The frequency and distribution of methylatable DNA sequences in leguminous plant protein coding genes

1983 ◽  
Vol 19 (5) ◽  
pp. 346-354 ◽  
Author(s):  
Michael McClelland
Keyword(s):  
Dna Sequences ◽  
Plant Protein ◽  
Leguminous Plant ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals Phylogeny of water birds inferred from mitochondrial DNA sequences of nine protein coding genes

2014 ◽  
Author(s):  
Tsendsesmee Lkhagvajav Treutlein ◽  
Javier Gonzalez ◽  
Michael Wink
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Mitochondrial Protein ◽  
Sister Relationship ◽  
Protein Coding ◽  
Water Bird ◽  
Protein Coding Genes ◽  
Reconstruction Methods ◽  
Mtdna Sequence ◽  
Water Birds

Background: The phylogeny of birds which are adapted to aquatic environments is controversial because of convergent evolution. Methods: To understand water bird evolution in more detail, we sequenced the majority of mitochondrial protein coding genes (6699 nucleotides in length) of 14 water birds, and reconstructed their phylogeny in the context of other taxa across the whole class of birds for which complete mitochondrial DNA (mtDNA) sequences were available. Results: The water bird clade, as defined by Hackett et al. (2008) based on nuclear DNA (ncDNA) sequences, was also found in our study by Bayesian Inference (BI) and Maximum Likelihood (ML) analyses. In both reconstruction methods, genera belonging to the same family generally clustered together with moderate to high statistical support. Above the family level, we identified three monophyletic groups: one clade consisting of Procellariidae, Hydrobatidae and Diomedeidae, and a second clade consisting of Sulidae, Anhingidae and Phalacrocoracidae, and a third clade consisting of Ardeidae and Threskiornithidae. Discussion: Based on our mtDNA sequence data, we recovered a robust direct sister relationship between Ardeidae and Threskiornithidae for the first time for mtDNA. Our comprehensive phylogenetic reconstructions contribute to the knowledge of higher level relationships within the water birds and provide evolutionary hypotheses for further studies.

scholarly journals Assembly and Annotation of an Ashkenazi Human Reference Genome

2020 ◽  
Author(s):  
Alaina Shumate ◽  
Aleksey V. Zimin ◽  
Rachel M. Sherman ◽  
Daniela Puiu ◽  
Justin M. Wagner ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Reference Genome ◽  
Gene Families ◽  
Gene Content ◽  
Specific Reference ◽  
Protein Coding ◽  
Human Reference Genome ◽  
Protein Coding Genes ◽  
Reference Genomes ◽  
Similar Gene

AbstractHere we describe the assembly and annotation of the genome of an Ashkenazi individual and the creation of a new, population-specific human reference genome. This genome is more contiguous and more complete than GRCh38, the latest version of the human reference genome, and is annotated with highly similar gene content. The Ashkenazi reference genome, Ash1, contains 2,973,118,650 nucleotides as compared to 2,937,639,212 in GRCh38. Annotation identified 20,157 protein-coding genes, of which 19,563 are >99% identical to their counterparts on GRCh38. Most of the remaining genes have small differences. 40 of the protein-coding genes in GRCh38 are missing from Ash1; however, all of these genes are members of multi-gene families for which Ash1 contains other copies. 11 genes appear on different chromosomes from their homologs in GRCh38. Alignment of DNA sequences from an unrelated Ashkenazi individual to Ash1 identified ~1 million fewer homozygous SNPs than alignment of those same sequences to the more-distant GRCh38 genome, illustrating one of the benefits of population-specific reference genomes.

scholarly journals Complete Mitochondrial and Plastid DNA Sequences of the Freshwater Green Microalga Medakamo hakoo

2021 ◽  
Author(s):  
Mari Takusagawa ◽  
Shoichi Kato ◽  
Sachihiro Matsunaga ◽  
Shinichiro Maruyama ◽  
Yayoi Tsujimoto-Inui ◽  
...  
Keyword(s):  
Green Alga ◽  
Dna Sequences ◽  
Plastid Dna ◽  
Mitochondrial Genomes ◽  
Genome Sequences ◽  
Protein Coding ◽  
Putative Protein ◽  
Protein Coding Genes ◽  
Organellar Genome ◽  
Green Microalga

Here we report the complete organellar genome sequences of Medakamo hakoo, a green alga identified in freshwater in Japan. It has 90.8-kb plastid and 36.5-kb mitochondrial genomes containing 80 and 33 putative protein coding genes, respectively, representing the smallest organellar genome among currently known core Trebouxiophyceae.

