The characteristics and expression profiles of the mitochondrial genome for the Mediterranean species of the Bemisia tabacicomplex
© Wang et al.; licensee BioMed Central Ltd. 2013
Received: 25 January 2013
Accepted: 12 June 2013
Published: 17 June 2013
The whiteflies under the name Bemisia tabaci (Gennadius) (Aleyrodidae: Hemiptera) are species complex of at least 31 cryptic species some of which are globally invasive agricultural pests. Previously, the mitochondrial genome (mitogenome) of the indigenous New World B. tabaci species was sequenced and major differences of gene order from the postulated whitefly ancestral gene order were found. However, the sequence and gene order of mitogenomes in other B. tabaci species are unknown. In addition, the sequence divergences and gene expression profiles of mitogenomes in the B. tabaci species complex remain completely unexplored.
In this study, we obtained the complete mitogenome (15,632 bp) of the invasive Mediterranean (MED), which has been identified as the type species of the B. tabaci complex. It encodes 37 genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNAs and 22 transfer RNAs (tRNA). Comparative analyses of the mitogenomes from MED and New World (previously published) species reveal that there are no gene arrangements. Based on the Illumina sequencing data, the gene expression profile of the MED mitogenome was analyzed. We found that a number of genes were polyadenylated and the partial stop codons in cox1, cox2 and nd5 are completed via polyadenylation that changed T to the TAA stop codon. In addition, combining the transcriptome with the sequence alignment data, the possible termination site of some PCGs were defined. Our analyses also revealed that atp6 and atp8, nd4 and nd4l, nd6 and cytb were found on the same cistronic transcripts, whereas the other mature mitochondrial transcripts were monocistronic. Furthermore, RT-PCR analyses of the mitochondrial PCGs expression in different developmental stages revealed that the expression level of individual mitochondrial genes varied in each developmental stage of nymph, pupa and adult. Interestingly, mRNA levels showed significant differences among genes located in the same transcription unit suggesting that mitochondrial mRNA abundance is heavily modulated by post-transcriptional regulation.
This work provides novel insights into the mitogenome evolution of B. tabaci species and demonstrates that utilizing RNA-seq data to obtain the mitogenome and analyze mitochondrial gene expression characteristics is practical.
KeywordsBemisia tabaci Gene expression Mediterranean Mitochondrial genome Mitogenomics Whitefly
Bemisia tabaci, the sweet potato whitefly, causes millions of dollars of crop damage globally [1, 2] and is considered one of the world’s top 100 invasive species according to the International Union for the Conservation of Nature and Natural Resources (IUCN) (http://www.issg.org). It is capable of causing extensive damage to major vegetable, grain legume and fiber crops and regarded as a regulated species by a number of countries or regions, e.g., Australia, Africa, China, the EU, and the USA. There are two main types of damage caused by B. tabaci; the first is caused by immature and adult stages feeding (they ingest phloem sap and this causes damage). The second type is indirect damage from excretion of honeydew onto the surfaces of leaves and fruit and this promotes the growth of sooty mold fungi which uses honey dew as a substrate and colonizes contaminated surfaces, further interfering with photosynthesis, ultimately resulting in reduced quality of fruit and fiber . In addition, B. tabaci is the vector of many economically important plant viral-pathogens, most being begomoviruses (Geminiviridae); a group recognized as the most important emerging plant virus group in subtropical and tropical world regions [4–6].
B. tabaci is now known as a species complex with dozens of morphologically indistinguishable species and contains both invasive and native members [7–10]. In 2007, the first global mitochondrial cytochrome oxidase I (mtCOI) dataset for B. tabaci was used to reconstruct the global phylogenetic relationships, indicating significant variation between and within genetic groups . Since that pivotal work in 2007, B. tabaci has been shown to be a species complex with at least 31 distinct genetic groups identified based on mtCOI [7, 8, 10–12]. What is more, by matching museum syntypes from the 1889 original specimen from Gennadius using mtCOI molecular maker, MED were recognized as the type species of the B. tabaci complex . With the taxonomy of the B. tabaci species complex becoming clearer, it is now possible to use this information to carry out detailed comparative studies. This includes uncovering and comparing the mitochondrial genomes (mitogenomes) of the different species in the B. tabaci complex. Thao et al. (2004) sequenced the mitogenomes of six whitefly species and found that four of them had an rearrangement of the cox3 - nd3 region compared to the hypothesized ancestral insect mitochondrial gene order . They suggest, based on this rearrangement that this region has been transposed, at least four times in the evolution of whiteflies. However, whether the gene order of mitogenome in other B. tabaci species, especially the invasive MED and MEAM1, differs from the ancestral whitefly mitogenome is still unknown. Furthermore, in the B. tabaci species complex, only the mitogenome of New World species is available , a detailed comparison of mitogenomes between members of the B. tabaci species complex is still lacking. In this study, we decided to explore variation in the mitogenomes of the B. tabaci species complex. This study will also add to the growing literature on insect comparative mitogenomics of closely related species [15–20].
