Characterization of Plastidial and Nuclear SSR Markers for Understanding Invasion Histories and Genetic Diversity of Schinus molle L.

Invasive plant species are expected to display high dispersal capacity but low levels of genetic diversity due to the founder effect occurring at each invasion episode. Understanding the history of invasions and the levels of genetic diversity of such species is an important task for planning management and monitoring strategy for these events. Peruvian Peppertree (Schinus molle L.) is a pioneer tree species native from South America which was introduced in North America, Europe and Africa, becoming a threat to these non-native habitats. In this study, we report the discovery and characterization of 17 plastidial (ptSSR) and seven nuclear (nSSR) markers for S. molle based on low-coverage whole-genome sequencing data acquired through next-generation sequencing. The markers were tested in 56 individuals from two natural populations sampled in the Brazilian Caatinga and Pampa biomes. All loci are moderately to highly polymorphic and revealed to be suitable for genetic monitoring of new invasions, for understanding the history of old invasions, as well as for genetic studies of native populations in their natural occurrence range and of orchards established with commercial purposes.

Download Full-text

Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish

Heredity ◽

10.1038/s41437-021-00438-5 ◽

2021 ◽

Author(s):

Axel Jensen ◽

Mette Lillie ◽

Kristofer Bergström ◽

Per Larsson ◽

Jacob Höglund

Keyword(s):

Genetic Diversity ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome Sequencing Data ◽

Peripheral Populations ◽

Whole Genome ◽

Runs Of Homozygosity ◽

Sequencing Data ◽

Isolated Populations ◽

Native Populations

AbstractThe use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.

Download Full-text

Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN)

BMC Genomics ◽

10.1186/s12864-021-08237-2 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Guilherme B. Neumann ◽

Paula Korkuć ◽

Danny Arends ◽

Manuel J. Wolf ◽

Katharina May ◽

...

Keyword(s):

Genetic Diversity ◽

Association Studies ◽

Bos Indicus ◽

Diversity Management ◽

Whole Genome Sequencing Data ◽

General Interest ◽

Whole Genome ◽

Sequencing Data ◽

Snp Chip ◽

Selection Of

Abstract Background German Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield. DSN cattle are kept as a genetic reserve with a current herd size of around 2500 animals. The ability to track sequence variants specific to DSN could help to support the conservation of DSN’s genetic diversity and to provide avenues for genetic improvement. Results Whole-genome sequencing data of 304 DSN cattle were used to design a customized DSN200k SNP chip harboring 182,154 variants (173,569 SNPs and 8585 indels) based on ten selection categories. We included variants of interest to DSN such as DSN unique variants and variants from previous association studies in DSN, but also variants of general interest such as variants with predicted consequences of high, moderate, or low impact on the transcripts and SNPs from the Illumina BovineSNP50 BeadChip. Further, the selection of variants based on haplotype blocks ensured that the whole-genome was uniformly covered with an average variant distance of 14.4 kb on autosomes. Using 300 DSN and 162 animals from other cattle breeds including Holstein, endangered local cattle populations, and also a Bos indicus breed, performance of the SNP chip was evaluated. Altogether, 171,978 (94.31%) of the variants were successfully called in at least one of the analyzed breeds. In DSN, the number of successfully called variants was 166,563 (91.44%) while 156,684 (86.02%) were segregating at a minor allele frequency > 1%. The concordance rate between technical replicates was 99.83 ± 0.19%. Conclusion The DSN200k SNP chip was proved useful for DSN and other Bos taurus as well as one Bos indicus breed. It is suitable for genetic diversity management and marker-assisted selection of DSN animals. Moreover, variants that were segregating in other breeds can be used for the design of breed-specific customized SNP chips. This will be of great value in the application of conservation programs for endangered local populations in the future.

Download Full-text

Global range expansion history of pepper (Capsicum spp.) revealed by over 10,000 genebank accessions

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2104315118 ◽

2021 ◽

Vol 118 (34) ◽

pp. e2104315118

Author(s):

Pasquale Tripodi ◽

Mark Timothy Rabanus-Wallace ◽

Lorenzo Barchi ◽

Sandip Kale ◽

Salvatore Esposito ◽

...