Plant Pan-Genomics Comes of Age

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Li Lei ◽  
Eugene Goltsman ◽  
David Goodstein ◽  
Guohong Albert Wu ◽  
Daniel S. Rokhsar ◽  
...  
Keyword(s):  
High Resolution ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Plant Biology ◽  
Annual Review ◽  
Publication Date ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Large Size ◽  
Sizable Fraction

A pan-genome is the nonredundant collection of genes and/or DNA sequences in a species. Numerous studies have shown that plant pan-genomes are typically much larger than the genome of any individual and that a sizable fraction of the genes in any individual are present in only some genomes. The construction and interpretation of plant pan-genomes are challenging due to the large size and repetitive content of plant genomes. Most pan-genomes are largely focused on nontransposable element protein coding genes because they are more easily analyzed and defined than noncoding and repetitive sequences. Nevertheless, noncoding and repetitive DNA play important roles in determining the phenotype and genome evolution. Fortunately, it is now feasible to make multiple high-quality genomes that can be used to construct high-resolution pan-genomes that capture all the variation. However, assembling, displaying, and interacting with such high-resolution pan-genomes will require the development of new tools. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Complete Mitochondrial Genomes of two Flying Fishes, Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii

2020 ◽  
Author(s):  
Liyan Qu ◽  
Heng Zhang ◽  
Fengying Zhang ◽  
Wei Wang ◽  
Fenghua Tang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Flying Fishes ◽  
Complete Mitochondrial Genomes

Background: Genome-scale approaches have played a significant role in the analysis of evolutionary relationships. Because of rich polymorphisms, high evolutionary rate and rare recombination, mitochondrial DNA sequences are commonly considered as effective markers for estimating population genetics, evolutionary and phylogenetic relationships. Flying fishes are important components of epipelagic ecosystems. Up to now, only few complete mitochondrial genomes of flying fishes have been reported. In the present study, the complete mitochondrial DNA sequences of the Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii had been determined. Methods: Based on the published mitogenome of Cheilopogon atrisignis (GenBank: KU360729), fifteen pairs of primers were designed by the software Primer Premier 5.0 to get the complete mitochondrial genomes of two flying fishes. According to the reported data, the phylogenetic position of two flying fishes were detected using the conserved 12 protein-coding genes. Result: The complete mitochondrial genomes of Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii are determined. They are 16532bp and 16525bp in length, respectively. And they both consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region. The OL regions are conserved in these two flying fishes and might have no function. From the tree topologies, we found C.p. japonicus and H. rondeletii clustered in a group. The findings of the study would contribute to the phylogenetic classification and the genetic conservation management of C.p. japonicus and H. rondeletii.

EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 689-691 ◽  
Author(s):  
Yoon-Seong Jeon ◽  
Kihyun Lee ◽  
Sang-Cheol Park ◽  
Bong-Soo Kim ◽  
Yong-Joon Cho ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Relevant Information ◽  
Biological Information ◽  
Sequence Alignments ◽  
Protein Coding ◽  
Structure Information ◽  
Biologically Relevant ◽  
Molecular Sequence ◽  
Protein Coding Genes

EzEditor is a Java-based molecular sequence editor allowing manipulation of both DNA and protein sequence alignments for phylogenetic analysis. It has multiple features optimized to connect initial computer-generated multiple alignment and subsequent phylogenetic analysis by providing manual editing with reference to biological information specific to the genes under consideration. It provides various functionalities for editing rRNA alignments using secondary structure information. In addition, it supports simultaneous editing of both DNA sequences and their translated protein sequences for protein-coding genes. EzEditor is, to our knowledge, the first sequence editing software designed for both rRNA- and protein-coding genes with the visualization of biologically relevant information and should be useful in molecular phylogenetic studies. EzEditor is based on Java, can be run on all major computer operating systems and is freely available from http://sw.ezbiocloud.net/ezeditor/.

scholarly journals Evolution of Pulmonate Gastropod Mitochondrial Genomes: Comparisons of Gene Organizations of Euhadra, Cepaea and Albinaria and Implications of Unusual tRNA Secondary Structures

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 749-758 ◽  
Author(s):  
Nika Yamazaki ◽  
Rei Ueshima ◽  
Jonathan A Terrett ◽  
Shin-ichi Yokobori ◽  
Masayuki Kaifu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Overlapping Genes ◽  
Protein Coding ◽  
Cepaea Nemoralis ◽  
Protein Coding Genes ◽  
Editing Process ◽  
Pulmonate Gastropod

Complete gene organizations of the mitochondrial genomes of three pulmonate gastropods, Euhadra herklotsi, Cepaea nemoralis and Albinaria coerulea, permit comparisons of their gene organizations. Euhadra and Cepaea are classified in the same superfamily, Helicoidea, yet they show several differences in the order of tRNA and protein coding genes. Albinaria is distantly related to the other two genera but shares the same gene order in one part of its mitochondrial genome with Euhadra and in another part with Cepaea. Despite their small size (14.1 – 14.5 kbp), these snail mtDNAs encode 13 protein genes, two rRNA genes and at least 22 tRNA genes. These genomes exhibit several unusual or unique features compared to other published metazoan mitochondrial genomes, including those of other molluscs. Several tRNAs predicted from the DNA sequences possess bizarre structures lacking either the T stem or the D stem, similar to the situation seen in nematode mt-tRNAs. The acceptor stems of many tRNAs show a considerable number of mismatched basepairs, indicating that the RNA editing process recently demonstrated in Euhadra is widespread in the pulmonate gastropods. Strong selection acting on mitochondrial genomes of these animals would have resulted in frequent occurrence of the mismatched basepairs in regions of overlapping genes.

