The Complete Chloroplast and Mitochondrial Genome Sequences of Boea hygrometrica: Insights into the Evolution of Plant Organellar Genomes

Abstract

The complete nucleotide sequences of the chloroplast (cp) and mitochondrial (mt) genomes of resurrection plant Boea hygrometrica (Bh, Gesneriaceae) have been determined with the lengths of 153,493 bp and 510,519 bp, respectively. The smaller chloroplast genome contains more genes (147) with a 72% coding sequence, and the larger mitochondrial genome have less genes (65) with a coding faction of 12%. Similar to other seed plants, the Bh cp genome has a typical quadripartite organization with a conserved gene in each region. The Bh mt genome has three recombinant sequence repeats of 222 bp, 843 bp, and 1474 bp in length, which divide the genome into a single master circle (MC) and four isomeric molecules. Compared to other angiosperms, one remarkable feature of the Bh mt genome is the frequent transfer of genetic material from the cp genome during recent Bh evolution. We also analyzed organellar genome evolution in general regarding genome features as well as compositional dynamics of sequence and gene structure/organization, providing clues for the understanding of the evolution of organellar genomes in plants. The cp-derived sequences including tRNAs found in angiosperm mt genomes support the conclusion that frequent gene transfer events may have begun early in the land plant lineage.

Effective Extraction and Assembly Methods for Simultaneously Obtaining Plastid and Mitochondrial Genomes

“…In some cases, plastid reads were initially separated from total reads employing the published plastid genomes [24], [25] and then used for de novo assembly of plastid genomes. However, the sequence differences between different materials, in particular, the large insertions and deletions, affect the efficiency of the assembly and lead to more gaps.…”

Selecting Molecular Markers for a Specific Phylogenetic Problem

“…This ensures comparisons among orthologous genes in almost all cases. Conversely, plant mitochondrial DNA have distinct gene compositions compared to those found in metazoans and fungi [26,27]. Plants exhibit mitochondrial genomes 10 to 100 times as large as most metazoans, and many gene duplications have been reported [28].…”

“…Plants exhibit mitochondrial genomes 10 to 100 times as large as most metazoans, and many gene duplications have been reported [28]. The symbiotic events that resulted in the origination of the eukaryotic mitochondria [29,30] and chloroplast [31] were unique, but due to recombinations and duplications, it would be best to use mitochondrial genomes for more restricted phylogenetic purposes [26,27,32] This is also true for chloroplast genomes that do not exhibit gene content stability among major lineages of plants [33].…”

Genome sequences published outside of Standards in Genomic Sciences, January-March 2012

“…Aspergillus flavus, sequence accession GSE32177 [79] Bacteriophage SPN3UB, sequence accession JQ288021 [80] Bamboo mitochondria, sequence accession JQ235166 to JQ235179 [81] Boea hygrometrica chloroplast, sequence accession JN107811 [82] Boea hygrometrica mitochondrial, sequence accession JN107812 [82] Canine Picornavirus, sequence accession JN831356 [83] Chandipura virus (CHPV) CIN0327, sequence accession GU212856.1 [84] Chandipura virus (CHPV) CIN0451, sequence accession GU212857.1 [84] Chandipura virus (CHPV) CIN0751, sequence accession GU212858.1 [84] Chandipura virus (CHPV) CIN0755, sequence accession GU190711.1 [84] Chinese Porcine Parvovirus Strain PPV2010, sequence accession JN872448 [85] Common midwife toad megavirus, sequence accession JQ231222 [86] Dengue Virus Serotype 4, sequence accession JN983813 [87] Duck Tembusu Virus, sequence accession JF270480 [88] Duck Tembusu Virus, sequence accession JQ314464 [88] Duck Tembusu Virus, sequence accession JQ314465 [88] Emiliania huxleyi Virus 202, sequence accession HQ634145 [89] Emiliania huxleyi Virus EhV-88, sequence accession JF974310 [89] Emiliania huxleyi EhV-201, sequence accession JF974311 [89] Emiliania huxleyi EhV-207, sequence accession JF974317 [89] Emiliania huxleyi EhV-208, sequence accession JF974318 [89] Glarea lozoyensis, sequence accession GUE00000000 [90] Nannochloropis gaditana, sequence accession AGNI00000000 [91] Oryza sativa cv., sequence accession DRA000499 [92] Partetravirus, sequence accession JN990269 [93] Porcine Bocavirus PBoV5, sequence accession JN831651 [94] Porcine epidemic diarrhea virus, sequence accession JQ282909 [95] Pseudomonas aeruginosa lytic bacteriophage PA1Ø, sequence accession HM624080 [96] Pseudomonas fluorescens phage OBP, sequence accesssion JN627160 [97] RNA Virus from Avocado, sequence accession JN880414 [98] Salmonella enterica Serovar Typhimuriu...…”