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Roger Moraga Martinez

Roger Moraga Martinez
Tea Break Bioinformatics Limited, New Zealand

MSc.

About

26
Publications
4,847
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284
Citations

Publications

Publications (26)
Article
Full-text available
Relationships with place provide critical context for characterizing biocultural diversity. Yet, genetic and genomic studies are rarely informed by Indigenous or local knowledge, processes, and practices, including the movement of culturally significant species. Here, we show how place‐based knowledge can better reveal the biocultural complexities...
Article
Full-text available
Species recovery programs are increasingly using genomic data to measure neutral genetic diversity and calculate metrics like relatedness. While these measures can inform conservation management, determining the mechanisms underlying inbreeding depression requires information about functional genes associated with adaptive or maladaptive traits. To...
Article
Full-text available
Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimise relatedness between individuals in an effort to avoid inbreeding, maximise diversity, and maintain e...
Poster
Full-text available
Reduced reproductive fitness due to maladaptive traits, like reduced fertility, hampers recovery efforts for critically endangered species. To identify putative structural variants on the Z-chromosome, we are developing a workflow to generate high resolution long-read sequence data for kākāpō (Strigops habroptilus) with known reproductive success...
Preprint
Full-text available
Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimise relatedness between individuals in an effort to avoid inbreeding, maximise diversity, and maintain e...
Poster
Full-text available
The advent of reduced representation genotyping-by-sequencing (GBS) provides a cost-effective high-throughput genotyping platform to many ‘orphan’ species. This enables downstream analyses including genomic selection, parentage assignment, conservation genetics, population genetics and genome wide association studies. There are many different workf...
Article
Full-text available
The merging of distinct genomes, allopolyploidization, is a widespread phenomenon in plants. It generates adaptive potential through increased genetic diversity, but examples demonstrating its exploitation remain scarce. White clover (Trifolium repens) is a ubiquitous temperate allotetraploid forage crop derived from two European diploid progenitor...
Poster
Full-text available
Memory requirements for large genome assemblies are notoriously expensive. Using fast NVMe solid-state drives as virtual memory under Linux, it is possible to assemble multi-gigabase genomes using a modest workstation.
Article
Full-text available
Threatened species recovery programmes benefit from incorporating genomic data into conservation management strategies to enhance species recovery. However, a lack of readily available genomic resources, including conspecific reference genomes, often limits the inclusion of genomic data. Here, we investigate the utility of closely related high-qual...
Article
Full-text available
Background The recent development of next-generation sequencing DNA marker technologies, such as genotyping-by-sequencing (GBS), generates thousands of informative single nucleotide polymorphism markers in almost any species, regardless of genomic resources. This enables poorly resourced or “orphan” crops/species access to high-density, high-throug...
Data
supplementary data for An entropy-reducing data representation approach for bioinformatic data by Mcculloch et al 2018
Presentation
Full-text available
This presentation proposes the use of straightforward whole-genome alignments as a proxy for accurately mapping Illumina short reads.
Article
Full-text available
Non-semantic approaches to bioinformatic data analysis have potential relevance where semantic resources such as annotated finished reference genomes are lacking, such as in the analysis and utilisation of growing amounts of sequence data from non-model organisms, often associated with sequence-based agricultural, aqua-cultural and environmental sa...
Article
Full-text available
Key message: Genomic prediction models for multi-year dry matter yield, via genotyping-by-sequencing in a composite training set, demonstrate potential for genetic gain improvement through within-half sibling family selection. Perennial ryegrass (Lolium perenne L.) is a key source of nutrition for ruminant livestock in temperate environments world...
Article
Full-text available
Here we report the draft genome of Yersinia entomophaga type strain MH96T. The genome shows 93.8% nucleotide sequence identity to that of Yersinia nurmii type strain APN3a-cT, and comprises a single chromosome of approximately 4,275,531 bp. In silico analysis identified that, in addition to the previously documented Y. entomophaga Yen-TC gene clust...
Chapter
Mixed-species pasture based on perennial ryegrass (Lolium perenne) and white clover (Trifolium repens) is the foundation for profitable production from temperate grasslands. In theory, genomic selection (GS) offers an opportunity to lift the rate of genetic gain in these species. Critical research questions include to what extent theoretical expect...
Poster
De novo assembly of reference genomes remains a challenge for some economic species. Polyploidy, a feature common to many plants, impedes assembly when reliant on short-read sequencing platforms. White clover, a prominent forage legume in grazed temperate pasture, has a relatively compact genome (≈1 Gb). It presents particular sequencing challenges...
Article
This review examines two classes of organism that live in symbiosis; grasses and fungi. Specifically it deals with grasses of the tribe Hordeeae (formerly Triticeae) of the subfamily Poöideae and the Epichloë fungi of family Clavicipitaceae. Epichloë endophytes, particularly asexual forms, have important roles in pastoral agricultural systems in th...
Article
Full-text available
Demand for palm oil has been increasing by an average of ∼8% the past decade and currently accounts for about 59% of the world's vegetable oil market. This drives the need to increase palm oil production. Nevertheless, due to the increasing need for sustainable production, it is imperative to increase productivity rather than the area cultivated. S...
Article
Full-text available
Proanthocyanidins (PAs) are polymeric flavonoids derived from the phenylpropanoid pathway, and they bind reversibly to forage proteins within the rumen, providing protection from bloat while enhancing protein utilisation and animal production. The occurrence of PAs varies greatly within forage legume species. Foliar PAs are present in Lotus cornicu...
Conference Paper
Polyploidy, a feature common to many crop species, impedes assembly when developing de novo reference genomes based on short-read sequencing platforms. White clover (Trifolium repensL.), an allopolyploid, is a principal legume in temperate pastoral systems. It produces high quality herbage, and fixes atmospheric nitrogen into plant available forms...
Conference Paper
White clover (Trifolium repens L.) is the dominant legume in temperate pasture systems, where it provides high quality feed for grazing ruminants. White clover synthesises both anthocyanins and condensed tannins (CT), but levels are negligible in leaf tissue. CT are particularly important in pastoral systems for improved animal health and productio...
Conference Paper
White clover (Trifolium repens L.), a principal legume in temperate pastoral systems, produces high quality herbage, offers compatibility and persistence in mixed swards, and through bacterial symbiosis fixes atmospheric nitrogen into plant available forms. Pastoral Genomics, a New Zealand Industry:Government-funded research consortium, is sequenci...

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