scholarly journals Mitochondrial genome annotation and phylogenetic placement of Oreochromis andersonii and O. macrochir among the cichlids of southern Africa

2018 ◽  
Author(s):  
Ian Bbole ◽  
Jin-Liang Zhao ◽  
Shou-Jie Tang ◽  
Cyprian Katongo
Keyword(s):  
Mitochondrial Dna ◽  
Southern Africa ◽  
Dna Sequences ◽  
Protein Coding ◽  
Important Species ◽  
Cichlid Species ◽  
Protein Coding Genes ◽  
Phylogenetic Placement ◽  
Biogeographic History ◽  
African Cichlids

AbstractGenetic characterization of southern African cichlids has not received much attention. Here, we describe the mitogenome sequences and phylogenetic positioning of Oreochromis andersonii and O. macrochir among the cichlids of southern Africa. The complete mitochondrial DNA sequences were determined for O. andersonii and O. macrochir, two important aquaculture and fisheries species endemic to southern Africa. The complete mitogenome sequence lengths were 16642 bp and 16644 bp for O. andersonii and O. macrochir respectively. The general structural organization follows that of other teleost species with 13 protein–coding genes, 2 rRNAs, 22 tRNAs and a non-coding control region. Phylogenetic placement of the two species among other African cichlids was performed using Maximum Likelihood (ML) and Bayesian Markov-Chain-Monte-Carlo (MCMC). The consensus trees confirmed the relative positions of the two cichlid species with O. andersonii being very closely related to O. mossambicus and O. macrochir showing a close relation to both species. Among the 13 mitochondrial DNA protein coding genes ND6 may have evolved more rapidly and COIII was the most conserved. There are signs that ND6 may have been subjected to positive selection in order for these cichlid lineages to diversity and adapt to new environments. More work is needed to characterize the southern Africa cichlids as they are important species for capture fisheries, aquaculture development and understanding biogeographic history of African cichlids. Bioconservation of some endangered cichlids is also essential due to the threat by invasive species.

scholarly journals Two new species of Verruconis from Hainan, China

MycoKeys ◽  
2019 ◽  
Vol 48 ◽  
pp. 41-53 ◽  
Author(s):  
Min Qiao ◽  
Weiguang Tian ◽  
Rafael F. Castañeda-Ruiz ◽  
JianPing Xu ◽  
Zefen Yu
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Sequence Data ◽  
Nuclear Ribosomal Dna ◽  
Closely Related Species ◽  
Protein Coding ◽  
Dna Sequence Data ◽  
Protein Coding Genes ◽  
Two New Species ◽  
New Perspective

Two new species of the genusVerruconis,V.hainanensisandV.pseudotricladiata, were described using combined morphological and DNA sequence data. The DNA sequences of respective strains including nuclear ribosomal DNA genes (nuSSU, ITS, nuLSU) and fragments of three protein-coding genes (ACT1, BT2, TEF1) were sequenced and compared with those from closely-related species to generaOchroconisandVerruconis(Family Sympoventuriaceae, Order Venturiales). Morphologically, both species showed typical ampulliform conidiophores and conidiogenous cells, features not seen in other species ofVerruconis. The conidia ofV.hainanensisare fusiform and those ofV.pseudotricladiataare Y or T shaped, similar to old members of a closely-related genusScolecobasidium. The addition of these two new species provides a new perspective on the heterogeneity ofScolecobasidium.

Mitochondrial genome sequences of representatives of three families of scorpionflies (Order Mecoptera) and evolution in a major duplication of coding sequence

Genome ◽  
2011 ◽  
Vol 54 (5) ◽  
pp. 368-376 ◽  
Author(s):  
Andrew T Beckenbach
Keyword(s):  
Dna Sequences ◽  
Complete Sequence ◽  
Trna Genes ◽  
Coding Region ◽  
Functional Protein ◽  
Protein Coding ◽  
Coding Sequence ◽  
Protein Coding Genes ◽  
Standard Set ◽  
Considerable Period

The complete mitochondrial DNA sequences of a hangingfly, Bittacus pilicornis (Mecoptera: Bittacidae), a snow scorpion fly, Boreus elegans (Mecoptera: Boreidae), and a nearly complete sequence from another scorpionfly species, Microchorista philpotti (Mecoptera: Nannochoristidae) were determined. The coding sequence of all three genomes includes the 37 genes normally found in insect mtDNAs, in the same gene order as first described in Drosophila. In addition to the standard set of genes, the Microchorista sequence includes a large duplication of the coding region. The duplication is at least 4 kb (and may be much larger) and includes the remnants of three protein-coding genes and seven tRNA genes. The duplication evidently arose as a single event, and the duplicated region can be aligned in its entirety with the corresponding region of the functional genome. Although most of the genes contain defects that render them nonfunctional, analysis shows that the protein-coding genes in the duplicated region evolved for a considerable period under constraints expected of functional protein-coding genes. It is evident, therefore, that for a period two copies of some of the mitochondrial genes were functional in this species, including genes coding for proteins.

Sign in / Sign up

Export Citation Format

Share Document