^{update October 2025}

J.S. Pat Heslop-Harrison, Trude Schwarzacher et al. – see https://www.le.ac.uk/biology/phh4/titles.html for earlier and possibly more recent papers

See also link to Authors at NCBI / NLM US for latest automated updates.

updated June 2025 – first-names and sometimes additional keywords have been added after some references to assist searching, Abstracts and full-text links where DOI is not open access are mostly given but please contact at phh4(a)le.ac.uk if not and I will send the PDF as permitted.

• 411. Biswas MK, Ahmed B, Hijri M, Schwarzacher T, Heslop-Harrison JS. 2025. Chloroplast genome diversity and marker potentials of diverse Ensete ventricosum accessions. International Journal of Molecular Sciences IJMS 26(19): 9561.  https://doi.org/10.3390/ijms26199561 Jump to EnsetecChloroplast Abstract
• 410. Shu X, Lu R, Heslop-Harrison P, Schwarzacher T, Wang Z, Qin Y, Wang N, Zhang F. 2025. Unraveling the evolutionary complexity of Lycoris: Insights into chromosomal variation, genome size, and phylogenetic relationships. Plant Diversity: on-line first version.  https://doi.org/10.1016/j.pld.2025.06.010. Jump to Lycoris Abstract
• 409. Dwivedi SL, Vetukuri RR, Kelbessa BG, Gepts P, Heslop-Harrison P, Araujo ASF, Sharma S, Ortiz R. 2025. Exploitation of rhizosphere microbiome biodiversity in plant breeding. Trends in Plant Science 30(9): 1033-1045. https://doi.org/10.1016/j.tplants.2025.04.004. ^{Sangam Dwivedi, Ramesh Raju Vetukuri, Bekele Gelena Kelbessa, Paul Gepts, Pat Heslop-Harrison, Ademir S. F. Araujo, Shilpi Sharma, Rodomiro Ortiz.}
• 408. Gui X, Cui D, Tian Y, Schwarzacher T, Heslop-Harrison JS, Liu Q. 2024. Genome-wide identification of Lectin Receptor-Like Kinases gene family in Avena sativa and their roles in salt stress tolerance. International Journal of Molecular Sciences IJMS 25(23): 12754 https://doi.org/10.3390/ijms252312754. Jump to Flavonoid Abstract ^{Full names: Gui Xiong, Dongli Cui, Yaqi Tian, Trude Schwarzacher, JS Pat Heslop-Harrison, Qing Liu RLK genes}
• 407. Laborne AM, Barrios-Leal DY, Heslop-Harrison JS, Manfrin MH, Kuhn GCS. 2024. Genome location, evolution and centromeric contribution of satellite DNAs shared between the two closely related species Drosophila serido and D. antonietae (repleta group, buzzatii cluster). Chromosoma 134(1): 1. /https://doi.org/10.1007/s00412-024-00827-9 . Jump to Drosophila Abstract Ana Mattioli Laborne Guto Gustavo Kuhn
• 406. Rocha-Reis DA, Rodrigues-Oliveira IH, Pasa R, Menegídio FB, Heslop-Harrison JS, Schwarzacher T, Kavalco KF. 2024.  In silico characterization of satellitomes and cross-amplification of putative satDNAs in two species of the Hypostomus ancistroides complex (Siluriformes, Loricariidae). Cytogenetic and Genome Research 164(2): 121-132. https://doi.org/10.1159/000539429 On-line first. Abstract: Fish-Satellitome
• 405. Dwivedi SL, Heslop-Harrison P, Amas J, Ortiz R, Edwards D. 2024. Epistasis and pleiotropy-induced variation for plant breeding. Plant Biotechnology Journal 22: 2788-2807. https://doi.org/10.1111/pbi.14405 . Abstract: Epistasis-Pleiotropy
• 404. Cui D, Xiong G, Ye L, Gornall R, Wang Z, Heslop-Harrison P, Liu Q. 2024. Genome-wide analysis of flavonoid biosynthetic genes in Musaceae (Ensete, Musella, and Musa species) reveals amplification of flavonoid 3’,5’-hydroxylase. AoB Plants 16(5): plae049. https://doi.org/10.1093/aobpla/plae049 Abstract: Flavonoids
• 403. Liu Q, Xiong G, Wang Z, Wu Y, Tu T, Schwarzacher T, Heslop-Harrison JS. 2024. Chromosome-level genome assembly of the diploid oat species Avena longiglumis. Scientific Data 11: 412. https://doi.org/10.1038/s41597-024-03248-6 Abstract: ALO-Genome BioRxiv version: Chromosome-scale genome assembly of the diploid oat Avena longiglumis reveals the landscape of repetitive sequences, genes and chromosome evolution in grasses  bioRxiv 2022.02.09.479819; doi: https://doi.org/10.1101/2022.02.09.479819
• 402. Liu Q, Ye L, Li M, Wang Z, Xiong G, Ye Y, Tu T, Schwarzacher T, Heslop-Harrison JS. 2023. Genome-wide expansion and reorganization during grass evolution: from 30 Mb chromosomes in rice and Brachypodium to 550 Mb in Avena. BMC Plant Biology 23:627. https://doi.org/10.1186/s12870-023-04644-7. Abstract: Genome Expansion
• 401. Jones A, Bridle S, Denby K, Bhunnoo R, Morton D, Stanbrough L, Coupe B, Pilley V, Benton T, Falloon P, Matthews T, Hasnain S, Heslop-Harrison JS (Pat), Beard SJ, Pierce J, Pretty J, Zurek M, Johnstone A, Smith P, Gunn N, Watson M, Pope E, Tzachor A, Douglas C, Reynolds C, Ward N, Fredenburgh J, Pettinger C, Quested T, Cordero JP, Mitchell C, Bewick C, Brown C, Brown C, Burgess P, Challinor A, Cottrell A, Crocker T, George T, Godfray C, Hails R, Ingram J, Lang T, Lyon F, Lusher S, MacMillan T, Newton S, Pearson S, Pritchard S, Sanders D, Bellamy AS, Steven M, Trickett A, Voysey A, Watson C, Whitby D, Whiteside K. 2023. Scoping potential routes to UK civil unrest via the food system: results of a structured expert elicitation. Sustainability 15(20) 14783. https://doi.org//10.3390/su152014783″
