Article

The complete mitochondrial genome and phylogeny of Indian oil sardine, Sardinella longiceps and Goldstripe Sardinella, Sardinella gibbosa from the Indian Ocean

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Abstract

The Indian oil Sardine, Sardinella longiceps and Goldstripe Sardinella, Sardinella gibbosa are the two commercially important, small pelagic fishes from Indian waters belonging to the family Clupeidae. Characterization of the complete mitogenome is very helpful in resolving taxonomic ambiguities and hence we characterized the complete mitogenome of S. longiceps and S. gibbosa from Indian waters. The assembled mitogenomes of S. longiceps and S. gibbosa are 16,613 and 16658 bp circles respectively, contained the 37 mitochondrial structural genes (2 rRNA, 22 tRNA, 13 protein-coding genes) with the gene order identical to that of typical vertebrates. In the phylogenetic tree, S. longiceps and S. gibbosa clustered with species belonging to the family Clupeidae. This study is the first report of the complete mitogenome of two commercially important clupeids from Indian waters which form the baseline for further studies on molecular systematics, population genetics, historic demography, adaptive variation and conservation of these species.

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... Seven positively selected sites (Two each in ND1 and ND5 genes and one each in ND4, CO1 and CO2 respectively) were specific to SEAS and two sites (one each in CO2 and CYTB) to NAS populations ( Supplementary Fig. A4). The control region contained different conserved sequence regions like Termination Associated Sequence (TAS) at the 3′ end and Conserved Sequence Box (CSB D, CSB1, CSB2, and CSB3) 41 . (Supplementary Fig. A3). ...
... Complete mitochondrial genomes of 45 individuals (15 each from the 3 eco-regions) were amplified and sequenced using 16 novel primer pairs (Supplementary Table T1) and the mitogenome of Sardinella longiceps was used as a template (GenBank Accession No: KR000002.1) 41 . Sequences were manually checked, aligned, and assembled in MEGA6 87 and Geneious R7 88 against the S. longiceps mitogenome 41 . ...
... 41 . Sequences were manually checked, aligned, and assembled in MEGA6 87 and Geneious R7 88 against the S. longiceps mitogenome 41 . Annotated mitogenome sequences have been submitted to NCBI, GenBank (Accession numbers MG251937-MG251981). ...
... Despite the evolutionary trend to reduce the size of the mitogenome, the presence and persistence of a non-coding region known as the control region indicate its functional importance. The functioning of conserved sequence elements in the control region as binding sites for nuclear-organized proteins that regulate mtDNA maintenance and expression substantiates the importance of this region (Anderson et al. 1981;Murakami et al. 2002;Pereira et al. 2008;Melo-Ferreira et al. 2014 strand promoter and LSP: light-strand promoter), termination associated sequences (TAS), conserved sequence blocks (CSBs)) and variable number of tandem repeats (VNTR) scattered among highly variable sequence elements (Brown et al. 1986;Wright 2000;Jamandre et al. 2014;Nicholls and Minczuk 2014;Jemt et al. 2015;Miya and Nishida 2015;Sebastian et al. 2017). It is believed that the major molecular machines in mitochondrial replication and gene expression regulation could be directly influenced by components of the control region (Pereira et al. 2008;Nicholls and Minczuk 2014;Jemt et al. 2015;D'Souza and Minczuk 2018). ...
... The DNA sequence of Clupeoids was aligned in MEGA v7 (Kumar et al. 2016) using CLUSTAL-W and a dataset of individual tRNAs and control regions was prepared. The conserved sequence blocks (CSBs) and highly variable regions with repeat units in the control region dataset were identified and annotated by comparing with CSBs reported from fishes (Jamandre et al. 2014;Sebastian et al. 2017). The nucleotide base composition of tRNAs and control region sequence blocks were calculated using Geneious R7 (Kearse et al. 2012). ...
Article
The vertebrate mitochondrial genome is characterized by an exceptional organization evolving towards a reduced size. However, the persistence of a non-coding and highly variable control region is against this evolutionary trend that is explained by the presence of conserved sequence motifs or binding sites for nuclear-organized proteins that regulate mtDNA maintenance and expression. We performed a comparative mitogenomic investigation of the non-coding control region to understand its evolutionary patterns in Clupeoid fishes which are widely distributed across oceans of the world, exhibiting exemplary evolutionary potential. We confirmed the ability of sequence flanking the conserved sequence motifs in the control region to form stable secondary structures. The existence of evolutionarily conserved secondary structures without primary structure conservation suggested the action of selective constraints towards maintaining the secondary structure. The functional secondary structure is maintained by retaining the frequency of discontinuous AT and TG repeats along with compensatory base substitutions in the stem forming regions which can be considered as a selective constraint. The nucleotide polymorphism along the flanking regions of conserved sequence motifs can be explained as errors during the enzymatic replication of secondary structure-forming repeat elements. The evidence for selective constraints on secondary structures emphasizes the role of the control region in mitogenome function. Maintenance of high frequency of discontinuous repeats can be proposed as a model of adaptive evolution against the mutations that break the secondary structure involved in the efficient regulation of mtDNA functions substantiating the efficient functioning of the control region even in a high nucleotide polymorphism environment.
... Seven positively selected sites (Two each in ND1 and ND5 genes and one each in ND4, CO1 and CO2 respectively) were specific to SEAS and two sites (one each in CO2 and CYTB) to NAS populations ( Supplementary Fig. A4). The control region contained different conserved sequence regions like Termination Associated Sequence (TAS) at the 3′ end and Conserved Sequence Box (CSB D, CSB1, CSB2, and CSB3) 41 . (Supplementary Fig. A3). ...
... Complete mitochondrial genomes of 45 individuals (15 each from the 3 eco-regions) were amplified and sequenced using 16 novel primer pairs (Supplementary Table T1) and the mitogenome of Sardinella longiceps was used as a template (GenBank Accession No: KR000002.1) 41 . Sequences were manually checked, aligned, and assembled in MEGA6 87 and Geneious R7 88 against the S. longiceps mitogenome 41 . ...
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Integrative approach revises the frequently misidentified species of Sardinella (Clupeidae) of the Indo-West Pacific Ocean
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Sambrook J, Russell D (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, New York Stern N, Rinkevich B, Goren M (2016) Integrative approach revises the frequently misidentified species of Sardinella (Clupeidae) of the Indo-West Pacific Ocean. J Fish Biol 89(5):2282-2305