Ranganathan Kamalakkannan

Central University of Kerala

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Muniyandi Nagarajan

Central University of Kerala

Vandana R. Prabhu

Central University of Kerala

Karippadakam Bhavana

International Institute of Information Technology, Hyderabad

Subhash Thomas

Central University of Kerala

Hijam Surachandra Singha

Central University of Kerala

Esther Rodríguez‐Belmonte

Universidade da Coruña

Juan-José Escuder‐Rodríguez

Universidade da Coruña

Priya Nimish Deo

Bharati Vidyapeeth Deemed University

Mariana Buongermino Pereira

Genomics England

Erik Kristiansson

Chalmers University of Technology

Cooperative Institutions

Central University of Kerala

University of Technology Malaysia

Amrita Vishwa Vidyapeetham

Universidade da Coruña

University of Gothenburg

Chalmers University of Technology

Pondicherry University

Universidade de Vigo

University of Bergen

Universidade de Santiago de Compostela

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Analysis of the mitochondrial genome of the Indian darter, Anhinga melanogaster, suggests a species status taxonomic rank

Molecular Biology Reports (2021)

Subhash Thomas Hijam Surachandra Singha Ranganathan Kamalakkannan Sarah Gaughan Karippadakam Bhavana

Rank (graph theory)

Melanogaster

10.1007/s11033-021-06737-8

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Citations (2)

Evidence for independent domestication of sheep mtDNA lineage A in India and introduction of lineage B through Arabian sea route

Scientific Reports (2021)

Ranganathan Kamalakkannan Satish Kumar Karippadakam Bhavana Vandana R. Prabhu Carolina Barros Machado

Abstract India ranks the second in the world in terms of its sheep population with approximately 74.26 million represented by 44 well-described breeds in addition to several non-descript populations. Genetic diversity and phylogeography of Indian sheep breeds remain poorly understood, particularly for south Indian breeds. To have a comprehensive view of the domestication history of Indian sheep, we sequenced the mitochondrial DNA (mtDNA) control region (D-loop) and cytochrome b gene ( CYTB ) of 16 Indian domestic sheep breeds, most of them (13) from the south India. We analysed these sequences along with published data of domestic and wild sheep from different countries, including India. The haplotype diversity was relatively high in Indian sheep, which were classified into the three known mtDNA lineages, namely A, B and C. Lineage A was predominant among Indian sheep whereas lineages B and C were observed at low frequencies but C was restricted to the breeds of north and east India. The median joining network showed five major expanding haplogroups of lineage A (A1–A5). Out of which, A2, A4 and A5 were more frequent in Indian sheep in contrast to breeds from other parts of the world. Among the 27 Indian sheep breeds analysed, Mandya and Sonadi breeds were significantly different from other Indian breeds in the MDS analyses. This was explained by a very high contribution of lineage B into these two breeds. The Approximate Bayesian Computation (ABC) provided evidence for the domestication of lineage A sheep in the Indian subcontinent. Contrary to the current knowledge, we also found strong support for the introduction of lineage B into Indian subcontinent through sea route rather than from the Mongolian Plateau. The neighbour-joining tree of domestic and wild sheep revealed the close genetic relationship of Indian domestic sheep with Pakistani wild sheep O. vignei blanfordi. Based on our analyses and archaeological evidences, we suggest the Indian subcontinent as one of the domestication centres of the lineage A sheep, while lineage B sheep might have arrived into India from elsewhere via Arabian sea route. To the best of our knowledge, this is the first comprehensive study on Indian sheep where we have analysed more than 740 animals belonging to 27 sheep breeds raised in various regions of India. Our study provides insight into the understanding of the origin and migratory history of Indian sheep.

Lineage (genetic)

Haplogroup

D-loop

mtDNA control region

10.1038/s41598-021-97761-y

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Consequences of Domestication on Gut Microbiome: A Comparative Study Between Wild Gaur and Domestic Mithun

Frontiers in Microbiology (2020)

Vandana R. Prabhu Wasimuddin Ranganathan Kamalakkannan Moolamkudy Suresh Arjun Muniyandi Nagarajan

Although the gut microbiome benefits the host in several ways, how anthropogenic forces impact the gut microbiome of mammals is not yet completely known. Recent studies have noted reduced gut microbiome diversity in captive mammals due to changes in diet and living environment. However, no studies have been carried out to understand how the gut microbiome of wild mammals responds to domestication. We analyzed the gut microbiome of wild and captive gaur and domestic mithun (domestic form of gaur) to understand whether the gut microbiome exhibits sequential changes from wild to captivity and after domestication. Both captive and domestic populations were characterized by reduced microbial diversity and abundance as compared to their wild counterparts. Notably, two beneficial bacterial families, Ruminococcaceae and Lachnospiraceae, which are known to play vital roles in herbivores' digestion, exhibited lower abundance in captive and domestic populations. Consequently, the predicted bacterial functional pathways especially related to metabolism and immune system showed lower abundance in captive and domestic populations compared to wild population. Therefore, we suggest that domestication can impact the gut microbiome more severely than captivity, which might lead to adverse effects on host health and fitness. However, further investigations are required across a wide range of domesticates in order to understand the general trend of microbiome shifts in domestic animals.