• 400. Liu Q, Cui D, Rouard M, Heslop-Harrison JS, Schwarzacher T, Wang Z. 2025. Haplotype-resolved T2T genome assemblies of Musella lasiocarpa characterize the mechanisms of chromosomal and genome evolution in Musaceae, and provide genetic insights into cold adaptation. Submitted https://doi.org/10.10 to come.” .
• 399. Masters LE, Tomaszewska P, Hackel J, Zuntini AR, Schwarzacher T, Heslop-Harrison JS, Vorontsova MS. 2024. Phylogenomic analysis reveals five independently evolved African forage grass clades in the genus Urochloa. Annals of Botany. 2024 Feb 14:mcae022. https://doi.org/10.1093/aob/mcae022 Preprint version: bioRxiv. 2023:2023-07  https://doi.org/10.1101/2023.07.03.547487.
• 398. Balzter H, Macul M, Delaney B, Tansey K, Espirito-Santo F, Ofoegbu C, Petrovskii S, Forchtner B, Nicholes N, Payo E, Heslop-Harrison P, Burns M, Basell L, Egberts E, Stockley E, Desorgher M, Upton C, Whelan M, Yildiz A. 2023. Loss and damage from climate change: knowledge gaps and interdisciplinary approaches.  Sustainability 15: 11864. https://doi.org/10.3390/su151511864 Heiko Balzter
• 397. Alisawi O, Richert-Pöggeler KR, Heslop-Harrison JS, Schwarzacher T. 2023. The nature and organisation of tandemly repeated satellite DNAs in Petunia hybrida, related, and ancestral genomes. Frontiers in Plant Science 14-1232588.. https://doi.org/10.3389/fpls.2023.1232588. “. Osamah Alisawi
• 396. White O, Biswas M, Abebe WM, Dussert Y, Kebede F, Nichols R, Buggs RJ, Demissew S, Woldeyes F, Papadopulos AS, Schwarzacher T, Heslop-Harrison JS, Wilkin P, Borrell JS. 2023  Maintenance and expansion of genetic and trait variation following domestication in a clonal crop. Molecular Ecology 32: 4165-4180. https://doi.org/10.1111/mec.17033.
• TS. Desjardins SD, Bailey JP, Zhang B, Zhao K, Schwarzacher T. 2023. New insights into the phylogenetic relationships of Japanese knotweed (Reynoutria japonica) and allied taxa in subtribe Reynoutriinae (Polygonaceae). PhytoKeys 220: 83-108. https://doi.org/10.3897/phytokeys.220.96922.
• TS. Schmidt N, Seibt KM, Weber B, Schwarzacher T, Schmidt T, Heitkam T. 2021. Broken, silent, and in hiding: tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris). Annals of Botany 128: 281-299. https://doi.org/10.1093/aob/mcab042
• 395. Wang Z-F, Rouard M, Droc G, Heslop-Harrison JS, Ge X-J. 2023. Genome assembly of Musa beccarii shows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes. Gigascience 12: 1-20. https://doi.org/10.1093/gigascience/giad005.
• 394. Liu Q, Yuan H, Xu J, Cui D, Xiong G, Schwarzacher T, Heslop-Harrison JS. 2023. The mitochondrial genome of the diploid oat Avena longiglumis. BMC Plant Biology 23: 218. https://doi.org/10.1186/s12870-023-04217-8
• 393. Gori GB, Aschner M, Borgert CJ, Cohen S, Dietrich DR, Galli CL, Greim H, Heslop-Harrison JS, Kacew S, Kaminski NE, Klaunig JE, Marquardt HWJ, Moretto A, Pelkonen O, Roberts R, Savolainen KM, Tsatsakis A, Yamazaki H. 2023. US regulations to curb alleged cancer causes are ineffectual and compromised by scientific, constitutional and ethical violations. Archives of Toxicology 97: 1813-1822. https://doi.org/10.1007/s00204-022-03429-5 THIS DOI LINK SEEMS TO BE BROKEN AT THE PUBLISHER SITE Oct2024. https://pmc.ncbi.nlm.nih.gov/articles/PMC10182921/ is the NCBI link working
• 392. Dwivedi SW, Heslop-Harrison JS, Spillane C, McKeown PC, Edwards D, Goldman I, Ortiz R. 2023. Evolutionary dynamics and adaptive benefits of deleterious mutations in crop genepools. Trends in Plant Science 28: 685-697. https://doi.org/10.1016/j.tplants.2023.01.006.
• 391. Schwarzacher T, Liu Q, Heslop-Harrison, JS. 2023. Plant cytogenetics: from chromosomes to cytogenomics, in: Tony Heitkam and Sònia Garcia (eds) Plant Cytogenetics: Methods and Protocols Methods in Molecular Biology MIMB, vol. 2672. https://doi.org/10.1007/978-1-0716-3226-0_1. Humana Press, New York. ISBN 978-1-0716-3226-0 (eBook). https://doi.org/10.1007/978-1-0716-3226-0.
• 390. Li L, Schwarzacher T, Tomaszewska P, Liu Q, Li X, Yi K, Wu W, Heslop-Harrison JS. 2023. Protocols for chromosome preparations: molecular cytogenetics and studying genome organization in coffee. In: ILW Ingelbrecht, M do Céu Lavado da Silva and J Jankowicz-Cieslak (eds) Mutation Breeding in Coffee with Special Reference to Coffee Leaf Rust. Springer Nature, Cham, Switzerland. ISBN Free download from 10/2023: 978-3-662-67273-0 maybe https://doi.org/978-3-662-67273-0.
• 389. Liu Q, Schwarzacher T, Heslop-Harrison JS. 2023. Polyploidy: its consequences and enabling role in plant diversification and evolution. Annals of Botany 131: 1-10. https://doi.org/10.1093/aob/mcac132.
• 388. Tomaszewska P, Schwarzacher T, Heslop-Harrison JS. 2022. Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids. Frontiers in Plant Science 13:1026364. https://doi.org/10.3389/fpls.2022.1026364.
• 387. Droc G, Martin G, Guignon V, Summo M, Sempéré G, Durant E, Soriano A, Baurens F-C, Cenci A, Breton C, Shah T, Aury J-M, Ge X-J, Heslop Harrison P, Yahiaoui N, D’Hont A, Rouard M. 2022. The Banana Genome Hub: a community database for genomics in the Musaceae. Horticulture Research 9: uhac221. https://doi.org/10.1093/hr/uhac221.
