Mr. Peter van Heusdenhttp://hdl.handle.net/10566/21632024-03-19T11:09:15Z2024-03-19T11:09:15ZTranscriptomics of the Rooibos (Aspalathus linearis) Species ComplexStander, Emily AmorWilliams, WesleyMgwatu, YamkelaHesse, Uljanavan Heusden, Peterhttp://hdl.handle.net/10566/68102021-09-28T00:01:18Z2020-01-01T00:00:00ZTranscriptomics of the Rooibos (Aspalathus linearis) Species Complex
Stander, Emily Amor; Williams, Wesley; Mgwatu, Yamkela; Hesse, Uljana; van Heusden, Peter
Rooibos (Aspalathus linearis), widely known as a herbal tea, is endemic to the Cape Floristic Region of South Africa (SA). It produces a wide range of phenolic compounds that have been associated with diverse health-promoting properties of the plant. The species comprises several growth forms that differ in their morphology and biochemical composition, only one of which is cultivated and used commercially. Here, we established methodologies for non-invasive transcriptome research of wild-growing South African plant species, including (1) harvesting and transport of plant material suitable for RNA sequencing; (2) inexpensive, high-throughput biochemical sample screening; (3) extraction of high-quality RNA from recalcitrant, polysaccharide- and polyphenol-rich plant material; and (4) biocomputational analysis of Illumina sequencing data, together with the evaluation of programs for transcriptome assembly (Trinity, IDBA-Trans, SOAPdenovo-Trans, CLC), protein prediction, as well as functional and taxonomic transcript annotation. In the process, we established a biochemically characterized sample pool from 44 distinct rooibos ecotypes (1–5 harvests) and generated four in-depth annotated transcriptomes (each comprising on average ≈86,000 transcripts) from rooibos plants that represent distinct growth forms and differ in their biochemical profiles. These resources will serve future rooibos research and plant breeding endeavors.
2020-01-01T00:00:00ZCapacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countriesVan Heusden, Peterhttp://hdl.handle.net/10566/68092021-09-24T00:00:47Z2020-01-01T00:00:00ZCapacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries
Van Heusden, Peter
Background
Whole-genome sequencing (WGS) is increasingly used for Mycobacterium tuberculosis (Mtb) research. Countries with the highest tuberculosis (TB) burden face important challenges to integrate WGS into surveillance and research.
Methods
We assessed the global status of Mtb WGS and developed a 3-week training course coupled with long-term mentoring and WGS infrastructure building. Training focused on genome sequencing, bioinformatics and development of a locally relevant WGS research project. The aim of the long-term mentoring was to support trainees in project implementation and funding acquisition. The focus of WGS infrastructure building was on the DNA extraction process and bioinformatics.
Findings
Compared to their TB burden, Asia and Africa are grossly underrepresented in Mtb WGS research. Challenges faced resulted in adaptations to the training, mentoring and infrastructure building. Out-of-date laptop hardware and operating systems were overcome by using online tools and a Galaxy WGS analysis pipeline. A case studies approach created a safe atmosphere for students to formulate and defend opinions. Because quality DNA extraction is paramount for WGS, a biosafety level 3 and general laboratory skill training session were added, use of commercial DNA extraction kits was introduced and a 2-week training in a highly equipped laboratory was combined with a 1-week training in the local setting.
Interpretation
By developing and sharing the components of and experiences with a sequencing and bioinformatics training program, we hope to stimulate capacity building programs for Mtb WGS and empower high-burden countries to play an important role in WGS-based TB surveillance and research.
2020-01-01T00:00:00ZChromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffoldingVij, ShubhaVan Heusden, PeterChristoffels, AlanMbandi, Stanley K.Mwangi, Sarahhttp://hdl.handle.net/10566/21332016-08-30T20:06:57Z2016-01-01T00:00:00ZChromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding
Vij, Shubha; Van Heusden, Peter; Christoffels, Alan; Mbandi, Stanley K.; Mwangi, Sarah
We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a
tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical
and genetic mapping along with shared synteny from closely related fish species to
derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50
size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various
regions across the species’ native range. SNP analyses identified high levels of genetic
diversity and confirmed earlier indications of a population stratification comprising three
clades with signs of admixture apparent in the South-East Asian population. The quality of
the Asian seabass genome assembly far exceeds that of any other fish species, and will
serve as a new standard for fish genomics.
2016-01-01T00:00:00ZTaste and odorant receptors of the coelecanth- a gene repertoire in transitionPicone, BarbaraHesse, UljanaPanji, SumirVan Heusden, PeterJonas, MarioChristoffels, Alanhttp://hdl.handle.net/10566/16082016-08-30T19:45:46Z2014-01-01T00:00:00ZTaste and odorant receptors of the coelecanth- a gene repertoire in transition
Picone, Barbara; Hesse, Uljana; Panji, Sumir; Van Heusden, Peter; Jonas, Mario; Christoffels, Alan
G-protein coupled chemosensory receptors (GPCR-CRs) aid in the perception of odors and tastes in vertebrates. So far, six GPCR-CR families have been identified that are conserved in most vertebrate species. Phylogenetic analyses indicate differing evolutionary dynamics between teleost fish and tetrapods. The coelacanth Latimeria chalumnae belongs to the lobe-finned fishes, which represent a phylogenetic link between these two groups. We searched the genome of L. chalumnae for GPCR-CRs and found that coelacanth taste receptors are more similar to those in tetrapods than in teleost fish: two coelacanth T1R2s co-segregate with the tetrapod T1R2s that recognize sweet substances, and our phylogenetic analyses indicate that the teleost T1R2s are closer related to T1R1s (umami taste receptors) than to tetrapod T1R2s. Furthermore, coelacanths are the first fish with a large repertoire of bitter taste receptors (58 T2Rs). Considering current knowledge on feeding habits of coelacanths the question arises if perception of bitter taste is the only function of these receptors. Similar to teleost fish, coelacanths have a variety of olfactory receptors (ORs) necessary for perception of water-soluble substances. However, they also have seven genes in the two tetrapod OR subfamilies predicted to recognize airborne molecules. The two coelacanth vomeronasal receptor families are larger than those in teleost fish, and similar to tetrapods, form V1R and V2R monophyletic clades. This may point to an advanced development of the vomeronasal organ as reported for lungfish. Our results show that the intermediate position of Latimeria in the phylogeny is reflected in its GPCR-CR repertoire.
2014-01-01T00:00:00Z