Keyword(s):

Genetic Diversity ◽

Genotyping By Sequencing ◽

Focal Region ◽

Nucleotide Polymorphisms ◽

Trade Routes ◽

Genebank Management ◽

Capsicum Spp ◽

History Of ◽

Cultural Commodity

Genebanks collect and preserve vast collections of plants and detailed passport information, with the aim of preserving genetic diversity for conservation and breeding. Genetic characterization of such collections has the potential to elucidate the genetic histories of important crops, use marker–trait associations to identify loci controlling traits of interest, search for loci undergoing selection, and contribute to genebank management by identifying taxonomic misassignments and duplicates. We conducted a genomic scan with genotyping by sequencing (GBS) derived single nucleotide polymorphisms (SNPs) of 10,038 pepper (Capsicum spp.) accessions from worldwide genebanks and investigated the recent history of this iconic staple. Genomic data detected up to 1,618 duplicate accessions within and between genebanks and showed that taxonomic ambiguity and misclassification often involve interspecific hybrids that are difficult to classify morphologically. We deeply interrogated the genetic diversity of the commonly consumed Capsicum annuum to investigate its history, finding that the kinds of peppers collected in broad regions across the globe overlap considerably. The method ReMIXTURE—using genetic data to quantify the similarity between the complement of peppers from a focal region and those from other regions—was developed to supplement traditional population genetic analyses. The results reflect a vision of pepper as a highly desirable and tradable cultural commodity, spreading rapidly throughout the globe along major maritime and terrestrial trade routes. Marker associations and possible selective sweeps affecting traits such as pungency were observed, and these traits were shown to be distributed nonuniformly across the globe, suggesting that human preferences exerted a primary influence over domesticated pepper genetic structure.

Download Full-text

Effects of habitat fragmentation on the genetic diversity and differentiation of Dendrolimus punctatus (Lepidoptera: Lasiocampidae) in Thousand Island Lake, China, based on mitochondrial COI gene sequences

Bulletin of Entomological Research ◽

10.1017/s0007485318000172 ◽

2018 ◽

Vol 109 (1) ◽

pp. 62-71 ◽

Cited By ~ 1

Author(s):

K. Lv ◽

J.-R. Wang ◽

T.-Q. Li ◽

J. Zhou ◽

J.-Q. Gu ◽

...

Keyword(s):

Genetic Diversity ◽

Habitat Fragmentation ◽

Geographic Distance ◽

Haplotype Diversity ◽

Shape Index ◽

Coi Gene ◽

Fragmented Landscape ◽

Dispersal Capacity ◽

Island Populations ◽

High Dispersal

AbstractThousand Island Lake (TIL) is a typical fragmented landscape and an ideal model to study ecological effects of fragmentation. Partial fragments of the mitochondrial cytochrome oxidase subunit I gene of 23 island populations of Dendrolimus punctatus in TIL were sequenced, 141 haplotypes being identified. The number of haplotypes increased significantly with the increase in island area and shape index, whereas no significant correlation was detected between three island attributes (area, shape and isolation) and haplotype diversity. However, the correlation with number of haplotypes was no longer significant when the ‘outlier’ island JSD (the largest island) was not included. Additionally, we found no significant relationship between geographic distance and genetic distance. Geographic isolation did not obstruct the gene flow among D. punctatus populations, which might be because of the high dispersal capacity of this pine moth. Fragmentation resulted in the conversion of large and continuous habitats into isolated, small and insular patches, which was the primary effect on the genetic diversity of D. punctatus in TIL. The conclusion to emphasize from our research is that habitat fragmentation reduced the biological genetic diversity to some extent, further demonstrating the importance of habitat continuity in biodiversity protection.