• 386. Rathore P, Schwarzacher T, Heslop-Harrison JP, Bhat V, Tomaszewska P. 2022. The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass, Cenchrus ciliaris. Frontiers in Plant Science 13: 952968. https://doi.org/10.3389/fpls.2022.952968. Priyanka Rathore, Vishnu Bhat
• 385. Biswas MK, Schwarzacher T, Heslop-Harrison JS. 2022. Large scale genome analysis: genome sequences, chromosomal reorganization, and repetitive DNA in Brassica juncea and relatives. In The Brassica juncea Genome eds Chittaranjan Kole, Trilochan Mohapatra. pp. 269-281. Springer. https://doi.org/10.1007/978-3-030-91507-0_15. Manosh Biswas
• 384. Biswas MK, Schwarzacher T, Heslop-Harrison JS. 2022. Large scale genome analysis: genome sequences, chromosomal reorganization, and repetitive DNA in Brassica juncea and relatives. In The Brassica juncea Genome eds Chittaranjan Kole, Trilochan Mohapatra. pp. 269-281. Springer. https://doi.org/10.1007/978-3-030-91507-0_15.
• 383. Mustafa SI, Heslop-Harrison JS, Schwarzacher T. 2022. The complete mitochondrial genome from Iraqi Meriz goats and the maternal lineage using whole genome sequencing data. Iranian Journal of Applied Animal Science Jun 1;12(2):321-8. https://journals.iau.ir/article_691854.html. Sarbast Mustafa
• 382. Yuan HY, Cui DL, Heslop-Harrison JS, Liu Q. 2023. Research progress of β-glucan synthase gene families in cereal crops. (in Chinese). Journal of Tropical and Subtropical Botany 31(2): 295–304. doi: https://doi.org/10.11926/jtsb.4645
• 381. Taheri S, Teo CH, Heslop-Harrison JS, Schwarzacher T, Tan YS, Wee WY, Khalid N, Biswas MK, Mutha NV, Mohd-Yusuf Y, Gan HM. 2022. Genome assembly and analysis of the flavonoid and phenylpropanoid biosynthetic pathways in Fingerroot ginger (Boesenbergia rotunda). International Journal of Molecular Sciences 23(13): 7269. https://doi.org/10.3390/ijms23137269.
• 380. Zhang F, Chen F, Schwarzacher T, Heslop-Harrison JS, Teng N. 2022. The nature and genomic landscape of repetitive DNA classes in Chrysanthemum nankingense shows recent genomic changes. Annals of Botany 131(1)215–228. https://doi.org/10.1093/aob/mcac066.
• 379. Wang Z, Rouard M, Biswas MK, Droc G, Cui D, Roux N, Baurens FC, Ge XJ, Schwarzacher T, Heslop-Harrison JS, Liu Q. 2022. A chromosome-level reference genome of Ensete glaucum gives insight into diversity, chromosomal and repetitive sequence evolution in the Musaceae. Gigascience 11: 1-21. https://doi.org/10.1093/gigascience/giac027.
• 378. Ran Li, Mian Gong, Xinmiao Zhang, Fei Wang, Zhenyu Liu, Lei Zhang, Mengsi Xu, Yunfeng Zhang, Xuelei Dai, Zhuangbiao Zhang, Wenwen Fang, Yuta Yang, Huanhuan Zhang, Weiwei Fu, Chunna Cao, Peng Yang, Zeinab Amiri Ghanatsaman, Niloufar Jafarpour Negari, Hojjat Asadollahpour Nanaei, Xiangpeng Yue, Yuxuan Song, Xianyong Lan, Weidong Deng, Xihong Wang, Ruidong Xiang, Eveline M. Ibeagha-Awemu, Pat (J.S.) Heslop-Harrison, Johannes A. Lenstra, Shangquan Gan, Yu Jiang. 2023. A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes. Genome Research 2023 Mar 1;33(3):463-77. https://genome.cshlp.org/content/33/3/463.short BioRxiv: doi: https://doi.org/10.1101/2021.12.22.472709
• 377. Zhou S, Richert-Pöggeler KR, Wang Z, Schwarzacher T, Heslop-Harrison JS, Liu Q. 2024. High throughput RNA sequencing discovers symptomatic and latent viruses: an example from ornamental Hibiscus.  Acta Horticulturae 1392 ISHS 2024. 10.17660/ActaHortic.2024.1392.4 bioRxiv 2022.01.25.477650; doi: https://doi.org/10.1101/2022.01.25.477650 Abstract Hibiscus-metaviromics
• 376. Tomaszewska P, Schwarzacher T, Heslop-Harrison JS. 2022. Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids. Frontiers in Plant Science 13:1026364. https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.1026364/full
• 375. Mustafa SI, Schwarzacher T, Heslop-Harrison JS. 2022. The nature and chromosomal landscape of endogenous retroviruses (ERVs) integrated in the sheep nuclear genome. DNA 2(1): 86-103. doi: https://doi.org/10.3390/dna2010007
• 374. Tomaszewska P, Vorontsova MS, Renvoize SA, Ficinski SZ, Tohme J, Schwarzacher T, Castiblanco V, de Vega JJ, Mitchell RA, Heslop-Harrison P. 2022. Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution in Urochloa (Brachiaria). Annals of Botany 131(1).: 87–108. doi:10.1093/aob/mcab147
• 373. Higgins J, Tomaszewska P, Pellny TK, Castiblanco V, Arango J, Tohme J, Schwarzacher T, Mitchell RA, Heslop-Harrison JS, De Vega JJ. 2022. Diverged subpopulations in tropical Urochloa (Brachiaria) forage species indicate a role for facultative apomixis and varying ploidy in their population structure and evolution. Annals of Botany 130: 657-669. doi:https://doi.org/10.1093/aob/mcac115
• 372. Hanley SJ, Pellny TK, de Vega JJ, Castiblanco V, Arango J, Eastmond PJ, Heslop-Harrison JSP, Mitchell RAC. 2021. Allele mining in diverse accessions of tropical grasses to improve forage quality and reduce environmental impact. Annals of Botany 128: 627-637. doi:10.1093/aob/mcab101
• 371. Richert-Pöggeler KR, Vijverberg K, Alisawi O, Chofong GN, Heslop-Harrison JSP, Schwarzacher T. 2021. Participation of multifunctional RNA in replication, recombination and regulation of Endogenous Plant PararetroViruses (EPRVs). Frontiers in Plant Science Jun 21;12: 689307. doi:10.3389/fpls.2021.689307
