食线虫真菌洛斯里被毛孢线粒体基因组的再分析

【目的】鉴定洛斯里被毛孢OWVT-1菌株的线粒体基因组,验证公布的USA-87-5菌株线粒体基因组中的错误,对洛斯里被毛孢正确的线粒体基因组序列进行注释并开展不同被毛孢物种间的比较线粒体基因组学分析。【方法】借助DNA高通量测序数据并通过必要的Sanger测序组装OWVT-1的线粒体基因组。通过PCR验证OWVT-1与公布的USA-87-5线粒体基因组序列差异的真实性。利用多种生物信息方法分析和注释洛斯里被毛孢的线粒体基因组。【结果】公布的洛斯里被毛孢USA-87-5菌株的线粒体基因组存在几处序列错误,包括3处长片段的插入缺失和多处短片段的插入缺失。实际上,洛斯里被毛孢USA-87-5与OWVT-1菌株的线粒体基因组序列完全相同。该菌的线粒体基因组全长62949 bp,在7个基因中共插入13个内含子,部分内含子和基因间区显现出序列退化的特征。洛斯里被毛孢、明尼苏达被毛孢、线虫被毛孢的线粒体基因组具有较强的共线性关系。除一些独立的ORF外,核心蛋白编码基因、rRNA基因和tRNA基因的排列顺序非常保守。基因间区的长短是影响3种被毛孢线粒体基因组大小最主要的因素。【结论】公布的洛斯里被毛孢USA-87-5菌株线粒体基因组中存在序列错误。本文新报道了OWVT-1菌株的线粒体基因组,并进行注释和比较线粒体基因组学分析。     

The complete nucleotide sequence of the mitochondrial genome of <Emphasis Type="Italic">Phthonandria atrilineata</Emphasis> (Lepidoptera: Geometridae)

Using long-polymerase chain reaction (Long-PCR) method, we determined the complete nucleotide sequence of the mitochondrial genome (mitogenome) of Phthonandria atrilineata. The complete mtDNA from P. atrilineata was 15,499 base pairs in length and contained 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a control region. The P. atrilineata genes were in the same order and orientation as the completely sequenced mitogenomes of other lepidopteran species. The nucleotide composition of P. atrilineata mitogenome was biased toward A + T nucleotides (81.02%), and the 13 PCGs show different A + T contents that range from 73.25% (cox1) to 92.12% (atp8). Phthonandria had the canonical set of 22 tRNA genes, that fold in the typical cloverleaf structure described for metazoan mt tRNAs, with the unique exception of trnS(AGN). The phylogenetic relationships were reconstructed with the concatenated sequences of the 13 PCGs of the mitochondrial genome, which confirmed that P. atrilineata is most closely related to the superfamily Bombycoidea.     

Complete mitochondrial genome of a carabid beetle,Damaster mirabilissimus mirabilissim (Coleoptera: Carabidae)

In the present study, we report the 16 823‐bp long complete mitochondrial genome (mitogenome) of a carabid beetle, Damaster mirabilissimus mirabilissim (Coleoptera: Carabidae), which is endangered in Korea. The gene arrangement of D. m. mirabilissim mitogenome is identical to the most common type found in insects. The start codon of the D. m. mirabilissim COI gene is a typical ATN codon. On the other hand, the initiation codon for ND1 gene is TTG, instead of ATN. All transfer RNAs (tRNAs) exhibit a stable canonical clover‐leaf structure, except for tRNA^Ser(AGN), the dihydrouridine arm of which forms a simple loop. The 1703‐bp long A+T‐rich region is the second longest among the complete adephagan mitogenome sequences, next to Macrogyrus oblongus belonging to Gyrinoidea. One of the unusual features of the genome is the presence of a tRNA^Leu(UUR)‐like sequence in the A+T‐rich region. This sequence displays the proper anticodon sequence and the potential to form secondary structures, but also harbors many mismatches in the stems.     

