Molecular Biology Reports

, Volume 46, Issue 1, pp 177–189 | Cite as

Assessment of genetic variation among wild Alpinia nigra (Zingiberaceae) population: an approach based on molecular phylogeny

  • Supriyo Basak
  • Ishani Chakrabartty
  • Vivek Hedaoo
  • Rahul G. Shelke
  • Latha RanganEmail author
Original Article


Genetic structure was evaluated among wild Alpinia nigra (Gaertn.) B.L. Burtt, populations. The information of genetic relatedness was developed using random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and barcoding loci (plastid and mitochondrial). The order (high to low) of Shannon’s information index (I) and Nei’s gene diversity (h) from the populations was: “IIT Guwahati” > “Amingaon” > “Saraighat”. Genetic diversity decreased and genetic differentiation increased among the three populations. We observed no isolation by distance thus lower amount of gene flow was observed. Narrow range of genetic distance among the three populations and appearance of two distinct clusters strengthened the geographical isolation in dendrogram and principal component analysis. No mutation among the three populations was observed for seven plastid loci and two mitochondrial tested suggesting the taxonomic homogeneity. The phylogeny based on nine barcoding loci supported our observation that individuals of IIT Guwahati were partially isolated from the outside populations. Our study will provide a backbone for developing strategies to resist habitat fragmentation of Zingiberaceous plants.


Alpinia nigra Genetic diversity DNA barcodes Habitat fragmentation ISSR marker Population differentiation RAPD marker 



Acetyl-CoA carboxylase-D


ATP synthase subunit b–ATP synthase subunit c


Apocytochrome b


Cytochrome oxidase subunit 1


Inter simple sequence repeats


Principle component analysis


Polymorphic information content


Polymerase chain reaction


Photosystem II reaction center protein K–Photosystem II reaction center protein I


Random amplified polymorphic DNA


Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit


RNA polymerase C


RNA polymerase B


Unweighted pair group method with arithmetic mean.



SB, IC and RGS thank MHRD for fellowship. LR thanks the Department of Biotechnology (DBT) Government of India for funding the project by way of DBT Twinning Programme for NE (BT/33/NE/TBP/2010) and Biosciences and Bioengineering Department, IIT Guwahati for providing all necessary infrastructural support.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11033_2018_4458_MOESM1_ESM.tif (1.6 mb)
Supplementary Fig. 1 The multiple sequence alignment of three populations of Guwahati city, Northeast India. arpoC1, bcob. The genes rpoC1 and cob were characterized by no mutation. It showed that all the three populations were A. nigra (TIF 1602 KB)
11033_2018_4458_MOESM2_ESM.tif (1.3 mb)
Supplementary Fig. 2 The multiple sequence alignment of the three populations of Guwahati city, Northeast India showed no mutation in the sequence. arpoB1, brbcL. This study confirmed that all the accessions are of A. nigra (TIF 1364 KB)
11033_2018_4458_MOESM3_ESM.tif (1.6 mb)
Supplementary Fig. 3 The multiple sequence alignment of the three populations of Guwahati Assam showed no mutation in the sequence. aaccD, bmatK. This study confirmed that there was no taxonomic ambiguity in our experimental design (TIF 1602 KB)
11033_2018_4458_MOESM4_ESM.tif (1.8 mb)
Supplementary Fig. 4 The multiple sequence alignment of inter-genic regions for three populations of Guwahati Assam showed no mutation in the sequence. aatpF-atpH, bpsbKpsbI. This study confirmed that all the accessions are of A. nigra (TIF 1797 KB)
11033_2018_4458_MOESM5_ESM.tif (1 mb)
Supplementary Fig. 5 The multiple sequence alignment of mitochondrial region (cox1) of the three populations of Guwahati Assam showed no mutation in the sequence. This study confirmed that all the accessions are of A. nigra (TIF 1067 KB)


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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  • Supriyo Basak
    • 1
    • 2
  • Ishani Chakrabartty
    • 1
  • Vivek Hedaoo
    • 1
  • Rahul G. Shelke
    • 1
  • Latha Rangan
    • 1
    Email author
  1. 1.Department of Biosciences and Bioengineering, Indian Institute of Technology GuwahatiGuwahatiIndia
  2. 2.Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina

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