• 370. Barile FA, Berry SC, Blaauboer B, Boobis A, Bolt HM, Borgert C, Dekant W, Dietrich D, Domingo JL, Galli CL, Gori GB, Hengstler JG, Heslop-Harrison P, Kacew S, Marquardt H, Mally A, Pelkonen O, Savolainen K, Testai E, Tsatsakis A, Vermeulen NP. 2021. The EU chemicals strategy for sustainability: in support of the BfR position. Archives of Toxicology Sep;95(9):3133-6. doi:10.1007/s00204-021-03125-w
• 369. Barile FA, Berry SC, Blaauboer B, Boobis A, Bolt HM, Borgert C, Dekant W, Dietrich D, Domingo JL, Galli CL, Gori GB, Hengstler JG, Kacew S, Marquardt H, Pelkonen O, Savolainen K, Heslop-Harrison JS, Tsatsakis A, Vermeulen NP. 2021. Critique of the “Comment” entitled “Pyrethroid exposure: Not so harmless after all” by Demeneix et al. (2020) published in the Lancet Diabetes Endocrinology. Toxicology Letters Apr 1;340:1-3. doi:10.1016/j.toxlet.2020.12.020
• 368. Tomaszewska P, Pellny TK, Hernández LM, Mitchell RAC, Castiblanco V, de Vega JJ, Schwarzacher T, Heslop-Harrison JS. 2021. Flow cytometry-based determination of ploidy from dried leaf specimens in genomically complex collections of the tropical forage grass Urochloa s.l. Genes Jun 23;12(7):957. doi:10.3390/genes12070957
• 367. Campos ML, Rocha-Reis DA, Heslop-Harrison JS, Schwarzacher T, Kavalco KF. 2021. Ten complete mitochondrial genomes of Gymnocharacini (Stethaprioninae, Characiformes): evolutionary relationships and a repetitive element in the Control Region (D-loop) Frontiers in Ecology and Evolution 22 July 2021. doi:10.3389/fevo.2021.650783
• 366. Agrawal N, Gupta M, Atri C, Akhatar J, Kumar S, Heslop-Harrison JS, Banga SS. 2021. Anchoring alien chromosome segment substitutions bearing gene(s) for resistance to mustard aphid in Brassica juncea-B. fruticulosa introgression lines and their possible disruption through gamma irradiation. Theoretical and Applied Genetics 134(10):3209-3224. doi:10.1007/s00122-021-03886-z
• 365.Gao JG, Heslop-Harrison P, Liu PL, Zhang RG. 2021. Panicum virgatum (Poaceae). Trends in Genetics Aug;37(8):771-772. doi:10.1016/j.tig.2021.04.009
• 364. Resende SV, Pasa R, Menegídio FB, Heslop-Harrison JS, Schwarzacher T, Kavalco KF. 2020. Complete mitochondrial genome of the endangered species Brycon nattereri (Characiformes, Characidae). F1000 Research 2020, 9:1343. doi: 10.12688/f1000research.26524.1
• 363. Agrawal N, Gupta M, Banga SS, Heslop-Harrison JS. 2021. Identification of chromosomes and chromosome rearrangements in crop Brassicas and Raphanus sativus: a cytogenetic toolkit using synthesized massive oligonucleotide libraries. Frontiers in Plant Science Dec 23;11: 598039. doi:10.3389/fpls.2020.598039
• 362. Escudeiro A, Adega F, Robinson TJ, Heslop-Harrison JS, Chaves R. 2021. Analysis of the Robertsonian (1;29) fusion in Bovinae reveals a common mechanism: insights into its clinical occurrence and chromosomal evolution. Chromosome Research 29, 301–312 . doi:10.1007/s10577-021-09667-0
• 361.Zaki NM, Schwarzacher T, Singh R, Madon M, Wischmeyer C, Hanim Mohd Nor N, Zulkifli MA, Heslop-Harrison JSP. 2021. Chromosome identification in oil palm (Elaeis guineensis) using in situ hybridization with massive pools of single copy oligonucleotides and transferability across Arecaceae species. Chromosome Research 2021 Oct 16. Online ahead of print. PMID: 34657216. doi: 10.1007/s10577-021-09675-0
• 360. Rocha-Reis DA, Pasa R, Menegidio FB, Heslop-Harrison JS, Schwarzacher T, Kavalco KF. 2020. The complete mitochondrial genome of two armored catfish populations of the genus Hypostomus (Siluriformes, Loricariidae, Hypostominae. Frontiers in Ecology and Evolution 04 December 2020.  doi: 10.3389/fevo.2020.579965
• 359. Nuraga GW, Feyissa T, Tesfaye K, Biswas MK, Schwarzacher T, Borrell JS, Wilkin P, Demissew S, Tadele Z, Heslop-Harrison JS. 2020. The genotypic and genetic diversity of enset (Ensete ventricosum) landraces used in traditional medicine is similar to the diversity found in starchy landraces. Frontiers in Plant Science 12, p. 756182. doi: 10.3389/fpls.2021.756182 .
• 358. Yemataw Z, Borrell JS, Biswas MK, White O, Mengesha W, Muzemil S, Jaypal N. Darbar JN, Ondo I, Heslop Harrison JS, Blomme G, Wilkin P. 2020. The distribution of enset pests and pathogens and a genomic survey of enset Xanthomonas wilt. bioRXiv doi: 10.1101/2020.06.18.144261 Posted 18 June, 2020.
• 357. Biswas MK, Darbar JN, Borrell JS, Bagchi M, Biswas D, Nuraga GW, Demissew S, Wilkin P, Schwarzacher T, Heslop-Harrison JS. 2020. The landscape of microsatellites in the enset (Ensete ventricosum) genome and web-based marker resource development. Scientific Reports Sep 17;10(1): 15312. doi: 10.1038/s41598-020-71984-x
• 356. Liu Q, Li X, Li M, Xu W, Schwarzacher T, Heslop-Harrison JS. 2020. Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny. BMC Plant Biology 20: 406. doi: 10.1186/s12870-020-02621-y
• 355. Tamrat S, Borrell JS, Biswas MK, Gashu D, Wondimu T, Vásquez-Londoño CA, Heslop-Harrison JS, Demissew S, Wilkin P, Howes M-JR. 2020. Micronutrient composition and microbial community analysis across diverse landraces of the Ethiopian orphan crop enset. Food Research International 2020: 109636. doi: 10.1016/j.foodres.2020.109636