Genetic differences among three species of the genus Trichiurus (Perciformes: Trichiuridae) based on mitochondrial DNA analysis

The mitochondrial DNA segment encoding the 16S ribosomal RNA (16S rRNA) gene sequence (ca. 600 bp) was compared among Trichiurus sp. 2 (sensu Nakabo, 2002) (obtained from various areas of Japan), T. japonicus Temminck and Schlegel (collected from various localities within Japan), and true T. lepturus Linnaeus (caught off the Atlantic coast of the United States and Brazil) of the family Trichiuridae using 10, 10, and 15 specimens, respectively. Based on phylogenetic analysis using a neighbor-joining (NJ) algorithm, the haplotypes of Trichiurus sp. 2, T. japonicus, and T. lepturus indicated three distinct monophyletic lineages, being supported by 100% bootstrap values with no haplotypes overlapping or sharing among the lineages. Trichiurus sp. 2, T. japonicus, and T. lepturus are genetically different from each other, suggesting that they are three distinct species.     

Complete mitochondrial genome sequence of the yellow-spotted long-horned beetle <Emphasis Type="Italic">Psacothea hilaris</Emphasis> (Coleoptera: Cerambycidae) and phylogenetic analysis among coleopteran insects

We have determined the complete mitochondrial genome of the yellow-spotted long horned beetle, Psacothea hilaris (Coleoptera: Cerambycidae), an endangered insect species in Korea. The 15,856-bp long P. hilaris mitogenome harbors gene content typical of the animal mitogenome and a gene arrangement identical to the most common type found in insect mitogenomes. As with all other sequenced coleopteran species, the 5-bp long TAGTA motif was also detected in the intergenic space sequence located between tRNA^Ser(UCN) and ND1 of P. hilaris. The 1,190-bp long non-coding A+T-rich region harbors an unusual series of seven identical repeat sequences of 57-bp in length and several stretches of sequences with the potential to form stem-and-loop structures. Furthermore, it contains one tRNA^Arg-like sequence and one tRNA^Lys-like sequence. Phylogenetic analysis among available coleopteran mitogenomes using the concatenated amino acid sequences of PCGs appear to support the sister group relationship of the suborder Polyphaga to all remaining suborders, including Adephaga, Myxophaga, and Archostemata. Among the two available infraorders in Polyphaga, a monophyletic Cucujiformia was confirmed, with the placement of Cleroidea as the basal lineage for Cucujiformia. On the other hand, the infraorder Elateriformia was not identified as monophyletic, thereby indicating that Scirtoidea and Buprestoidea are the basal lineages for Cucujiformia and the remaining Elateriformia.     

Complete mitochondrial genome of Tubulipora flabellaris (Bryozoa: Stenolaemata): the first representative from the class Stenolaemata with unique gene order

Mitochondrial genomes play a significant role in the reconstruction of phylogenetic relationships within metazoans. There are still many controversies concerning the phylogenetic position of the phylum Bryozoa. In this research, we have finished the complete mitochondrial genome of one bryozoan (Tubulipora flabellaris), which is the first representative from the class Stenolaemata. The complete mitochondrial genome of T. flabellaris is 13,763 bp in length and contains 36 genes, which lacks the atp8 gene in contrast to the typical metazoan mitochondrial genomes. Gene arrangement comparisons indicate that the mitochondrial genome of T. flabellaris has unique gene order when compared with other metazoans. The four known bryozoans complete mitochondrial genomes also have very different gene arrangements, indicates that bryozoan mitochondrial genomes have experienced drastic rearrangements. To investigate the phylogenetic relationship of Bryozoa, phylogenetic analyses based on amino acid sequences of 11 protein coding genes (excluding atp6 and atp8) from 26 metazoan complete mitochondrial genomes were made utilizing Maximum Likelihood (ML) and Bayesian methods, respectively. The results indicate the monopoly of Lophotrochozoa and a close relationship between Chaetognatha and Bryozoa. However, more evidences are needed to clarify the relationship between two groups. Lophophorate appeared to be polyphyletic according to our analyses. Meanwhile, neither analysis supports close relationship between Branchiopod and Phoronida. Four bryozoans form a clade and the relationship among them is T. flabellaris + (F. hispida + (B. neritina + W. subtorquata)), which is in coincidence with traditional classification system.     