In addition to using the mitogenome for evolutionary study, we are also interested in the function of the mitochondrial genes. The mitochondrion is an important organelle responsible for numerous important cellular functions in insects such as energy transduction, apoptosis, detoxification, signal transduction and ATP production [21, 22]. With few exceptions, insect mitogenomes contain 37 genes encoding 13 protein coding genes (PCGs), 2 ribosomal RNAs (rrnL and rrnS) and 22 transfer RNAs (tRNAs) . The gene organization of mitogenomes is different between insects [25, 26] and mechanisms of mitochondrial gene expression have been investigated in various organisms [27–29]. Studying the mitochondrial gene organization and expression may facilitate the elucidation of mitogenome evolution and characterization of key components regulating insect biology . At present, large amount of information about mitochondrial expression profile has focused on studies of humans, mice or Drosophila. Relatively little is known about the features of non-model insect mitogenomes, such as polyadenylation and modes of gene transcription [28, 31–33].
Next-generation sequencing (NGS) data is important to predict processed mitochondrial transcripts and reveal transcription process in mitogenomes [21, 34, 35]. For example, the transcription profile of genes encoded in the mitogenome of Drosophila and the legume pod borer Maruca vitrata has been revealed using NGS data [21, 34]. For B. tabaci, the transcriptome of MED has been sequenced and a total of 43 million reads were obtained . A large number of sequencing reads could be mapped to the mitogenome of the New World B. tabaci species (data not shown). Therefore, a second goal of this study is to utilize NGS data to analyzing the characteristics of whitefly mitochondrial gene expression, including the translation start site of PCGs, polyadenylation and polycistronic transcripts.
Obtaining the MED mitogenome sequences with the NGS data
Without prior amplification of specific regions of the mitogenome, DNA sequence data obtained by NGS methodology can generate sequences of the mitogenome . In this study, 43 million Illumina sequencing reads of MED  were used to retrieve the MED mitogenome sequences by mapping them to the available mitogenome of B. tabaci New World species (GenBank accession number: AY521259). A total of 635,172 reads were mapped to the New World species reference mitogenome. These reads were assembled into eight contigs distributed in different parts of the New World mitogenome (Additional file 1). The missing base positions were 1–104, 624–800, 2042–2211, 2237–2282, 7523–7595, 11209–11434, 11537–11614 and 13566–13762. Specific primers were then designed to close these gaps (Additional file 2).
The MED mitogenome
Mitochondrial genes of MED as determined by DOGMA
Sequence divergence between mitogenoms of the MED and New World B. tabacispecies
Sequence divergence of mitogenome between the invasive MED and New World cryptic species
% mean of difference
Transcript reads mapping to the MED mitogenome
Reads mapped to tRNAs and control regions
Reads mapped to tRNA, PCGs and control regions can reveal different features for each of the segments. In the MED mitogenome, the read coverage of tRNAs was relatively low compared to that of PCGs and no reads were recovered for some of tRNAs. In addition, a number of reads were mapped to putative control regions, indicating the existence of non-coding RNA (ncRNA). The expression levels for the first and the second control regions were 0.44 and 90.93, respectively, suggesting that the two putative control regions were transcribed at different levels. However, both functional and comparative studies are needed to examine whether these two putative control regions are real control regions [48, 49]. In addition, some reads were also mapped to the intragenic spacer region and the expression level varied (Figure 5). These results suggest that while the control and intervening spacer regions are transcribed, their expression levels are lower than that of PCGs. Interestingly, the same phenomenon has been found in the mitogenomes of mouse, pig and salamander [33, 50]. The latest research also revealed that the mammalian mitogenomes encode abundant ncRNAs besides the 37 known mitochondrial genes . Whether these ncRNAs may play a role in post-transcriptional processing or simply reflect polycistronic transcription warrants further investigation.