Download Full-text

Introgression of Eastern Chinese and Southern Chinese haplotypes contributes to the improvement of fertility and immunity in European modern pigs

GigaScience ◽

10.1093/gigascience/giaa014 ◽

2020 ◽

Vol 9 (3) ◽

Cited By ~ 3

Author(s):

Hao Chen ◽

Min Huang ◽

Bin Yang ◽

Zhongping Wu ◽

Zheng Deng ◽

...

Keyword(s):

Geographic Origin ◽

Whole Genome Sequencing Data ◽

Biological Functions ◽

Sequencing Data ◽

Phenotypic Characteristics ◽

Large White ◽

Wild Boars ◽

Domestic Pigs ◽

Southern Chinese ◽

History Of

Abstract Background Pigs were domesticated independently from European and Asian wild boars nearly 10,000 years ago. Chinese indigenous pigs have been historically introduced to improve Europe local pigs. However, the geographic origin and biological functions of introgressed Chinese genes in modern European pig breeds remain largely unknown. Results Here we explored whole-genome sequencing data from 266 Eurasian wild boars and domestic pigs to produce a fine-scale map of introgression between French Large White (FLW) and Chinese pigs. We show that FLW pigs had historical admixture with both Southern Chinese (SCN) and Eastern Chinese (ECN) pigs ∼200–300 years ago. Moreover, a set of SCN haplotypes was shown to be beneficial for improving disease resistance and ECN haplotypes are favorable for improved reproductive performance in FLW pigs. In addition, we confirm human-mediated introgression events at the AHR locus, at which the haplotype of most likely ECN origin contributes to increased fertility of FLW pigs. Conclusions This study advances our understanding of the breeding history of global domestic pigs and highlights the importance of artificial introgression in the formation of phenotypic characteristics in domestic animals.

Download Full-text

Construction of the third generation Zea mays haplotype map

10.1101/026963 ◽

2015 ◽

Cited By ~ 21

Author(s):

Robert Bukowski ◽

Xiaosen Guo ◽

Yanli Lu ◽

Cheng Zou ◽

Bing He ◽

...

Keyword(s):

Zea Mays ◽

Whole Genome Sequencing Data ◽

Limiting Factor ◽

Computational Pipeline ◽

Research Groups ◽

Sequencing Data ◽

The Third ◽

The World ◽

Set Up

ABSTRACTBackgroundCharacterization of genetic variations in maize has been challenging, mainly due to deterioration of collinearity between individual genomes in the species. An international consortium of maize research groups combined resources to develop the maize haplotype version 3 (HapMap 3), built from whole genome sequencing data from 1,218 maize lines, covering pre-domestication and domesticated Zea mays varieties across the world.ResultsA new computational pipeline was set up to process over 12 trillion bp of sequencing data, and a set of population genetics filters were applied to identify over 83 million variant sites.ConclusionsWe identified polymorphisms in regions where collinearity is largely preserved in the maize species. However, the fact that the B73 genome used as the reference only represents a fraction of all haplotypes is still an important limiting factor.

Download Full-text

Population-level genome-wide STR typing in Plasmodium species reveals higher resolution population structure and genetic diversity relative to SNP typing

10.1101/2021.05.19.444768 ◽

2021 ◽

Author(s):

Jiru Han ◽

Jacob E Munro ◽

Anthony Kocoski ◽

Alyssa E Barry ◽

Melanie Bahlo

Keyword(s):

Genetic Diversity ◽

Large Scale ◽

Tandem Repeats ◽

Plasmodium Species ◽

Whole Genome Sequence ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Genome Wide ◽

Field Samples

Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. falciparum and P. vivax have been made available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).