银色裂腹鱼线粒体基因组序列特征与系统进化分析

银色裂腹鱼(Schizothorax argentatus)在我国仅分布于新疆地区的伊犁河流域,是我国裂腹鱼类中珍稀濒危品种之一,具有较高的科研和经济价值。本研究采用高通量测序技术获得了银色裂腹鱼长度为16580 bp的线粒体基因组全序列,其基因组成和排列顺序均与典型的脊椎动物相似,共有13个蛋白质编码基因、22个tRNA基因、2个rRNA基因和1个非编码区(D-loop)。碱基组成分别为A(30.25%)、G(17.28%)、C(27.20%)和T(25.27%),呈现明显的AT偏好性和反G偏倚。tRNA基因中仅tRNA-Ser(GCU)因缺少二氢尿嘧啶茎而无法形成典型的三叶草结构。ND6基因的AT-skew和GC-skew值波动最大,揭示该基因经历的选择和突变压力可能与其他基因不同。银色裂腹鱼线粒体控制区包含了3个不同的结构域:终止序列区(ETAS)、中央保守区(CSB-F、CSB-E、CSB-D和CSB-B)和保守序列区(CSB1、CSB2和CSB3),且在CSB3下游约50 bp处识别到鲤形目(Cypriniformes)鱼类中普遍存在的保守序列片段TT(AT)nGTG。基于28种裂腹鱼属鱼类线粒体基因组全序列构建的系统发育关系表明银色裂腹鱼分化时间较早,与其他类群亲缘关系较远,这可能与其所生活的水域地理位置和水文环境有密切关系。     

肺囊康定产生菌Glarea lozoyensis线粒体基因组序列的再分析

[目的] Glarea lozoyensis是抗真菌药物卡泊芬净的产生菌,其突变菌株ATCC 74030的线粒体基因组已被报道。我们此前的研究发现诱变剂能引起该菌某些细胞核基因的突变,但诱变剂是否也能引起线粒体DNA序列的改变并不清楚。[方法] 组装野生型菌株ATCC 20868的线粒体基因组,并与发表的突变型菌株ATCC 74030的线粒体基因组进行比较。通过PCR验证野生和突变菌株线粒体基因组间表现差异之处,并利用正确的线粒体基因组序列进行新的分析。[结果] 我们成功组装出野生型菌株ATCC 20868的线粒体基因组,通过比较其与发表的ATCC 74030的线粒体基因组序列,发现存在6处单核苷酸变异位点和2处具有长度差异的区域。然而,随后的PCR验证和序列比较并没有发现2个菌株间存在这些差异。最初观察到的碱基差异是因为发表的ATCC 74030线粒体基因组存在序列错误。有趣的是,在Glarea lozoyensis的线粒体基因组中,我们发现存在3个具有内含子的tRNA基因和1个rnpB基因。同时,该菌线粒体基因组中存在多种重复序列,在其线粒体和细胞核基因组间也存在明显的DNA片段重复事件。[结论] 诱变剂没有引起G. lozoyensis线粒体DNA的任何改变;发表的ATCC 74030的线粒体基因组存在序列错误。我们报道G. lozoyensis正确的线粒体基因组序列,并且发现该菌线粒体和细胞核基因组间频繁的基因交流。     

Grain protein variability among species of Triticum and Aegilops: quantitative SDS-PAGE studies

Summary Total proteins were extracted from degermed seeds of various species of Triticum and Aegilops with solutions containing sodium dodecyl sulfate (SDS) and mercaptoethanol. The reduced, dissociated proteins were fractionated according to molecular weight (MW) by high-resolution polyacrylamide gel electrophoresis in buffers containing SDS (SDS-PAGE). Stained SDS-PAGE patterns were measured by densitometric scanning over a suitable range of optical density. The data were normalized to equivalent total areas for each of the densitometric scans by means of a computer program that also permitted the construction of patterns of hypothetical amphiploids by averaging patterns of two or three diploid species. The grain proteins of most species examined had distinctive qualitative and quantitative aspects that were characteristic of the species even though nearly every accession or cultivar of a species exhibited at least minor differences in pattern from other accessions or cultivars. The main protein components (probably prolamins) of Triticum monococcum ssp. monococcum, T. monococcum ssp. boeoticum, T. urartu, and Aegilops squarrosa had MW's in the range 29–36 X 10³ whereas the most important components of Ae. speltoides, Ae. longissima, and Ae. searsii had MW's in the range 37–55 × 10³. Changes in the quantitative expression of particular genes, especially those coding for storage protein components, may have been associated with speciation. The strong predominance of proteins with MW's in the range 29–36 × 10³ in some accessions of AB genome tetraploids, such as T. turgidum ssp. dicoccoides, may indicate contributions to the B genome of these tetraploids by T. monococcum ssp. boeoticum, T. urartu, or Ae. squarrosa.     