Polyadenylation of mitochondrial PCGs
MED mitochondrial polycistronic transcripts
The expression profile of contigs transcribed from the MED mitogenome
Genes within contig
Contig length (bp)
Single nucleotide polymorphism (SNP) in the MED mitogenome
The SNP sites in the complete mitogenome
Three_base_ref- > three_base_alt
aa_ref- > aa_alt
ATG- > ATA
M- > M
GAA- > AAA
E- > K
GGA- > AGA
G- > S
GTC- > GTT
V- > V
ACG- > ACA
T- > T
Detecting PCG gene expression in different developmental stages
Next-generation sequencing is developing rapidly and many datasets have been generated in organisms whose mitochondrial genome is unknown . However, many of the valuable RNA-seq datasets were not analyzed in details. In this study, we have demonstrated that to obtain the mitogenome (at least partially) based on existed RNA-seq data is possible. This strategy can be valuable for the cloning of mitogenomes from other non-model organisms with a sequenced transcriptome. For the B. tabaci complex, even though the mitogenome of New World species has been sequenced, we thought that utilizing Illumina sequence reads to obtain the MED mitogenome was more efficient. Because the mitogenomes of New World and MED species are quite diverged (about 20%), some primers directly designed according to the mitochondrial sequence of New World species may not be used to clone MED genes. However, PCR primers can be designed according to the MED Illumina reads mapped to the New World mitogenome with nearly 100% confidence, therefore improve the probability of success (see Additional file 1). As many transcriptomes have been generated from different species, the transcriptome led approach is a useful way to extend existing data. In addition, this method may possibly be a solution or a guide for difficult to sequence mitogenomes.
The mitogenome of MED, which is the type species of the B. tabaci complex, shows similarities to the previously published mitogenome of the New World species. Both the mitogenomes have the identical set of genes in the same gene order with two putative control regions (Figure 1). However, the MED genome is slightly longer due to the presence of additional variable repeat sequences in the second control region. Codon usage differs between MED and New World mitogenomes. Overall, the MED mitogenome has 21.30% sequence divergence from that of the New World species, which is higher than the divergence at the cox1 barcode region (14.9%). This is probably due to the fact that the cox1 sequences are more constrained than the other 12 PCGs and the presence of divergent noncoding regions (Table 2 and Figure 1). This finding is consistent with the previous claim that mitochondrial genes are susceptible to rapid evolution inferred from higher mutation rates and limited DNA repair mechanisms. The analysis of synonymous and non-synonymous sites of PCGs between MED and New World showed that atp8 was evolving under high selective pressure (Figure 2), whereas cox1, cox2, cox3 and atp6 had the lowest substitution rates. This finding suggests that cox1, cox2, cox3, and atp6 may be used for reconstructing evolutionary relationships at the species level, while atp8 may be suitable for population level phylogenetic analysis.
EST data is important to define gene boundaries, predict processed mitochondrial transcripts and reveal transcription process of mitogenome. Mapping MED RNA-seq data to its mitogenome revealed a number of interesting characteristics about the MED mitogenome, such as gene expression, noncoding RNA, RNA polyadenylation and cistronic transcript. Noncoding RNAs play important roles in the splicing site recognition during the processing of transcripts if they have the ability to form stable stem-loop structures [46, 63]. Intergenic noncoding RNAs were found in the MED mitogenome. Previous RNA-seq analyses had revealed that a number of intergenic noncoding RNAs are expressed [64, 65] and noncoding RNAs appear to contain functional information , including transcription, RNA splicing, editing, translation and turnover . UTRs and intronic regions flanking nuclear genes are critical for regulating its expression, but mitogenome lacks of these regions, indicating that the mitochondrial noncoding RNA may serve as a backup mechanism to coordinate gene expression . Whether noncoding RNAs found in MED mitogenome have similar functions warrants further investigation. From the transcriptome data, rrnL had the highest expression level. In Drosophila, the mitochondrial termination factor mTERF binds just downstream of the 3′ end of the ribosomal gene cluster and is responsible for the higher expression levels of rRNAs . In New World mitogenome, the putative mTERF binding site (ACTAA) should locate in the non-coding DNA between nd1 and tRNA-Ser, similar to Philaenus (AACTAT) which is the hemipteran and very similar to Lepidoptera . In MED mitogenome, although there is no non-coding region between nd1 and tRNA-Ser, the same consensus sequence (ACTAA) was discovered at the 3' end of nd1. Interestingly, there are instances in beetles of frame shift mutations causing the mTERF site to become part of the coding region despite no changes to the sequence of the recognition site . Therefore, we propose this region as the mTERF binding site in the MED mitogenome. Interestingly, the mTERF domain-containing protein 1-like and domain-containing protein 2-like were found in transctiptome data of MED (data unpublished). This further suggests that the mTERF binding site exists in the MED mitogenome.
