Molecular Phylogeny of Palms - Genomics of Cultivated Palms - page 88

Table 9.1 Genomics of Phylogeny of Palms

Region Type of Region,

Location

Approximate
Size (bp)

No. of PI Sites Reference

rbcL Coding, plastid 1500 92, 553, 55, 57 [18,19,21,22]

rps 16 Intron, plastid 680-960 74, 298, 47 [18,19,22]

trnL-F Intergenic, plastid 740-950 63, 219, 57, 42 [18,19,20,22]

matK-trnK Coding, intergenic,

plastid

1800-1850 553 [19]

atpB Coding, plastid 1300-1500 31 [22]

9.6 Plastid Regions in Classification of Palms

Three plastid regions (coding [rbcL] region, intron region [ rps 16 intron], and inter-
generic spacer region [trnL-F]) were analyzed for potential parsimony informative
(PI) sites in palms [18] . In a study by Asmussen and Chase, the rbcL and rps 16
introns produced a high number of PI sites [18] . Comparative figures of PI sites
in different plastid DNA regions [18-22] , as reported by different researchers, are
given in Table 9.1 . The number of sites in different reports varies probably due to the
number of species included in the study and sequence variation in the available set.

9.7 Nuclear DNA Regions in Phylogeny of Palms

Low-copy nuclear genes are good candidates for use in studying palm phylogeny.
Specific coding regions of malate synthase (MS) exons were used for palms. The
genes gave better phylogenetic resolution than noncoding plastid loci for palms
at the family level. However, many clades were not resolved with sufficient boot-
strap values [23] . RPB2 [13] and PRK are widely used in phylogenetic research of
palms. Thomas et al. used the RPB and PRK sequence variation in concluding the
monophyletic nature of the Chamaedorea genus [24] and the individuality of gen-
era Heterospathe and Rhopaloblaste members of the Areceae taxon [25] . These two
low-copy gene sequences also confirmed the many independent origins of the West
Indian Palm flora [26] . The importance of RPB2 and PRK in classification of the
Arecinae subtribe is dealt with in Chapter 6 under Section 6.2.
When used in 65 taxa, the nuclear rDNA 18 S SU gene sequence gave a topology
similar to that of the plastid DNA-based study [22] . Sequences of WRKY transcrip-
tion factors [27] were cloned in a set of palms of subtribe Attaleinae identified the
genus Syagrus as a sister group of the coconut. Phytochrome genes, being repeated
in plant families, are not suitable for phylogenetic research [28] . But recently, stud-
ies by Ludeña et al. [29] found AGA1 (Agamous 1) and phytochrome B (PHYB)
to be single-copy genes in palms. The phylogenetic structure obtained with AGA1
and PHYB genes clarified the intergeneric relationships within the Bactridinae. The