Gut microbiome

10.3389/fmicb.2020.00133

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Citations (29)

Metagenomics: Implications in oral health and disease

Elsevier eBooks (2024)

Vandana R. Prabhu Karippadakam Bhavana Priya Nimish Deo Aparna Suresh Ranganathan Kamalakkannan

10.1016/b978-0-323-91631-8.00020-2

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Metagenomics: Implications in Oral Health and Disease

Elsevier eBooks (2017)

Muniyandi Nagarajan Vandana R. Prabhu Ranganathan Kamalakkannan

Oral Microbiome

Dysbiosis

Oral microbiology

Human Microbiome Project

Commensalism

10.1016/b978-0-08-102268-9.00009-4

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The complete mitochondrial genome of Indian gaur, Bos gaurus and its phylogenetic implications

Scientific Reports (2020)

Ranganathan Kamalakkannan Karippadakam Bhavana Vandana R. Prabhu Dhandapani Sureshgopi Hijam Surachandra Singha

Abstract The gaur is the largest extant cattle species and distributed across South and Southeast Asia. Around 85% of its current global population resides in India, however there has been a gradual decrease in the gaur population over the last two decades due to various anthropogenic activities. Mitochondrial genome is considered as an important tool for species identification and monitoring the populations of conservation concern and therefore it becomes an obligation to sequence the mitochondrial genome of Indian gaur. We report here for the first time 16,345 bp mitochondrial genome of four Indian gaur sequenced using two different approaches. Mitochondrial genome consisted of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. Among the 37 genes, 28 were positioned on the H-strand and 9 were positioned on the L-strand. The overall base composition appeared to be 33.5% A, 27.2% T, 25.9% C and 13.4% G, which yielded a higher AT content. The phylogenetic analysis using complete mitochondrial genome sequences unambiguously suggested that gaur is the maternal ancestor of domestic mithun. Moreover, it also clearly distinguished the three sub species of B. gaurus i.e. B. gaurus gaurus, B. gaurus readei and B. gaurus hubbacki . Among the three sub species, B. gaurus gaurus was genetically closer to B. gaurus readei as compared to B. gaurus hubbacki . The findings of our study provide an insight into the genetic structure and evolutionary history of Indian gaur.

Heavy strand

10.1038/s41598-020-68724-6

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Citations (23)

Mitochondrial genome of the Indian spot-billed duck and its phylogenetic and conservation implications

Scientific Reports (2024)

Muniyandi Nagarajan Ranganathan Kamalakkannan Vandana R. Prabhu Karippadakam Bhavana A. Gopalakrishnan

The Indian spot-billed duck, Anas poecilorhyncha is a large dabbling and non-migratory breeding bird. The identification and phylogenetic relationship of A. poecilorhyncha remain uncertain due to the presence of overlapping meristic characters and hybridization with closely related species. Molecular data aids when there are challenges in morphological identification. However, genetic characterization of A. poecilorhyncha has been paid less attention. Apart from their functional and physiological role, mitochondrial genome can also be used for various purposes, including species identification, phylogenetic analysis, understanding the domestication history of species etc. Therefore, the present study aimed to sequence the mitochondrial genome of A. poecilorhyncha and its closely related domestic species A. platyrhynchos (mallard duck) to understand their mitochondrial genome structure and phylogenetic relationships. The length of mitochondrial genome of A. poecilorhyncha and A. platyrhynchos was 16,608 and 16,604 bp respectively. Mitochondrial genome contained 37 genes and a non-coding control region. Overall, the characteristics of mitochondrial genome of both species were found to be conserved. The phylogenetic tree exhibited seven major clades (A to G) with a high bootstrap support. Notably, the Indian A. poecilorhyncha population formed a distinct clade (C) whereas the A. poecilorhyncha that were probably sampled from China grouped along with A. zonorhyncha (clade B). Besides, one of the A. poecilorhyncha probably sampled from China was placed in the clade A, which predominantly consisted of A. platyrhynchos. It suggests that Indian A. poecilorhyncha population is genetically different from Chinese A. poecilorhyncha population. Further, it sheds light on the importance of conducting a comprehensive phylogenetic study on these species. The newly sequenced mitochondrial genome of A. poecilorhyncha and A. platyrhynchos would be useful not only to have a better understanding of the phylogeny and evolution of Anas species but also to help in the conservation of A. poecilorhyncha which is under constant threat from rapid urbanization, interspecific hybridization and other human activities.

10.1038/s41598-024-75665-x

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Complete mitochondrial genome of Indian mithun, Bos frontalis and its phylogenetic implications

Molecular Biology Reports (2019)

Vandana R. Prabhu Moolamkudy Suresh Arjun Karippadakam Bhavana Ranganathan Kamalakkannan Muniyandi Nagarajan

10.1007/s11033-019-04675-0

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Citations (23)

Genetic diversity and maternal lineages of south Indian goats

Molecular Biology Reports (2018)

Ranganathan Kamalakkannan Jesna Jose Subhash Thomas Vandana R. Prabhu Muniyandi Nagarajan