Hi Devina. Being a member of Asparagales I would try with ndhF (provided you use primers specific for monocots) and matK. They are easy to amplify and usually they yield enough variability. However, bear in mind that diversification in Aloe might be the result of rapid radiation with incomplete lineage sorting (ILS) and plastid horizontal transfer. This results in conflicting phylogenetic signal and lack of resolution in your trees (soft polytomies) .This complication get worse in case you're using plants coming from nurseries in your sampling (breeders hybridise different species to get novel cultivars). Hope this is helpful.

Cheers,

Javier

Dear Devina Lobine 

I hope this may help you.

Cryptic structural changes (deletions, inversions and translocations), which are not evident in the gross morphology of chromosomes, may account for considerable genetic variation that is undetectable in the conservative relative size of the long and the small chromosomes and bimodality of the karyotype of Aloe. For instance, the 18S-5.8S-26S ribosomal DNA region is known to vary considerably in Aloe while the 5S region is very stable (Adams et al. 2000). Each of the species characterised in this study possessed four pairs of long chromosomes (L) that comprise about 78% of the entire complement (2n) length, whilst the short chromosomes cover 22%. More than three quarters of the genome is therefore accommodated in the four pairs of long chromosomes, and the majority of cytogenetic differences among species are likewise expected at the structural level rather than the chromosome level.

Fentaw, Eshetu, Kifle Dagne, Nina Rønsted, Sebsebe Demissew, and Olwen M. Grace. “Karyotypes in Ethiopian Aloe Species (Xanthorrhoeaceae: Asphodeloideae).” Kew Bull 68, no. 4 (December 2013): 599–607. doi:10.1007/s12225-013-9475-8.

Aloe species, which have been used as medicinal plants, belong to the Asphodelaceae family consisting of 530 species. In this study, genetic diversity and phylogenetic relationships among 40 Aloe species including a putative interspecies hybrid were analyzed using PCR band profiles from eight chloroplast intergenic space markers and nucleotide sequence diversity in the psbK–psbI intergenic region. A phylogenetic tree based on psbK–psbI sequences supported the revised classification of the genus Aloe as polyphyletic with several species be re-allocated into three genera Kumara, Aloidendron, and Aloiampelos. Further, the origin of the putative interspecies Aloe hybrid was characterized through molecular cytogenetics. Fluorescence and genomic in situ hybridization illustrated that the hybrid has a bimodal karyotype with a chromosome complement of 2n = 14, of which complementary halves were derived from two parental species, A. vera and A. arborescens. These findings revealed that the hybrid species was allodiploid. The phylogenetic analysis showed that A. arborescens was the maternal genome donor of the hybrid, as both have identical chloroplast genome sequences. We thus conclude that the allodiploid hybrid should be called A. arborescens × A.vera.

Lee, Yun Sun, Hye Mi Park, Nam-Hoon Kim, Nomar E. Waminal, Yeon Jeong Kim, Ki-Byung Lim, Jin Hong Baek, Hyun Hee Kim, and Tae-Jin Yang. “Phylogenetic Relationship of 40 Species of Genus Aloe L. and the Origin of an Allodiploid Species Revealed by Nucleotide Sequence Variation in Chloroplast Intergenic Space and Cytogenetic in Situ Hybridization.” Genetic Resources and Crop Evolution (March 28, 2015). doi:10.1007/s10722-015-0243-5.

Kind regards

Jose Macedo

Hi Devina. Being a member of Asparagales I would try with ndhF (provided you use primers specific for monocots) and matK. They are easy to amplify and usually they yield enough variability. However, bear in mind that diversification in Aloe might be the result of rapid radiation with incomplete lineage sorting (ILS) and plastid horizontal transfer. This results in conflicting phylogenetic signal and lack of resolution in your trees (soft polytomies) .This complication get worse in case you're using plants coming from nurseries in your sampling (breeders hybridise different species to get novel cultivars). Hope this is helpful.

Cheers,

Javier

I agree with Javier, 

trnK-matK-trnK- spacer to psbA is a good region in case of variability and amplification

Thanks everyone.

Javier can please suggest any paper.

I have amplified the matk and psbA-trnH region but there is not enough phylogenetic signal.

Regards

Devina