• TS. Sepsi A, Schwarzacher T. 2020. Chromosome-nuclear envelope tethering – a process that orchestrates homologue pairing during plant meiosis? Journal of Cell Science 133(15): doi: 10.1242/jcs.243667
• 354. Autrup H, Barile FA, Berry C, Blaauboer BJ, Boobis A, Bolt H, Borgert CJ, Dekant W, Dietrich D, Domingo JL, Gori GB, Greim H, Hengstler J, Kacew S, Marquardt H, Pelkonen O, Savolainen K, Heslop-Harrison P, Vermeulen NP. 2020. Human exposure to synthetic endocrine disrupting chemicals (S-EDCs) is generally negligible as compared to natural compounds with higher or comparable endocrine activity. How to evaluate the risk of the S-EDCs? Computational Toxicology 14: 100124. doi:10.1016/j.comtox.2020.100124. ALSO published as “Guest Editorial” Archives of Toxicology. Archiv für Toxikologie 94(7): 2549-2557. doi: 10.1007/s00204-020-02800-8 AND J Toxicol Environ Health A. 2020 Jul 17;83(13-14):485-494. doi: 10.1080/15287394.2020.1756592. Epub 2020 Jun 18 AND Chem Biol Interact. 2020 Aug 1;326:109099. doi: 10.1016/j.cbi.2020.109099. Epub 2020 May 1. PMID: 32370863 AND Toxicol Lett. 2020 Oct 1;331:259-264. doi: 10.1016/j.toxlet.2020.04.008. Epub 2020 Apr 30 AND Toxicol In Vitro. 2020 Sep;67:104861. doi: 10.1016/j.tiv.2020.104861. Epub 2020 Apr 30.
• 353. Heslop-Harrison P. 2019. Book review: Tropical Plant Collections: Legacies from the Past? Essential Tools for the Future? Scientia Danica. Series B, Biologica eds Ib Friis and Henrik Balslev. 2017. 306 pp. ISBN 978-87-7304-407-0.Annals of Botany 123(6): vii-viii (freely accessible). doi: 10.1093/aob/mcz049
• 352. Liu Q, Li X, Zhou X, Li M, Zhang F, Schwarzacher T, Heslop-Harrison JS. 2019. The repetitive DNA landscape in Avena (Poaceae): chromosome and genome evolution defined by major repeat classes in whole-genome sequence reads. BMC Plant Biology Dec;19(1):226. pp 1-17 doi:10.1186/s12870-019-1769-z
• 351. Heslop-Harrison P. 2019. Editorial: Introducing Commentaries to Annals of Botany. Annals of Botany 124(2): iv–v (freely accessible). doi:10.1093/aob/mcz090
• 350. Escudeiro A, Adega F, Robinson TJ, Heslop-Harrison JS, Chaves R. 2019. Conservation, divergence and functions of centromeric satellite DNA families in the Bovidae. Genome Biology and Evolution 11(4): 1152-1165 (open access). https://doi.org/10.1093/gbe/evz061 
• 349. Borrell JS, Biswas MK, Goodwin M, Blomme G, Schwarzacher T, Heslop-Harrison JS, Wendawek AM, Berhanu A, Kallow S, Janssens S, Molla EL, Davis AP, Woldeyes F, Willis K, Demissew S, Wilkin P. 2019. Enset in Ethiopia: a poorly characterized but resilient starch staple. Annals of Botany 123(5): 747-766 (freely accessible). https://doi.org/10.1093/aob/mcy214
• 348. Escudeiro A, Ferreira D, Mendes-da-Silva A, Heslop-Harrison JS, Adega F, Chaves R. 2019. Bovine satellite DNAs–a history of the evolution of complexity and its impact in the Bovidae family. European Zoological Journal 86(1): 20-37 (open access). https://doi.org/10.1080/24750263.2018.1558294
• 347. Wilkin P, Davis A, Demissew S, Etherington T, Goodwin M, Heslop-Harrison P, Schwarzacher T, Willis K. 2018. A perspective to enhance innovative research with emphasis on varietal diversity and sustainable utilization of enset (Ensete ventricosum). Ethiopian Journal of Biological Sciences 17(Suppl.): 201–209. https://doi.org/10.3389/fpls.2018.00717
• 346. Nielen S, Forster BP, Heslop-Harrison JS. 2018. Mutagen effects in the first generation after seed treatment: biological effects of mutation treatments. Chapter 4 In: FAO/IAEA. Manual on Mutation Breeding – Third edition. Spencer-Lopes MM, Forster BP, Jankuloski L (eds), Food and Agriculture Organization of the United Nations. Rome, Italy. 301 pp. Free download of whole book:http://www.fao.org/3/I9285EN/i9285en.pdf
• 345. Baudouin L, Heslop-Harrison P, Pereira MG. 2018. 3.9.2 Preparing the era of marker-assisted breeding – Chapter 3. Where we need to be to secure diversity and promote use. In Bourdeix R & Prades A (Eds.), A Global Strategy for the Conservation and Use of Coconut Genetic Resources 2018-2028. pp 169-171. Montpellier, France. Bioversity International. ISBN 13:978-92-9043-984-4 Download from Bioversity Website.
• 344. Sepsi A, Fábián A, Jäger K, Heslop-Harrison JS, Schwarzacher T. 2018. ImmunoFISH: simultaneous visualisation of proteins and DNA sequences gives insight into meiotic processes in nuclei of grasses. Frontiers in Plant Science 9: article 1193. https://doi.org/10.3389/fpls.2018.01193
• 343. Velmurugan J, Milbourne D, Connolly V, Heslop-Harrison JS, Anhalt UC, Lynch MB, Barth S. 2018. An immortalized genetic mapping population for perennial ryegrass: a resource for phenotyping and complex trait mapping. Frontiers in Plant Science 9: article 717. https://doi.org/10.3389/fpls.2018.00717
• 342. Mhiret WN, Heslop-Harrison JS. 2018. Biodiversity in Ethiopian linseed (Linum usitatissimum L.): molecular characterization of landraces and some wild species. Genetic Resources and Crop Evolution 65: 1603-1614. https://doi.org/10.1007/s10722-018-0636-3 and author version https://molcyt.wordpress.com/?p=1301&preview=true