The potato mitochondrial initiator methionine tRNA gene and its flanking regions: an illustration of the diversity of mitochondrial genome rearrangements among plant species

The initiator methionine transfer RNA (tRNAf ^Met) gene was identified on a 347 bpEco RI-Hind III DNA fragment of the potato mitochondrial (mt) genome. The sequence of this gene shows 1 to 7 nucleotide differences with the other plant mt tRNAsf ^Met or tRNAf ^Met genes studied so far. Whereas the tRNAf ^Met gene is present as a single copy in the potato mt genome, a tRNA pseudogene corresponding to 60% of a complete tRNA (from the 5 end to the variable region) and located at 105 nucleotides upstream of the tRNAf ^Met gene on the opposite strand was shown to be repeated at least three times. Furthermore, the physical environment of the tRNAf ^Met gene in the mt genome is very different among plants, which suggests that the tRNAf ^Met gene region has often been implicated in recombination events of plant mt genomes leading to important rearrangements in gene order.     

The complete mitochondrial genome of Gomphocerus tibetanus Uvarov, 1935 (Orthoptera: Acrididae: Gomphocerinae)

The complete nucleotide sequence of the mitochondrial genome (mitogenome) of Gomphocerus tibetanus Uvarov, 1935 (Orthoptera: Acrididae: Gomphocerinae) was determined. It is 15,571 bp in length and contains 74.8% A + T. All Gomphocerus tibetanus protein-coding sequences start with a typical ATN codon. The usual termination codons (TAA and TAG) were found from 13 PCGs except COI and COII which took incomplete codon T as termination codons. All tRNA genes could be folded into the typical cloverleaf secondary structure, except tRNA^Ser(AGN) lacking of dihydrouridine (D) arm. The sizes of the large and small ribosomal RNA genes are 1313 and 822 bp, respectively. The A + T content of the A + T-rich region is 82.3%. A preliminary analysis on characteristics of Gomphocerinae mitogenome was made by comparision among three Gomphocerinae mitogenomes and Locusta migratoria.     

The complete mitochondrial genome structure of snow leopard <Emphasis Type="Italic">Panthera uncia</Emphasis>

The complete mitochondrial genome (mtDNA) of snow leopard Panthera uncia was obtained by using the polymerase chain reaction (PCR) technique based on the PCR fragments of 30 primers we designed. The entire mtDNA sequence was 16 773 base pairs (bp) in length, and the base composition was: A—5,357 bp (31.9%); C—4,444 bp (26.5%); G—2,428 bp (14.5%); T—4,544 bp (27.1%). The structural characteristics [0] of the P. uncia mitochondrial genome were highly similar to these of Felis catus, Acinonyx jubatus, Neofelis nebulosa and other mammals. However, we found several distinctive features of the mitochondrial genome of Panthera unica. First, the termination codon of COIII was TAA, which differed from those of F. catus, A. jubatus and N. nebulosa. Second, tRNA^{Ser (AGY)}, which lacked the ‘‘DHU’’ arm, could not be folded into the typical cloverleaf-shaped structure. Third, in the control region, a long repetitive sequence in RS-2 (32 bp) region was found with 2 repeats while one short repetitive segment (9 bp) was found with 15 repeats in the RS-3 region. We performed phylogenetic analysis based on a 3 816 bp concatenated sequence of 12S rRNA, 16S rRNA, ND2, ND4, ND5, Cyt b and ATP8 for P. uncia and other related species, the result indicated that P. uncia and P. leo were the sister species, which was different from the previous findings.     

