Nuclear DNA in Molecular systematics Nuclear DNA Nuclear

Nuclear DNA in Molecular systematics

Nuclear DNA - Nuclear DNA is double stranded DNA located in chromosomes / nucleus of a cell. - 6 -30 billion bp per haploid genome in gymnosperm, 250 million to 15 billion bp per haploid genome in angiosperm, 3 billion bp per haploid genome in human. - The difference in genome size is mainly due to the amount of repetitive DNA. Repetitive DNA is distributed throughout the genome. - For example, pine (Pinus stobus) genome contains 75% repetitive DNA and 25% low number single copy DNA. Only 0. 1% of the genome is expressed as m. RNA.

Nuclear DNA - Recombination occurs between homologous chromosomes. - Biparentally inherited. - Mutational rate is high.

Molecular Systematics - Nuclear DNA regions commonly used for plant/animal systematics study is nuclear ribosomal DNA (nr. DNA) including 18 S, 28 S, ITS and 5 S. - nr. DNA occurs in high number of copy in the genome, and it experiences concerted evolution.

Nuclear Ribosomal DNA A typical plant r. DNA repeat unit shown to scale. EST = external transcribed region; ITS = internal transcribed region.

Molecular Systematics - nr. DNA sometimes is claimed to be problematic in some plant families. - Copies of the ITS regions may display a high degree of polymorphism within plant genomes, and relationships among paralogues can be difficult to interpret at species level.

Nuclear DNA in Plant Systematics - Other nuclear DNA regions used in plant systematics are genes Adh. C, Pgi. C, malate synthase, phosphoribulokinase etc. [lowcopy nuclear genes] - These low-copy nuclear gene sequences are found to be informative and provide robust resolved phylogeny. - e. g. in Gossypium, the base substitution of Adh. C sequences are three- to sixfold higher than that of cp. DNA.

Tree length = 277 CI = 0. 9206 RI = 0. 9415 100 H. subalata 100 H. nervosa H. dyeri 86 H. pubescens 94 64 62 H. beccariana H. pierrei H. mengerawan Subsection Dryobalanoides H. dryobalanoides 70 Dryobalanoides clade 100 Hopea clade 52 D r y o b a l a n o i d e s H. sangal H. odorata 100 H. myrtifolia H. ferruginea 98 18 -bp deletion in the Pgi. C Subsection Sphaerocarpae Subsection Hopea H. apiculata H. bilitonensis H. helferi H. nutans Subsection Pierrea H o p e a H. wightiana Neobalanocarpus heimii Upuna borneensis Phylogeny based on the Pgi. C sequences. Outgroup