptera: Colletidae).

Bees are one of the most well-known and important type of pollinators in agriculture and natural ecosystems, and maintaining their diversity in nature...
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