1. Nuclear DNA in Molecular systematics

2. -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 mRNA. Nuclear DNA

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

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

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

6. -nrDNA 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. Molecular Systematics

7. -Other nuclear DNA regions used in plant systematics are genes AdhC, PgiC, malate synthase, phosphoribulokinase etc. [low- copy 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 AdhC sequences are three- to sixfold higher than that of cpDNA. Nuclear DNA in Plant Systematics

8. H. nervosa H. dyeri H. dryobalanoides H. beccariana H. pierrei H. mengerawan H. myrtifolia H. ferruginea H. sangal H. nutans H. odorata H. helferi H. apiculata H. wightiana Neobalanocarpus heimii 100 98 100 94 86 100 Subsection Hopea Subsection Dryobalanoides Subsection Sphaerocarpae Subsection Pierrea Hopea clade Dryobalanoides clade Outgroup 18-bp deletion in the PgiC HopeaHopea DryobalanoidesDryobalanoides Phylogeny based on the PgiC sequences. Upuna borneensis H. subalata 70 100 H. bilitonensis Tree length = 277 CI = 0.9206 RI = 0.9415 52 H. pubescens 62 64