Epistasis-Pleiotropy

404. Sangam L. Dwivedi, Pat Heslop-Harrison, Junrey Amas, Rodomiro Ortiz and David Edwards. 2024. Epistasis and pleiotropy-induced variation for plant breeding. Plant Biotechnology Journal 22: 2788-2807. https://doi.org/10.1111/pbi.14405
Keywords: artificial intelligence, conserved pleiotropy, epistasis, interactions, genetic correlation, genomic selection, heterosis, high value and multi-role pleiotropy genes, machine learning algorithms, nonpleiotropy, loci, trade-off.
Summary
Epistasis refers to nonallelic interaction between genes that cause bias in estimates of genetic parameters for a phenotype with interactions of two or more genes affecting the same trait. Partitioning of epistatic effects allows true estimation of the genetic parameters affecting phenotypes. Multigenic variation plays a central role in the evolution of complex characteristics, among which pleiotropy, where a single gene affects several phenotypic characters, has a large influence. While pleiotropic interactions provide functional specificity, they increase the challenge of gene discovery and functional analysis. Overcoming pleiotropy-based phenotypic trade-offs offers potential for assisting breeding for complex traits. Modelling higher order nonallelic epistatic interaction, pleiotropy and non-pleiotropy-induced variation, and genotype x environment interaction in genomic selection may provide new paths to increase the productivity and stress tolerance for next generation of crop cultivars. Advances in statistical models, software and algorithm developments, and genomic research have facilitated dissecting the nature and extent of pleiotropy and epistasis. We overview emerging approaches to exploit positive (and avoid negative) epistatic and pleiotropic interactions in a plant breeding context, including developing avenues of artificial intelligence, novel exploitation of large-scale genomics and phenomics data, and involvement of genes with minor effects to analyse epistatic interactions and pleiotropic quantitative trait loci, including missing heritability.

Abstract Genome Expansion 402. Liu Q, Ye L, Li M, Wang Z, Xiong G, Ye Y, Tu T, Schwarzacher T, Heslop-Harrison JS. 2023. Genome-wide expansion and reorganization during grass evolution: from 30 Mb chromosomes in rice and Brachypodium to 550 Mb in Avena. BMC Plant Biology 23:627. https://doi.org/10.1186/s12870-023-04644-7.

The BOP (Bambusoideae, Oryzoideae, and Pooideae) clade of the Poaceae has a common ancestor, with similarities to the genomes of rice, Oryza sativa (2n = 24; genome size 389 Mb) and Brachypodium, Brachypodium distachyon (2n = 10; 271 Mb). We exploit chromosome-scale genome assemblies to show the nature of genomic expansion, structural variation, and chromosomal rearrangements from rice and Brachypodium, to diploids in the tribe Aveneae (e.g., Avena longiglumis, 2n = 2x = 14; 3,961 Mb assembled to 3,850 Mb in chromosomes).
Most of the Avena chromosome arms show relatively uniform expansion over the 10-fold to 15-fold genome-size increase. Apart from non-coding sequence diversification and accumulation around the centromeres, blocks of genes are not interspersed with blocks of repeats, even in subterminal regions. As in the tribe Triticeae, blocks of conserved synteny are seen between the analyzed species with chromosome fusion, fission, and nesting (insertion) events showing deep evolutionary conservation of chromosome structure during genomic expansion. Unexpectedly, the terminal gene-rich chromosomal segments (representing about 50 Mb) show translocations between chromosomes during speciation, with homogenization of genome-specific repetitive elements within the tribe Aveneae. Newly-formed intergenomic translocations of similar extent are found in the hexaploid A. sativa. The study provides insight into evolutionary mechanisms and speciation in the BOP clade, which is valuable for measurement of biodiversity, development of a clade-wide pangenome, and exploitation of genomic diversity through breeding programs in Poaceae.

