Amin Eimanifar

The complete mitochondrial genome of the Cape honey bee, Apis mellifera capensis Esch. (Insecta: hymenoptera: apidae)

Abstract We characterized the complete mitogenome sequence of the Cape honey bee, Apis mellifera capensis, from South Africa. The circle genome is 16,470 bp in length, with the base composition of 43.2% A, 9.6% C, 5.6% G, and 41.5% T. The assembled mitogenome has 13 protein-coding genes (PCGs), 22 transfer RNAs, two ribosomal RNA genes, and one control region. All protein-coding genes are initiated by ATT, ATC, ATG or ATA codons and are terminated by the typical stop codon TAA. The heavy strand encodes four protein-coding genes, eight tRNAs, and two rRNAs. The light strand encodes nine protein-coding genes and 14 tRNAs. The complete mitogenome sequence of A.m. capensis is identical to the gene arrangement found in other A. mellifera mitogenomes and it provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis of members of the genus Apis.

Fine-scale population genetic structure in Artemia urmiana (Günther, 1890) based on mtDNA sequences and ISSR genomic fingerprinting

We investigated the genetic variability and population structure of the halophilic zooplankter Artemia urmiana from 15 different geographical locations of Lake Urmia using nucleotide sequences of COI (mtDNA cytochrome c oxidase subunit I) and genomic fingerprinting by ISSR-PCR (inter-simple sequence repeats). According to sequence data, A. urmiana exhibits a high level of haplotype diversity with a low level of nucleotide diversity. The haplotype spanning network recognized 36 closely related unique haplotypes. ISSR profiles confirmed a substantial amount of genomic diversity with a low level of population structure. No apparent genetic structure was recognized in Lake Urmia but rather a random geographic distribution of genotypes indicating a high degree of panmixia. The population genetic data indicate the possibility of an individual’s relationship, implying that differentiation of individuals is not affected by ecological factors. Therefore, the A. urmiana population from Lake Urmia should be considered as a single management unit for conservation.

The complete mitochondrial genome and phylogenetic placement of Apis nigrocincta Smith (Insecta: Hymenoptera: Apidae), an Asian, cavity-nesting honey bee

Abstract The complete mitochondrial genome of Apis nigrocincta was sequenced. The mitochondrial genome is a circular molecule of 15,855 bp, including 37 classical eukaryotic mitochondrial regions and an A + T-rich region. Gene directions and arrangements are similar to those of other Apis mitogenomes. Most genes initiated with ATT, though ATG and ATA were also used as start codons. Twelve of 13 protein-coding genes terminated with TAA, though ND2 terminated with TAG. Four PCG genes, eight tRNAs and both rRNAs were encoded on the heavy strand while all others were encoded on the light strand (9 PCGs and 14 tRNAs). Overall, the GC content composed 15.6% of the mitogenome. All of the 22 tRNA genes, ranging from 66 to 114 bp, have a typical cloverleaf structure. A phylogenetic tree showed that A. nigrocincta clustered closest to A. cerana. The complete mitogenome of A. nigrocincta provides essential information on the biogeography and evolution of this Asian honey bee species.

The complete mitochondrial genome of Apis mellifera meda (Insecta: Hymenoptera: Apidae)

Abstract The complete mitochondrial genome of the western honey bee subspecies Apis mellifera meda was sequenced. This mitochondrial genome is 16,248 bp in length, with 37 classical eukaryotic mitochondrial genes and an A + T-rich region. Gene direction and arrangement are similar to those of other Apis mitogenomes. All genes initiate with ATT (six genes), ATG (four genes), ATA (two genes), and ATC (one gene) start codons and terminate with a TAA stop codon. Four genes are encoded on the heavy and nine on the light strands, respectively. All of the 22 tRNA genes, ranging from 66 to 78 bp, have a typical cloverleaf structure. The complete mitogenome of A.m. meda provides information on the biogeography and evolution of A. mellifera subspecies.

The complete mitochondrial genome of an east African honey bee, Apis mellifera monticola Smith (Insecta: Hymenoptera: Apidae)

Abstract The complete mitochondrial genome of Apis mellifera monticola was sequenced and annotated. The genome is 16,343 bp in length and encodes all 37 mitochondrial genes with an A + T content of 84.8%. Gene directions and arrangements are identical to those of other sequenced mitogenomes in Apis. Most genes initiated with ATT, though ATG, ATA, and ATC also were used as start codons. All genes terminated with TAA. Four PCG genes, eight tRNAs and both rRNAs are encoded on the heavy strand while all others are coded on the light strand (nine PCGs and 14 tRNAs). Overall, the GC content composed 15.2% of the mitogenome. All of the 22 tRNA genes, ranging from 63 to 78 bp, have a typical cloverleaf structure. A phylogenetic tree showed that A.m. monticola clusters with other African subspecies.