The complete mitochondrial genome sequence of the little egret (Egretta garzetta)

Many phylogenetic questions in the Ciconiiformes remain unresolved and complete mitogenome data are urgently needed for further molecular investigation. In this work, we determined the complete mitogenome sequence of the little egret (Egretta garzetta). The genome was 17,361 bp in length and the gene organization was typical of other avian mtDNA. In protein-coding genes (PCGs), a C insertion was found in ND3, and COIII and ND4 terminated with incomplete stop codons (T). tRNA-Val and tRNA-Ser (AGY) were unable to fold into canonical cloverleaf secondary structures because they had lost the DHU arms. Long repetitive sequences consisting of five types of tandem repeats were found at the 3′ end of Domain III in the control region. A phylogenetic analysis of 11 species of Ciconiiformes was done using complete mitogenome data and 12 PCGs. The tree topologies obtained with these two strategies were identical, which strongly confirmed the monophyly of Ardeidae, Threskiorothidae and Ciconiidae. The phylogenetic analysis also revealed that Egretta was more closely related to Ardea than to Nycticorax in the Ardeidae, and Platalea was more closely related to Threskiornis than to Nipponia in the Threskiornithidae. These findings contribute to our understanding of the phylogenetic relationships of Ciconiiformes based on complete mitogenome data.     

Chemical ecology of oribatid mites III. Chemical composition of oil gland exudates from two oribatid mites, Trhypochthoniellus sp. and Trhypochthonius japonicus (Acari: Trhypochthoniidae)

The composition of oil gland exudates from two oribatid mites, Trhypochthoniellus sp. and Trhypochthonius japonicus, was studied with reference to the related species Trhypochthoniellus crassus. Trhypochthoniellus sp. contained a mixture of seven compounds; (Z,Z)-6,9-heptadecadiene, geranial, 3-hydroxybenzene-1,2-dicarbaldehyde (γ-acaridial), neryl formate, neral, (Z)-8-heptadecene and geranyl formate in decreasing order of abundance. The profile of the components from T. japonicus consisted of two types depending on the locality of sampling with unknown reason; one possessing a mixture of eight compounds [(Z,E)-farnesal, γ-acaridial, (Z,Z)-6,9-heptadecadiene, (E,E)-farnesal, (Z)-8-heptadecene and geranial in decreasing order] together with two unknown compounds, and the other composed of the same set of compounds together with 2-hydroxy-6-methylbenzaldehyde as the most abundant component. Relative abundance among common components was consistent between the two types of T. japonicus. Profiles of components differed among three species including T. crasus. The phylogenetic relationship between Oribatida and Astigmata was discussed based on secretory compounds commonly distributed between these two suborders. This revised version was published online in July 2006 with corrections to the Cover Date.     

Unlike in other monocotyledonous plants such as wheat and rice, the region containing the tRNA (UCC), tRNA (UCU) and CF1 ATPase α-subunit genes has not undergone recombination in the leek chloroplast DNA

The nucleotide sequence of a 1.1 kbp BamHI fragment of the leek chloroplast DNA (Allium porrum., fam. Liliaceae) has been determined. The fragment contains the 3' part of the tRNA^Gly (UCC) gene and the tRNA^Arg (UCU) gene on the same strand, and the 3' end of the atpA gene encoding the CF₁ ATPase α-subunit which is located on the opposite strand. The gene arrangement and nucleotide sequence of this fragment are similar to those of the corresponding region in the tobacco chloroplast DNA but differ significantly from what has been observed in other monocotyledonous plants such as wheat and rice, in which the region containing these genes has undergone intensive rearrangement.     

The complete mitochondrial genome of the intertidal copepod Tigriopus sp. (Copepoda, Harpactidae) from Korea and phylogenetic considerations

This paper reports on the basic characteristics of the mitochondrial genome of the intertidal copepod Tigriopus sp. from Korea, including its structural organization, base composition of rRNAs and protein-encoding genes, and the secondary structure of tRNAs. We amplified the complete mitochondrial DNA of the intertidal copepod Tigriopus sp. from Korea (sampling site Busan) by long-polymerase chain reaction (long-PCR) with conserved primers and sequenced this mitogenome by primer walking using flanking sequences as sequencing primers. The primer informations were obtained as expressed sequence tags (ESTs) from Tigriopus sp. The resultant Tigriopus sp. mitochondrial DNA sequence was 14,301 bp with a conserved structural organization, compared to that of T. japonicus from Japan with significant differences in several protein-coding regions including rRNAs, although the genomic organization of the mitochondrial genome was identical. In order to investigate biogeographic differences within the genus Tigriopus, we analyzed the CO1 gene by sequencing. This way, we compared several Tigriopus species from Korea, Japan, Hong Kong and Taiwan as well as other related species such as T. californicus, T. brevicornis and T. fulvus. The results further support the notion that the copepods display significantly different genomes within the same genus. These findings provide valuable genomic information for further studies on the population genetics and speciation processes within the genus Tigriopus.     