ALO-genome

403. Liu Q, Xiong G, Wang Z, Wu Y, Tu T, Schwarzacher T, Heslop-Harrison JS. 2024. Chromosome-level genome assembly of the diploid oat species Avena longiglumis. Scientific Data in press April 2024 #SDATA-23-02613B. https://doi.org/10.1038/s41597-024-03248-6

Diploid wild oat Avena longiglumis has nutritional and adaptive traits which are valuable for common oat (A. sativa) breeding. The combination of Illumina, Nanopore and Hi-C data allowed us to assemble a high-quality chromosome-level genome of A. longiglumis (ALO), evidenced by contig N50 of 12.68 Mb with 99% BUSCO completeness for the assembly size of 3,960.97 Mb. A total of 40,845 protein-coding genes were annotated. The assembled genome was composed of 87.04% repetitive DNA sequences. Dotplots of the genome assembly (PI657387) with two published ALO genomes were compared to indicate the conservation of gene order and equal expansion of all syntenic blocks among three genome assemblies. Two recent whole-genome duplication events were characterized in genomes of diploid Avena species. These findings provide new knowledge for the genomic features of A. longiglumis, give information about the species diversity, and will accelerate the functional genomics and breeding studies in oat and related cereal crops.

Hibiscus-metaviromics 377. Zhou S, Richert-Pöggeler KR, Wang Z, Schwarzacher T, Heslop-Harrison JS, Liu Q. 2022. High throughput RNA sequencing discovers symptomatic and latent viruses: an example from ornamental Hibiscus.  Acta Horticulturae 1392 10.17660/ActaHortic.2024.1392.4 bioRxiv 2022.01.25.477650; doi: https://doi.org/10.1101/2022.01.25.477650 Abstract ISHS Acta Horticulturae 1392: XV International Symposium on Virus Diseases of Ornamental Plants High throughput RNA sequencing discovers symptomatic and latent viruses: an example from ornamental hibiscus
Authors: S. Zhou, K.R. Richert-Pöggeler, Z. Wang, T. Schwarzacher, J.S. Heslop-Harrison, Q. Liu
Keywords: RNA-seq, hibiscus, genome analysis, electron microscopy DOI: 10.17660/ActaHortic.2024.1392.4

Hibiscus rosa-sinensis L. (Hibiscus, Malvaceae) is an ornamental species grown widely in landscape plantings. We collected leaves from a plant on an urban sidewalk near a market in Guangzhou that showed multiple symptoms of leaf rolling, deformation and chlorosis. Initial evaluation by electron microscopy using negative staining of dip preparations revealed the presence of Tobamovirus-like particles. Total RNA was extracted and without any RNA selection based on sequence, was used for cDNA library construcHition and high-throughput survey sequencing. Chloroplast, ribosomal, and mitochondrial sequences were filtered out of the 814 Mb of clean sequence data (from 2,712,161 paired reads of 150 bp), eliminating 79.1% of reads. 1,135,848×150 bp of the sequence was retained and screened for viral sequences. Assembly of these sequences revealed nine virus species from seven virus genera: tobacco mosaic virus, tobacco mild green mosaic virus and hibiscus latent Singapore virus (Tobamovirus), turnip mosaic virus (Potyvirus), potato virus M (Carlavirus), hibiscus chlorotic ringspot virus (Betacarmovirus), Fabavirus sp. (Fabavirus), cotton leaf curl Multan virus (Begomovirus) and Chenopodium quinoa mitovirus 1 (a putative Mitovirus replicating in mitochondria). Mapping the reads to complete virus reference sequences showed high and uniform coverage of the genomes from 3,729× coverage for turnip mosaic virus to 22× for cotton leaf curl Multan virus. By comparison, nuclear reference genes actin showed 14× coverage and polyubiquitin 27×. Notable variants from reference sequences (SNPs) were identified. With the low cost of sequencing and potential for semi-automated bioinformatic pipelines, the whole-RNA approach has huge potential for identifying multiple undiagnosed viruses in ornamental plants, resulting in the ability to take preventive measures in production facilities against virus spread and to improve product quality for the mutual benefit of producers and consumers.

Fish-Satellitome

Fish-Satellitome

In silico Characterization of Satellitomes and Cross-Amplification of Putative satDNAs in Two Species of the Hypostomus ancistroides Complex (Siluriformes, Loricariidae)
Dinaíza Abadia Rocha-Reis; Igor Henrique Rodrigues-Oliveira; Rubens Pasa; Fabiano Bezerra Menegídio; John Seymour (Pat) Heslop-Harrison; Trude Schwarzacher; Karine Frehner Kavalco
Cytogenet Genome Res 121–132.
https://doi.org/10.1159/000539429
Introduction: The mapping of the satellite DNA on chromosomes is vital to understanding the distribution and evolution of repetitions in the genome since these chromosomal studies have shown the origin, evolutionary mode, and function of repetitive sequences. This study aimed to prospect the satellitome and determine its location in the genome of two cryptic species of Hypostomus, H. aff. ancistroides and H. ancistroides, with and without XX/XY sexual chromosome system. Methods: Mitotic chromosomes and DNA extraction were obtained according to protocols. After the whole genome sequencing, the satDNAs were retrieved, amplified, and hybridized in chromosome preparations for male and female individuals. Results: We found 30 satellite families (47 variants, two superfamilies) in H. ancistroides and 38 satellite families (45 variants, four superfamilies) in H. aff. ancistroides. The sequences varied from 14 bp to 2,662 bp in H. ancistroides and from 14 bp to 2,918 bp in H. aff. ancistroides. We did not observe any tandem repeats that were exclusive to each of the libraries; however, many sequences showed very different abundances and copy numbers between the libraries. Four satDNAs did not hybridize on the chromosomes of either species. Conversely, one satDNA hybridized in both species, HxySat1-80. However, the phenotypes found varied among species, populations, and in the same individual. There was no sign of HanSat3-464 and HanSat11-335 in any individuals of H. aff. ancistroides, but markings were in the chromosomes of H. ancistroides. HxySat12-1127 and HxySat8-52, on the other hand, were only hybridized in H. aff. ancistroides, while H. ancistroides had a negative sign. No hybridization of satDNAs was found in the X and Y sex chromosomes as they were mostly composed of euchromatin. Conclusion: We distinguish H. aff. ancistroides as genetically different from H. ancistroides, recognizing that such characteristics go far beyond morphological, karyotypic, and molecular data. Our data support the differential abundance and location of satellite DNAs and confirm that many organisms, including fish, have repetitive sequences that validate the library hypothesis. All found and validated satDNAs and the characterization of the satellitomes of the two species represent important contributions to cytogenomic studies of the genus Hypostomus.
Keywords: Chromosomal evolution, Cytogenomics, Fluorescent in situ hybridization, Repetitive DNA, Satellite DNA