Download Full-text

Population Genetics of New Zealand Nemadactylus macropterus (tarakihi) and Characterisation of their Mitochondrial Genome

10.26686/wgtn.17142476.v1 ◽

2021 ◽

Author(s):

◽

Alexander Halliwell

Keyword(s):

Genetic Diversity ◽

New Zealand ◽

Genetic Structure ◽

East Coast ◽

Demographic History ◽

Variable Region ◽

Sequencing Data ◽

Commercial Catch ◽

History Of ◽

Hyper Variable Region

<p>Nemadactylus macropterus, commonly known as tarakihi in New Zealand is highly regarded by commercial and recreational fishers and considered a taonga by iwi and customary fisheries. For many years N. macropterus was New Zealand’s second most important commercial catch and is currently the third most valuable inshore commercial finfish fishery in which 90% is consumed by the domestic market. However, despite the apparent importance, relatively little is known about the population structure of the N. macropterus. In 2017 the first fully quantitative stock assessment was conducted on the east coast N. macropterus fisheries as one stock. Alarmingly, the east coast fishery was estimated to be 15.9% of the unexploited spawning biomass and predicted to have been declining for the past thirty years. In an effort to rebuild the fishery, several rebuild plans have been purposed and commercial catch limits have been reduced. In order to rebuild and successfully manage a viable future N. macropterus fishery, an understanding of demographic connectivity and genetic connectivity among N. macropterus populations is essential. The overall goal of this thesis research was to investigate the population genetic structure, genetic diversity and demographic history of N. macropterus using fish sampled from around New Zealand. This was achieved by analysing hyper variable region one of mitochondrial DNA for 370 N. macropterus collected from 14 locations. No genetic differentiation was observed among the 14 locations, an indication that N. macropterus have a panmictic genetic structure. Furthermore, N. macropterus display a relatively high level of genetic diversity and appear to have a large stable population with a long evolutionary history. The Bayesian skyline analysis indicates the N. macropterus historic population has gone through two expansions. The mostly likely cause of this is an expansion before and after the last glacial maximum. The genetic diversity and demographic history of N. sp was also studied using samples collected from around the Three Kings Islands of New Zealand. The complete mitochondrial genome of N. macropterus was reconstructed from bulk DNA sequencing data and a set of specific mtDNA primers were developed to amplify hyper variable region one. The DNA sequencing data provided by these primers with the addition of published control region sequences was used to reconstruct the Nemadactylus phylogeny.</p>

Download Full-text

Novel functional sequences uncovered through a bovine multiassembly graph

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2101056118 ◽

2021 ◽

Vol 118 (20) ◽

pp. e2101056118

Author(s):

Danang Crysnanto ◽

Alexander S. Leonard ◽

Zih-Hua Fang ◽

Hubert Pausch

Keyword(s):

Genetic Diversity ◽

Reference Genome ◽

Bos Taurus ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Reference Allele ◽

Genomic Analyses ◽

Reference Quality ◽

Reference Genomes

Many genomic analyses start by aligning sequencing reads to a linear reference genome. However, linear reference genomes are imperfect, lacking millions of bases of unknown relevance and are unable to reflect the genetic diversity of populations. This makes reference-guided methods susceptible to reference-allele bias. To overcome such limitations, we build a pangenome from six reference-quality assemblies from taurine and indicine cattle as well as yak. The pangenome contains an additional 70,329,827 bases compared to the Bos taurus reference genome. Our multiassembly approach reveals 30 and 10.1 million bases private to yak and indicine cattle, respectively, and between 3.3 and 4.4 million bases unique to each taurine assembly. Utilizing transcriptomes from 56 cattle, we show that these nonreference sequences encode transcripts that hitherto remained undetected from the B. taurus reference genome. We uncover genes, primarily encoding proteins contributing to immune response and pathogen-mediated immunomodulation, differentially expressed between Mycobacterium bovis–infected and noninfected cattle that are also undetectable in the B. taurus reference genome. Using whole-genome sequencing data of cattle from five breeds, we show that reads which were previously misaligned against the Bos taurus reference genome now align accurately to the pangenome sequences. This enables us to discover 83,250 polymorphic sites that segregate within and between breeds of cattle and capture genetic differentiation across breeds. Our work makes a so-far unused source of variation amenable to genetic investigations and provides methods and a framework for establishing and exploiting a more diverse reference genome.

Download Full-text