The use of a non-coding region of chloroplast DNA in phylogenetic studies of the subtribeSonchinae (Asteraceae:Lactuceae)

1999 ◽  
Vol 215 (1-4) ◽  
pp. 85-99 ◽  
Author(s):  
Seung-Chul Kim ◽  
Daniel J. Crawford ◽  
Robert K. Jansen ◽  
Arnoldo Santos-Guerra
Keyword(s):  
Chloroplast Dna ◽  
Coding Region ◽  
Phylogenetic Studies

scholarly journals An additional promoter within the protein-coding region of thepsbD-psbC gene cluster in tobacco chloroplast DNA

1989 ◽  
Vol 17 (23) ◽  
pp. 9583-9591 ◽  
Author(s):  
Wen Biao Yao ◽  
Bing Yuan Meng ◽  
Minoru Tanaka ◽  
Masahiro Sugiura
Keyword(s):  
Chloroplast Dna ◽  
Gene Cluster ◽  
Coding Region ◽  
Protein Coding ◽  
Tobacco Chloroplast

A new species of the genus Tuberfemurus (Orthoptera: Tetrigoidea: Cladonotinae) with comments on the characters of mitochondrial genome

Zootaxa ◽  
2021 ◽  
Vol 5071 (3) ◽  
pp. 437-446
Author(s):  
MENG-QI WANG ◽  
YAO DENG ◽  
DE-LONG GUAN ◽  
BEN-YONG MAO ◽  
MIAO LI
Keyword(s):  
New Species ◽  
Mitochondrial Genome ◽  
Stop Codon ◽  
Complete Mitochondrial Genome ◽  
Hind Femur ◽  
Start Codon ◽  
Gene Arrangement ◽  
Coding Region ◽  
Phylogenetic Studies ◽  
A New Species

A new species, Tuberfemurus viridulus sp. nov. is described and illustrated with photographs. The new species is similar to T. torulisinotus Deng, 2019, but differs from the latter by broader vertex, invisible frontal costa in profile, distinctly truncate apex of hind pronotal process, and two large triangular projections on lower outer carinae of hind femur. An updated key to species of Tuberfemurus is provided. Simultaneously, the complete mitochondrial genome of Tuberfemurus viridulus sp. nov. is sequenced and analyzed. The total length of the assembled mitogenome is 15,060 bp with 37 typical mitochondrial genes and a non-coding region (A + T-rich region). The order and orientation of the gene arrangement pattern are identical to that of most Tetrigoidea species. All PCGs initiate with the standard start codon of ATN, except ATP6 with GAC and ND1 with TTG; and terminate with the complete stop codon (TAA/TAG) or with an incomplete T- codon. This data could provide the genome information available for Tetrigoidea and facilitate phylogenetic studies of related insects.  

Chloroplast DNA and Phylogenetic Studies in the Asteridae

1990 ◽  
pp. 119-134 ◽  
Author(s):  
RICHARD G. OLMSTEAD ◽  
ROBERT K. JANSEN ◽  
HELEN J. MICHAELS ◽  
STEPHEN R. DOWNIE ◽  
JEFFREY D. PALMER
Keyword(s):  
Chloroplast Dna ◽  
Phylogenetic Studies

The complete mitochondrial genomes of four Baikal molluscs from the endemic family Baicaliidae (Caenogastropoda: Truncatelloida)

2020 ◽  
Vol 86 (3) ◽  
pp. 201-209
Author(s):  
T E Peretolchina ◽  
T Ya Sitnikova ◽  
D Yu Sherbakov
Keyword(s):  
Lake Baikal ◽  
Ribosomal Rna ◽  
Rrna Genes ◽  
Trna Genes ◽  
Coding Region ◽  
Base Pairs ◽  
Protein Coding ◽  
Phylogenetic Studies ◽  
Canonical Base ◽  
Complete Mitochondrial Genomes

Abstract Here, we present the complete mitochondrial (mt) genomes of four members of the Baicaliidae Fisher, 1885, a truncatelloidean family that is endemic to Lake Baikal (East Siberia). The mt genomes are those of Korotnewia korotnevi (15,171 bp), Godlewskia godlewskii (15,224 bp), Baicalia turriformis (15,127) and Maackia herderiana (15,154 bp). All these mt genomes contain 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. We detected non-canonical base pairs in some of the tRNA genes and variable numbers of non-coding spacers; some tRNAs do not have a TψC loop. We found gene order to be highly conserved in these Lake Baikal species and similar to the majority of caenogastropod mt genomes available on GenBank. A position of the putative control region is delimited to the non-coding region between trnF and the cox3 gene. It contains the ‘GAA(A)nT’ motif at the 3′ end and is similar to the replication origin found in most Caenogastropoda studied to date. We also compared the evolutionary rates of different genes to evaluate their use in different kinds of population or phylogenetic studies of this group of gastropods.

THE NATURE OF NUCLEOTIDE SEQUENCE DIVERGENCE BETWEEN BARLEY AND MAIZE CHLOROPLAST DNA

Genetics ◽  
1984 ◽  
Vol 106 (4) ◽  
pp. 735-749
Author(s):  
Gerard Zurawski ◽  
Michael T Clegg ◽  
Anthony H D Brown
Keyword(s):  
Chloroplast Dna ◽  
Dna Sequences ◽  
Large Subunit ◽  
Leader Region ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Bisphosphate Carboxylase ◽  
Noncoding Regions ◽  
The Third ◽  
Maize Chloroplast

