Detecting population structure of Paleosuchus trigonatus (Alligatoridae: Caimaninae) through microsatellites markers developed by next generation sequencing

Muniz, Fábio; Ximenes, Aline Mourão; Bittencourt, Pedro; Hernández-Rangel, Sandra M.; Campos, Zilca; Hrbek, Tomas; Farias, Izeni Pires

doi:10.1007/s11033-019-04709-7

Cited by 13 publications

(2 citation statements)

References 65 publications

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“…The SSR density detected in this study is nearly similar with Jujube (321.56 SSRs/Mb) [49]. Plants exhibit variation of SSRs Repeat units within their genomes, for example, in Paleosuchus trigonatus, di-nucleotide repeat motif predominated [50], whereas tetra-nucleotide repeats were the most frequent in Coffea canephora [51], and tri-nucleotide repeat motifs being most frequent in Hyalessa fuscata [52]. The mono-nucleotide repeat motifs predominated in our study, which is similar to Alibertia edulis [53].…”

Section: Discussionsupporting

confidence: 74%

Development and Utilization of Microsatellite Markers to Assess Genetic Variation Coupled with Modelling Range Shifts of Dodonaea Viscosa in Isolated Taita Hills and Mount Kenya Forests

Saina

Gichira

Ngarega

et al. 2021

Preprint

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For the protection and maintenance of fragmented and highly disturbed habitats, understanding genetic variation is essential. The Taita Hills of Kenya is the northernmost part of the Eastern Arc Mountains and has been identified as one of the top 10 biodiversity hotspots globally. The current forests in the Taita Hills have been highly fragmented over the past century. In order to appraise the influence of anthropological disturbance and fragmentation on the genetic variation of Dodonaea viscosa (Sapindaceae), we studied its preliminary genetic variability and population structure using newly developed microsatellite (SSR) markers, combined with ecological niche modeling analyses. We utilized the Illumina paired-end technology to sequence the D. viscosa’s genome and developed its microsatellite markers. In total, 646,428 sequences were analyzed and 49,836 SSRs were identified from 42,638 sequences. A total of 18 primer pairs were designed to test polymorphism among 92 individuals across eight populations. The average observed heterozygosity and expected heterozygosity ranged from 0.119 to 0.982 and from 0.227 to 0.691, respectively. Analysis of molecular variance (AMOVA) revealed 78% variance within individuals and only 20% among the eight populations. According to SDM results, D. viscosa’s suitable habitats have been gradually reducing since the last glacial maximum (LGM), and the situation will worsen under the extreme pessimist scenario of RCP 8.5. Moreover, genetic diversity was significantly greater in larger fragments. Therefore, urgent conservation management of smaller fragmented patches is necessary to protect this disturbed region and maintain the genetic resources.

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Section: Discussionsupporting

confidence: 74%

Development and Utilization of Microsatellite Markers to Assess Genetic Variation Coupled with Modelling Range Shifts of Dodonaea Viscosa in Isolated Taita Hills and Mount Kenya Forests

Saina

Gichira

Ngarega

et al. 2021

Preprint

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“…Together they are combined into a single clade of diapsid reptiles—Archosauria [ 4 , 5 ]. The order Crocodylia is divided into three families (Alligatoridae, Crocodylidae, and Gavialidae), and the number of currently described species ranges from 23 to 27 [ 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 ]. Cytogenetic data for Crocodylia are usually restricted to the description of chromosome numbers, karyotype composition, and some conventional banding; only a few studies have used molecular cytogenetic tools [ 14 , 15 , 16 , 17 , 18 , 19 ].…”

Section: Introductionmentioning

confidence: 99%

The Cytogenetic Map of the Nile Crocodile (Crocodylus niloticus, Crocodylidae, Reptilia) with Fluorescence In Situ Localization of Major Repetitive DNAs

Romanenko

Prokopov

Proskuryakova

et al. 2022

IJMS

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Tandemly arranged and dispersed repetitive DNA sequences are important structural and functional elements that make up a significant portion of vertebrate genomes. Using high throughput, low coverage whole genome sequencing followed by bioinformatics analysis, we have identified seven major tandem repetitive DNAs and two fragments of LTR retrotransposons in the genome of the Nile crocodile (Crocodylus niloticus, 2n = 32). The repeats showed great variability in structure, genomic organization, and chromosomal distribution as revealed by fluorescence in situ hybridization (FISH). We found that centromeric and pericentromeric heterochromatin of C. niloticus is composed of previously described in Crocodylus siamensis CSI-HindIII and CSI-DraI repetitive sequence families, a satellite revealed in Crocodylus porosus, and additionally contains at least three previously unannotated tandem repeats. Both LTR sequences identified here belong to the ERV1 family of endogenous retroviruses. Each pericentromeric region was characterized by a diverse set of repeats, with the exception of chromosome pair 4, in which we found only one type of satellite. Only a few repeats showed non-centromeric signals in addition to their centromeric localization. Mapping of 18S–28S ribosomal RNA genes and telomeric sequences (TTAGGG)n did not demonstrate any co-localization of these sequences with revealed centromeric and pericentromeric heterochromatic blocks.

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Genetic Diversity of New World Crocodilians

Amavet

Zucoloto

Hrbek

et al. 2020

Conservation Genetics of New World Crocodilians

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Detecting population structure of Paleosuchus trigonatus (Alligatoridae: Caimaninae) through microsatellites markers developed by next generation sequencing

Cited by 13 publications

References 65 publications

Development and Utilization of Microsatellite Markers to Assess Genetic Variation Coupled with Modelling Range Shifts of Dodonaea Viscosa in Isolated Taita Hills and Mount Kenya Forests

Development and Utilization of Microsatellite Markers to Assess Genetic Variation Coupled with Modelling Range Shifts of Dodonaea Viscosa in Isolated Taita Hills and Mount Kenya Forests

The Cytogenetic Map of the Nile Crocodile (Crocodylus niloticus, Crocodylidae, Reptilia) with Fluorescence In Situ Localization of Major Repetitive DNAs

Genetic Diversity of New World Crocodilians

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