Enhancement of the salt tolerance of Triticum turgidum L. by the Kna1 locus transferred from the Triticum aestivum L. chromosome 4D by homoeologous recombination

Durum wheat, Triticum turgidum L. (2n= 4x=28, genome formula AABB) is inferior to bread wheat, T. aestivum L. (2n=6x=42, genome formula AABBDD), in the ability to exclude Na⁺ under salt strees, in the ratio of the accumulated K⁺ to Na⁺ in the leaves under salt stress, and in tolerance of salt stress. Previous work showed that chromosome 4D has a major effect on Na⁺ and K⁺ accumulation in the leaves of bread wheat. The 4D chromosome was recombined with chromosome 4B in the genetic background of durum wheat. The recombinants showed that Na⁺ exclusion and enhanced K⁺/Na⁺ ratio in the shoots were controlled by a single locus, Kna1, in the long arm of chromosome 4D. The recombinant families were grown in the field under non-saline conditions and two levels of salinity to determine whether Kna1 confers salt tolerance. Under salt stress, the Kna1 families had higher K⁺/Na⁺ ratios in the flag leaves and higher yields of grain and biomass than the Kna1 ^- families and the parental cultivars. Kna1 is, therefore, one of the factors responsible for the higher salt tolerance of bread wheat relative to durum wheat. The present work provides conceptual evidence that tolerance of salt stress can be transferred between species in the tribe Triticeae.     

Complete mitochondrial genome of the atlas moth, Attacus atlas (Lepidoptera: Saturniidae) and the phylogenetic relationship of Saturniidae species

Mitochondrial genome (mitogenome) can provide information for genomic structure as well as for phylogenetic analysis and evolutionary biology. In this study, we present the complete mitogenome of the atlas moth, Attacus atlas (Lepidoptera: Saturniidae), a well-known silk-producing and ornamental insect with the largest wing surface area of all moths. The mitogenome of A. atlas is a circular molecule of 15,282 bp long, and its nucleotide composition shows heavily biased towards As and Ts, accounting for 79.30%. This genome comprises 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A + T-rich region. It is of note that this genome exhibits a slightly positive AT skew, which is different from the other known Saturniidae species. All PCGs are initiated by ATN codons, except for COI with CGA instead. Only six PCGs use a common stop codon of TAA or TAG, whereas the remaining seven use an incomplete termination codon T or TA. All tRNAs have the typical clover-leaf structure, with an exception for tRNA^Ser(AGN). The A. atlas A + T-rich region contains non-repetitive sequences, but harbors several features common to the Bombycoidea insects. The phylogenetic relationships based on Maximum Likelihood method provide a well-supported outline of Saturniidae, which is in accordance with the traditional morphological classification and recent molecular works.     

TheTy1-copia group retrotransposons inVicia species: copy number, sequence heterogeneity and chromosomal localisation

We present an in-depth study of theTy1-copia group of retrotransposons within the plant genusVicia, which contains species with widely differing genome sizes. We have compared the numbers and sequence heterogeneities of these genetic elements in three diploidVicia species chosen to represent large (V. faba, 1C=13.3 pg), medium (V. melanops, 1C=11.5 pg) and small (V. sativa, 1C=2.3 pg) genomes within the genus. The copy numbers of the retrotransposons are all high but vary greatly, withV. faba containing approximately 10⁶ copies,V. melanops about 1000 copies andV. sativa 5000 copies. The degree of sequence heterogeneity ofTy1-copia group elements correlates with their copy number within each genome, but neither heterogeneity nor copy number are related to the genome size of the host. In situ hybridization to metaphase chromosomes shows that the retrotransposons inV. faba are distributed throughout all chromosomes but are much less abundant in certain heterochromatic regions. These results are discussed in the context of plant retrotransposon evolution.