ABSTRACT Analysis of a 2175-base pair (bp) SmaI-HindIII fragment of barley chloroplast DNA revealed that rbcL (the gene for the large subunit of ribulose 1,5-bisphosphate carboxylase) and atpB (the gene for the β subunit of ATPase) are transcribed divergently and are separated by an untranscribed region of 155-166 bp. The rbcL mRNA has a 320-residue untranslated leader region, whereas the atpB mRNA has a 296- to 309-residue leader region. The sequence of these regions, together with the initial 113 bp of the atpB-coding region and the initial 1279 bp of the rbcL-coding region, is compared with the analogous maize chloroplast DNA sequences. Two classes of nucleotide differences are present, substitutions and insertions/deletions. Nucleotide substitutions show a 1.9-fold bias toward transitions in the rbcL-coding region and a 1.5-fold bias toward transitions in the noncoding region. The level of nucleotide substitutions between the barley and maize sequences is about 0.065/bp. Seventy-one percent of the substitutions in the rbcL-coding region are at the third codon position, and 95% of these are synonymous changes. Insertion/deletion events, which are confined to the noncoding regions, are not randomly distributed in these regions and are often associated with short repeated sequences. The extent of change for the noncoding regions (about 0.093 events/bp) is less than the extent of change at the third codon positions in the rbcL-coding region (about 0.135 events/bp), including insertion/delection events. Limited sequence analysis of the analogous DNA from a wild line (Hordeum spontaneum) and a primitive Iranian barley (H. vulgare) suggested a low rate of chloroplast DNA evolution. Compared to spinach chloroplast DNA, the barley rbcL-atpB untranslated region is extremely diverged, with only the putative rbcL promoters and ribosome-binding site being extensively conserved.

An atpE-specific promoter within the coding region of the atpB gene in tobacco chloroplast DNA

1994 ◽  
Vol 26 (3) ◽  
pp. 263-268 ◽  
Author(s):  
Sanjay Kapoor ◽  
Tatsuya Wakasugi ◽  
Hiroshi Deno ◽  
Masahiro Sugiura
Keyword(s):  
Chloroplast Dna ◽  
Coding Region ◽  
Tobacco Chloroplast

A reassessment of tribal affinities of the enigmatic genera Printzia and Isoetopsis (Asteraceae), based on three chloroplast sequences

2002 ◽  
Vol 50 (6) ◽  
pp. 677 ◽  
Author(s):  
Randall J. Bayer ◽  
Edward W. Cross
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Dna ◽  
Dna Sequences ◽  
Trnl Intron ◽  
Coding Region ◽  
Strong Affinity ◽  
Taxonomic History ◽  
Chloroplast Dna Sequences ◽  
Chemical Characters

The tribal affinities of two dubiously placed genera of the Asteraceae, Printzia and Isoetopsis, were assessed by using three chloroplast DNA sequences, the trnL/F spacer, the trnL intron and the matK coding region. The outgroup was represented by two species of the tribe Barnadesieae, whereas one to six genera (43 species including Printzia and Isoetopsis) of the tribes of the Asteroideae [Anthemideae (six genera), Astereae (five) Calenduleae (two), Gnaphalieae (six), Heliantheae s.l. (five), Inuleae s.str. (three), Plucheeae (two), Senecioneae (four)] and Cichorioideae [Arctotideae (one), Cardueae (two), Lactuceae (two), Liabeae (one), Mutisieae (one), Vernonieae (one)] were chosen as the ingroup. Phylogenetic analysis indicates that both Printzia and Isoetopsis have a strong affinity with members of the tribe Astereae. At some point in their taxonomic history, both genera had been placed in this tribe and there are good morphological and chemical characters that justify this placement.

scholarly journals Phylogenic study of Lemnoideae (duckweeds) through complete chloroplast genomes for eight accessions

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4186 ◽  
Author(s):  
Yanqiang Ding ◽  
Yang Fang ◽  
Ling Guo ◽  
Zhidan Li ◽  
Kaize He ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Chloroplast Genome ◽  
Morphological Characters ◽  
Repeat Sequence ◽  
Genome Comparison ◽  
Protein Coding ◽  
Phylogenetic Studies ◽  
Chloroplast Genomes ◽  
Effective Option ◽  
Total Dna

Background Phylogenetic relationship within different genera of Lemnoideae, a kind of small aquatic monocotyledonous plants, was not well resolved, using either morphological characters or traditional markers. Given that rich genetic information in chloroplast genome makes them particularly useful for phylogenetic studies, we used chloroplast genomes to clarify the phylogeny within Lemnoideae. Methods DNAs were sequenced with next-generation sequencing. The duckweeds chloroplast genomes were indirectly filtered from the total DNA data, or directly obtained from chloroplast DNA data. To test the reliability of assembling the chloroplast genome based on the filtration of the total DNA, two methods were used to assemble the chloroplast genome of Landoltia punctata strain ZH0202. A phylogenetic tree was built on the basis of the whole chloroplast genome sequences using MrBayes v.3.2.6 and PhyML 3.0. Results Eight complete duckweeds chloroplast genomes were assembled, with lengths ranging from 165,775 bp to 171,152 bp, and each contains 80 protein-coding sequences, four rRNAs, 30 tRNAs and two pseudogenes. The identity of L. punctata strain ZH0202 chloroplast genomes assembled through two methods was 100%, and their sequences and lengths were completely identical. The chloroplast genome comparison demonstrated that the differences in chloroplast genome sizes among the Lemnoideae primarily resulted from variation in non-coding regions, especially from repeat sequence variation. The phylogenetic analysis demonstrated that the different genera of Lemnoideae are derived from each other in the following order: Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia. Discussion This study demonstrates potential of whole chloroplast genome DNA as an effective option for phylogenetic studies of Lemnoideae. It also showed the possibility of using chloroplast DNA data to elucidate those phylogenies which were not yet solved well by traditional methods even in plants other than duckweeds.

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