The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, requires the elimination of poorly aligned positions and divergent regions, since they may not be homologous or may have been saturated by multiple substitutions. A computerized method that eliminates such positions and at the same time tries to minimize the loss of informative sites is presented here. The method is based on the selection of blocks of positions that fulfill a simple set of requirements with respect to the number of contiguous conserved positions, lack of gaps, and high conservation of flanking positions, making the final alignment more suitable for phylogenetic analysis. To illustrate the efficiency of this method, alignments of 10 mitochondrial proteins from several completely sequenced mitochondrial genomes belonging to diverse eukaryotes were used as examples. The percentages of removed positions were higher in the most divergent alignments. After removing divergent segments, the amino acid composition of the different sequences was more uniform, and pairwise distances became much smaller. Phylogenetic trees show that topologies can be different after removing conserved blocks, particularly when there are several poorly resolved nodes. Strong support was found for the grouping of animals and fungi but not for the position of more basal eukaryotes. The use of a computerized method such as the one presented here reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers.

/pdf/selection-of-conserved-blocks-from-multiple-alignments-for-i0qfazjwh5.pdf

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis

An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence (1,830,137 base pairs) of the genome from the bacterium Haemophilus influenzae Rd. This approach eliminates the need for initial mapping efforts and is therefore applicable to the vast array of microbial species for which genome maps are unavailable. The H. influenzae Rd genome sequence (Genome Sequence DataBase accession number L42023) represents the only complete genome sequence from a free-living organism.

https://science.sciencemag.org/content/sci/269/5223/496.full.pdf

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.

C. elegans cell survival gene ced-9 encodes a functional homolog of the mammalian proto-oncogene bcl-2

We have determined the complete sequence of the mitochondrial DNA in the model plant species Arabidopsis thaliana, affording access to the first of its three genomes. The 366,924 nucleotides code for 57 identified genes, which cover only 10% of the genome. Introns in these genes add about 8%, open reading frames larger than 100 amino acids represent 10% of the genome, duplications account for 7%, remnants of retrotransposons of nuclear origin contribute 4% and integrated plastid sequences amount to 1%-leaving 60% of the genome unaccounted for. With the significant contribution of duplications, imported foreign DNA and the extensive background of apparently functionless sequences, the mosaic structure of the Arabidopsis thaliana mitochondrial genome features many aspects of size-relaxed nuclear genomes.

The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides

https://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/227477/1/j.cell.2017.09.030.pdf

Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome

Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of plant mitochondrial genome

The tropane alkaloid scopolamine is synthesized in the pericycle of branch roots in certain species of the Solanaceae The enzyme responsible for the synthesis of scopolamine from hyoscyamine is hyoscyamine 6[beta]-hydroxylase (H6H) The gene for H6H was isolated from Hyoscyamus niger It has an exon/intron organization very similar to those for ethylene-forming enzymes, suggesting a common evolutionary origin The 827-bp 5[prime] flanking region of the H6H gene was fused to the [beta]-glucuronidase (GUS) reporter gene and transferred to three solanaceous species by Agrobacterium-mediated transformation systems: H niger and belladonna (Atropa belladonna), which have high and low levels, respectively, of H6H mRNA in the root, and tobacco (Nicotiana tabacum), which has no endogenous H6H gene Histochemical analysis showed that GUS expression occurred in the pericycle and at the root meristem of transgenic H niger hairy roots, but only at the root meristem of hairy roots and plants of transgenic tobacco In transgenic hairy roots and regenerated plants of belladonna, the root meristem was stained with GUS activity, except for a few transformants in which the vascular cylinder was also stained These studies indicate that the cell-specific expression of the H6H gene is controlled by some genetic regulation specific to scopolamine-producing plants

Species-dependent expression of the hyoscyamine 6 beta-hydroxylase gene in the pericycle.

The mitochondrial DNA (mtDNA) from the cultured cells of a cytoplasmic male-sterile line (A-58CMS) of rice (Oryza sativa) was cloned and its physical map was constructed. There was structural alteration on the mitochondrial genome during the cell culture. Detailed restriction analysis of cosmid clones having mtDNA fragments suggested either that the master genome has a 100-kb duplication (the genome size becomes 450 kb) or that a master circle is not present in the genome (the net structural complexity becomes 350 kb). The physical map of plant mitochondrial genomes thus far reported is illustrated in a single circle, namely a master circle. However, no circular DNA molecule corresponding to a master circle has yet been proved. In the present report, representation of plant mitochondrial genomes and a possibility for mitochondrial genome without a master circle are discussed.

Mitochondrial genome structure of rice suspension culture from cytoplasmic male-sterile line (A-58CMS): reappraisal of the master circle.

Libraries of cosmid and plasmid clones covering the entire region of mtDNA from the liverwortMarchantia polymorpha were constructed. These clones were used for the determination of the complete nucleotide sequence of the liverwort mtDNA totally 186,608 bp (GenBank no. M68929) and including genes for 3 species of ribosomal RNAs, 29 genes for 27 species of transfer RNAs, and 30 genes for functionally known proteins (16 ribosomal proteins, 3 subunits of cytochromec oxidase, apocytochromeb protein, 3 subunits of H+-ATPase, and 7 subunits of NADH ubiquinone oxidoreductase). The genome also contains 32 unidentified open reading frames. Thus the complete nucleotide sequences from both chloroplast and mitochondrial genomes have been determined in the same organism. Plasmid clones are available upon the request.

Complete nucleotide sequence of the mitochondrial DNA from a liverwort,Marchantia polymorpha

In the plant kingdom, the endosymbiotic event of a mitochondrial ancestor probably happened first to plant cell progenitors followed by the endosymbiosis of a chloroplast ancestor, namely cyanobacteria. In this paper we describe the characterization of plant mitochondrial genome focussing on (1) the complexity of plant mitochondrial genomes, (2) the genetic codes utilized in plant mitochondrial genomes, (3) the properties of open reading frames encoded by introns (group I and group II) of plant mitochondrial genes, and (4) RNA editing which has been reported in wheat mitochondrial genome (C to U conversion), and (5) evolutionary events of gene migration from mitochondrial and chloroplast genomes to nuclear genomes.

Takeshi Kanegae

Papers

Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of plant mitochondrial genome

Species-dependent expression of the hyoscyamine 6 beta-hydroxylase gene in the pericycle.

Mitochondrial genome structure of rice suspension culture from cytoplasmic male-sterile line (A-58CMS): reappraisal of the master circle.

Complete nucleotide sequence of the mitochondrial DNA from a liverwort,Marchantia polymorpha

Evolution of Organellar Genomes