In MED, atp8/6, nd4l/nd4 and nd6/cytb genes were found in the same dicistronic transcripts in mature mRNA. Generation of polycistronic transcripts is a common feature of many mitochondria and the co-transcription of genes is likely used for the regulation of gene expression . Previous research has demonstrated that mRNAs that are smaller than ~400 nucleotides interact with 28S subunit of the ribosome less readily than larger mRNAs and for efficient binding, thus a minimum transcript length of ~400 nucleotides is necessary [71, 72]. This may partially explain why some mRNAs (i.e. nd4l/nd4 and atp8/6) in the MED mitogenome are dicistronic. In these dicistronic mRNAs, both nad4l and atp8 are shorter than ~400 nucleotides. Therefore, both nad4l and atp8 need to form a dicistronic mRNA with downstream genes to initiate the protein translation efficiently . In dicistronic transcripts, the downstream gene lose the 5' untranslated region, which are capable of forming extensive secondary structures and play important roles in post-transcriptional events [73–75]. In dicistronic transcripts of MED, absence of 5' untranslated regions of atp6, nd4, cytb genes may increase the efficiency of translation, suggesting a different role for the persistence of dicistronic molecules . Interestingly, for the dicistronic nd6/cytb and atp8/atp6 transcripts, poly(A) stretches were found in the 3' end of nd6 and atp8 genes. Similarly, in the tricistronic transcript (atp8/atp6/cox3) of Drosophila, poly(A) stretches were found in the 3' terminus of atp8 and atp6, which suggest the variation in mitochondrial transcript cleavage events may occur in the insects [27, 33]. Analyses of mitochondrial transcripts in additional species are needed to reveal the mechanism of the polycistronic processing in mitochondria.
The poly(A) tail has been identified to possibly contribute to translational control [73, 74] and mRNA degradation . In this study, PCGs of the MED mitogenome were found to have varying lengths of poly(A) tails and some of the poly(A) tails were critical to generate the UAA termination codon. Previous studies on mRNA polyadenylation concluded that the central sequence motif AAUAAA was essential for mRNA polyadenylation and 3' end formation, but recent studies of EST databases suggest that the frequency of the motif appeared low . In our study, different possible poly(A) signals were also found in eight PCGs of the MED mitogenome.
In summary, the mitogenome of the invasive B. tabaci MED species contains the same gene rearrangement as that of the New World species. Using transcriptome data, the expression profile and the termination location of some genes were determined. In addition, polyadenylation, polycistronic transcripts and SNPs were discovered in B. tabaci mitogenome for the first time. The results presented here also demonstrate that utilizing RNA-seq data to analyze gene expression characteristics of mitogenome is practical. The MED and New World mitogenomes are interesting but the real utility of the sequence data comes from a comparative approach and it is our recommendation to sequence all of the mitogenomes for the species. With the inclusion of additional mitogenomes, patterns of mitochondrial gene expression and differences of energy usage in invasive and indigenous species could be tested.
Mitogenome sequence mapping and assembly
The complete mitogenome sequence of the New World species of B. tabaci was downloaded from GenBank: AY 521259 and was used as reference for alignment. MED transcriptome reads were directly mapped onto the New World mitogenome using Blastn . As the mitogenome of New World and MED differ, when reads of MED were mapped to the New World mitogenome two mismatches were allowed. Then, reads mapped to the New World mitogenome were collected and assembled. Based on the position and sequence information of the assembled contigs, PCR primers were designed to complete the mitogenome sequence of MED (Additional file 2).
PCR amplification, cloning and sequencing
The method of obtaining MED whitefly DNA samples was described in Wang et al. . Total genomic DNA of multiple individuals was isolated using the DNeasy animal tissue kit (Qiagen, Germany) following the manufacturer’s protocol. PCR was carried out in an S1000 Thermal Cycler (Bio-Rad). A 25 μL PCR reaction contained 0.5 μL 10 μmol primers, 2.5 μL 10 × PCR buffer, 2.0 μL 10 mM dNTP, 0.4 μL LA Taq polymerase (Takara, Japan). Short PCRs (<2.0 kb) were carried out using Taq DNA polymerase (Takara, Japan) with the following PCR conditions: 95°C for 2 min, followed by 35 cycles of 96°C for 30 s, 44-52°C for 30 s, 72°C for 3 min, as well as a final cycle of 72°C for 10 min. Long PCRs were carried out using LA Taq DNA polymerase with the following PCR conditions: 95°C for 2 min, followed by 35 cycles of 96°C for 30 s, 48-56°C for 30 s, 72°C for 3 min and a final cycle of 72°C for 10 min. PCR fragments were purified and ligated into the pGEM-T Easy Vector (Promega, USA) and sequenced in both directions using the ABI BigDye 3.1 at GenScript (Nanjing, China).