The complete mitochondrial genome of the hybrid honey bee, Apis mellifera capensis × Apis mellifera scutellata, from South Africa

Abstract We characterized the complete mitogenome sequence of the South African hybrid honey bee Apis mellifera capensis × Apis mellifera scutellata using genome skimming. The mitochondrial genome was a circular molecule 16,340 bp in length with a gene organization identical to that of the other A. mellifera mitogenomes. The base composition is 43.2% A, 9.7% C, 5.6% G, and 41.5% T, with an A + T content of 84.7%. The mitogenome had 13 protein-coding genes (PCGs), 22 transfer RNAs, two ribosomal RNAs genes, and one control region. All PCGs were initiated by ATT, ATG, ATA, and ATC codons and were terminated by a TAA stop codon. The heavy strand encodes four PCGs, eight tRNAs, and two rRNAs. The light strand encodes nine PCGS and 14 tRNAs. A phylogenetic analysis of the PCGs reveals a close relationship between this hybrid honey bee and other Apis spp.

Analysis of the genetic variability of Artemia franciscana Kellogg, 1906 from the Great Salt Lake (USA) based on mtDNA sequences, ISSR genomic fingerprinting and biometry

The genetic structure of the brine shrimp Artemia franciscana, an extremophile halophilic microcrustacean, from the Great Salt Lake (USA), was investigated by analysis of nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I (COI), genomic fingerprinting by ISSR-PCR (inter-simple sequence repeats polymerase chain reaction) and biometry. Samples from six different geographical localities of Great Salt Lake revealed ten distinct haplotypes with a mean high level of haplotype diversity (HD = 0.6). Phylogenetic and genetic fingerprinting analyses supported the null hypothesis, that the brine shrimps of this lake form a panmictic gene pool with a low level of genetic differentiation index (FST = 0.05) and a high rate of gene flow (Nm = 2.8) between geographical areas. Moreover, morphological parameters revealed no population structure among all examined populations. Neutrality tests and mismatch distribution revealed that A. franciscana has undergone a recent population expansion. In spite of hypersaline conditions in the Northern (Gunnison Bay) regions of the Great Salt Lake, the genetic population structures of different areas of the lake are not linked to ecological or limnological conditions. Therefore, A. franciscana from the Great Salt Lake should be considered as a single management unit for conservation.

Artemia biodiversity in Asia with the focus on the phylogeography of the introduced American species Artemia franciscana Kellogg, 1906

Asia harbors a diverse group of sexual and asexual Artemia species, including the invasive Artemia franciscana, which is native to the Americas. The phylogeny of Asian Artemia species and the phylogeography of the introduced A. franciscana from 81 sampling localities in Eurasia, Africa and America were elucidated using mitochondrial (COI) and nuclear DNA (ITS1) sequences. According to a COI phylogeny, 6 distinctive genetic groups were recognized, with a complex phylogeographic structure among Asian Artemia. A haplotype complex which includes parthenogenetic lineages is distributed in 39 inland geographical localities in Asia, illustrating a wide distribution with a narrow genetic structure on this continent. The invasive A. franciscana was discovered in 31 geographical localities along the southern and eastern coastal regions of Asia. Three sexual species (A. sinica, A. tibetiana and A. urmiana) have a restricted distribution in certain geographical localities in Asia. In contrast to COI phylogeny reconstruction, ITS1 sequences showed inconsistency with the COI tree, indicating incomplete lineage sorting which provided the low genetic divergence in the Asian clade. Asian A. franciscana showed higher haplotype diversity as compared to the source population from the Great Salt Lake (USA), which could be attributed to multiple introductions by mass dispersal in Asia via human activities. The invasive success of A. franciscana in Asia could lead to a long-term biodiversity disturbance of the autochthonous Artemia species on the continent.

The complete mitochondrial genome of the Egyptian honey bee, Apis mellifera lamarckii (Insecta: Hymenoptera: Apidae)

Abstract The complete mitochondrial genome of the western honey bee subspecies Apis mellifera lamarckii was sequenced. This mitochondrial genome is 16,589 bp in length with 37 classical eukaryotic mitochondrial genes and an A + T-rich region. Gene directions and arrangements are similar to those of other Apis mitogenomes. Seven genes begin with ATT, four with ATG, and two with ATA (none with ATC) and all genes terminate with TAA. Four genes are encoded on the heavy strand and nine are encoded on light strand. All of the 22 tRNA genes, ranging from 66 to 80 bp, have a typical cloverleaf structure. A phylogenetic tree showed that A.m. lamarckii clusters with other A. mellifera subspecies, as expected.

Genetic variation and evolutionary origins of parthenogenetic Artemia (Crustacea: Anostraca) with different ploidies

Using two nuclear (ITS1 and Na+/K+ ATPase) and three mitochondrial (COI, 16S and 12S) markers, we determined the genetic variation and evolutionary relationship of parthenogenetic and bisexual Artemia. Our analyses revealed that mitochondrial genes had higher genetic variation than nuclear genes and that the 16S showed more variety than the other mitochondrial genes in parthenogenetic populations. Triploid parthenogens showed lower genetic variation than diploid ones, whereas the tetra‐ and pentaploids had greater genetic distance than diploid parthenogens. No shared haplotype was found between individuals of parthenogenetic populations and Asian bisexual species with the exception of Na+/K+ ATPase (Artemia tibetiana). Only mitochondrial markers can demonstrate phylogenetic relationships, and showed that the parthenogenetic Artemia is a polyphyletic group in which the diploid lineages share a common ancestor with Artemia urmiana while tetraploids are closely related to Artemia sinica. The triploid and pentaploid linages are likely to be directly derived from diploid and tetraploid parthenogens, respectively. Subsequently, west Asia is origin for di‐/triploids, and tetra‐/pentaploids rose from East Asia.