Annotation of the MED mitogenome
DOGMA  was used to annotate the PCGs, rRNA genes of MED mitochondrial DNA. tRNAs were identified using tRNAscan-SE (invertebrate mitochondrial genetic code and ‘mito/chloroplast’ source) . tRNA genes that could not be identified using tRNAscan-SE, sequences were aligned with published Aleyrodidae mitochondrial sequences (see below for species). BioEdit was used to calculate A/T content and also to translate DNA into amino acids . AT and GC skews were calculated by (A-T)/(A+T) and (G-C)/(G+C) respectively . The complete mitogenome of MED was deposited in GenBank: JQ906700.
Comparison of mitogenomes
The numbers of synonymous substitutions (Ks) and non-synonymous substitutions (Ka) for each gene were calculated with the software of DnaSP Version 5.10.01 [82, 83]. For the sequence divergence analyses, pair-wise alignments were generated for all the 13 PCGs orthologous gene pairs based on protein sequences and DNA sequences using the MegaBlast algorithm. According to the mitochondrial codons, the divergence was determined for the contexts of nd, 4d, CpG and non-CpG sites . The ratio of transitions over transversions (Ts/Tv) was caculated for the all coding region as well. The mitogenome sequences of Tetraleurodes acaciae (AY521626), Neomaskellia andropogonis (AY572539), Aleurochiton aceris (AY572538), Trialeurodes vaporariorum (AY521265), Aleurodicus dugesii (AY521251), Pachypsylla venusta (AY278317) and Schizaphis graminum (AY531391) were obtained from GenBank. The MED and New World partial cox1 sequences were extracted from GenBank AM176574 and AY057133, respectively.
Mapping reads to the MED mitogenome, expression profiling and SNP analysis
TopHat (Version:1.4.1) was used to align the MED NGS reads with the MED mitogenome with the following parameters: -g1 -r 200 –mate-std-dev20 -I 10000 . The numbers of mapped reads for each gene were summed and divided by gene length to calculate the expression level of each mitochondrial gene. To detect polyadenylation, reads containing more than eight continuous A or T from the transcript data were aligned to the 13 mitochondrial genes using Blast. Reads that hit at or downstream of stop codons of PCGs were selected. Based on the mapping results, SAMTools (V0.1.13) were used to discovery the possible SNP sites with depth of at least 10 reads . The analyses of amino acid mutation at PCGs and intergenic region were performed by a custom-written algorithm (available upon request) using mitochondrial codons.
Verification of dicistronic transcripts
The method of obtaining RNA from MED females had been described . RNA was treated with DNase and 1st Strand cDNA was synthesized following the protocol of PrimeScript II 1st Strand cDNA Synthesis Kit (Takara). Three pairs of primers for the three dicistronic transcripts were designed respectively. PCR were performed with cDNA as template.
qPCR analysis of PCG expression
Total RNA was extracted from the three MED samples (nymph, pupa and adult) using SV total RNA isolation system (Promega) following the manufacturer’s protocol . The nymph sample include first- to third-instars. The SYBR® Prime Script™ RT-PCR Kit II (Takara) was used to synthesize cDNA and then qPCR was used to detect the expression of 11 mitochondrial genes. The ABI PRISM 7500 Fast Real-Time PCR System (Applied Biosystems) with SYBR-Green detection was employed to perform qPCRs. For normalization, β-actin was selected as the endogenous control. Every gene was analyzed three times and the relative expression levels were calculated by the 2-△△Ct method. As an endogenous control, the expression of β-actin was measured in parallel .
Cytochrome oxidase, subunit I
Cytochrome oxidase, subunit II
ATP synthase, subunit 8
ATP synthase, subunit 6
NADH dehydrogenase, subunit 5
NADH dehydrogenase, subunit 4
NADH dehydrogenase, subunit 4L
NADH dehydrogenase, subunit 6
NADH dehydrogenase, subunit 1
NADH dehydrogenase, subunit 2
NADH dehydrogenase, subunit 3
cytochrome oxidase, subunit III
NADH dehydrogenase, subunit 2
Small subunit of mitochondrial ribosomal DNA
Large subunit of mitochondrial ribosomal DNA.
Acknowledgments and funding information
We thank Dr. Shu-Jun Wei and Dr. Xue-Xin Chen for advices on this research. This work was supported by the National Natural Science Foundation of China (grant number 31272104) and the National Basic Research Program of China (grant number 2009CB119203). A New Zealand-China Scientist Exchange Programme administered by The Royal Society of New Zealand and the Chinese Ministry and Science and Technology (MOST) funded LMB.
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