Flavonoids

Genome-wide analysis of flavonoid biosynthetic genes in Musaceae (Ensete, Musella, and Musa species) reveals amplification of flavonoid 3’,5’-hydroxylase
Dongli Cui, Gui Xiong, Lyuhan Ye, Richard Gornall, Ziwei Wang, Pat Heslop-Harrison, Qing Liu
AoB PLANTS, plae049, https://doi.org/10.1093/aobpla/plae049

Flavonoids in Musaceae are involved in pigmentation and stress responses, including cold resistance, and are a component of the healthy human diet. Identification and analysis of the sequence and copy number of flavonoid biosynthetic genes are valuable for understanding the nature and diversity of flavonoid evolution in Musaceae species. In this study, we identified 71 to 80 flavonoid biosynthetic genes in chromosome-scale genome sequence assemblies of Musaceae, including those of Ensete glaucum, Musella lasiocarpa, Musa beccarii, M. acuminata, M. balbisiana, and M. schizocarpa, checking annotations with BLAST and determining the presence of conserved domains. The number of genes increased through segmental duplication and tandem duplication. Orthologues of both structural and regulatory genes in the flavonoid biosynthetic pathway are highly conserved across Musaceae. The flavonoid 3’,5’-hydroxylase gene F3’5’H was amplified in Musaceae and ginger compared with grasses (rice, Brachypodium, Avena longiglumis, and sorghum). One group of genes from this gene family amplified near the centromere of chromosome 2 in the x = 11 Musaceae species. Flavonoid biosynthetic genes displayed few consistent responses in the yellow and red bracts of Musella lasiocarpa when subjected to low temperatures. The expression levels of MlDFR2/3 (dihydroflavonol reductase) increased while MlLAR (leucoanthocyanidin reductase) was reduced by half. Overall, the results establish the range of diversity in both sequence and copy number of flavonoid biosynthetic genes during evolution of Musaceae. The combination of allelic variants of genes, changes in their copy numbers, and variation in transcription factors with the modulation of expression under cold treatments and between genotypes with contrasting bract-colours suggests the variation may be exploited in plant breeding programmes, particularly for improvement of stress-resistance in the banana crop.

Anthocyanins, banana, diversification, F3’5’H, F3’H, flavonoids, genetics, genomics, ginger, monocotyledons, Musaceae

Lycoris

Unraveling the Evolutionary Complexity of Lycoris: Insights into Chromosomal Variation, Genome Size, and Phylogenetic Relationships Xiaochun Shu, Ruisen Lu, Pat Heslop-Harrison, Trude Schwarzacher, Zhong Wang, Yalong Qin, Ning Wang, Fengjiao Zhang. Plant Diversity 2025

•Correlations between Lycoris genome size and ploidy-level groups (i.e., diploid or aneuploid) suggest roles for post-polyploid diploidization, aneuploidy, and dysploidy in speciation.

•Phylogenetic analyses based on chloroplast genomes and nuclear DNA sequences revealed significant discordance, indicating a complex reticulate evolution and historical hybridization, which may complicate morphological classification.

•We propose a putative speciation pathway involving multiple hybridization and polyploidization, with allopolyploidy playing a predominant role.

Hybridization and polyploidy are key drivers of species diversity and genome variation in Lycoris, but their cytological and evolutionary consequences remain poorly understood. Here, we investigated chromosome numbers and genome sizes in 64 accessions representing the morphological diversity across the genus. Chromosome numbers ranged from 12 to 33, with seven accessions newly identified, including L. chunxiaoensis (2n = 33), two putative L. guangxiensis (2n = 19), and five natural hybrids (2n = 16, 18, 29, 33). Genome sizes varied from 18.03 Gb (L. wulingensis) to 32.62 Gb (L. caldwellii). Although no significant correlation was found between genome size and chromosome number across all accessions, a strong correlation within ploidy-level groups (i.e., diploid or aneuploid) suggested roles for post-polyploid diploidization, aneuploidy, and dysploidy in speciation. Phylogenetic analyses based on chloroplast genomes and nuclear DNA sequences revealed significant discordance, indicating a complex reticulate evolution and historical hybridization, which may complicate morphological classification. Chromosome number aligned more closely with morphological groups, underscoring the necessity of integrating cytological, molecular, and morphological data for accurate taxonomy, particularly in large-genome taxa. Based on this evidence, we propose a putative speciation pathway involving multiple hybridization and polyploidization events, with allopolyploidy playing a predominant role. Furthermore, our results indicate that the species L. insularis and L. longifolia are geographic populations of L. sprengeri and L. aurea, respectively, and confirmed the distribution of L. traubii and L. albiflora in mainland China. These findings offer new insights into the mechanisms underlying speciation, interspecific relationships, and the evolutionary history of Lycoris. Keywords: Lycoris Chromosome variation Genome size Hybridization Polyploidy Phylogenetics

Drosophila

Satellite DNAs are highly repetitive, tandemly arranged sequences, typically making up large portions (> 20%) of the eukaryotic genome. Most satDNAs are fast evolving and changes in their abundance and nucleotide composition may be related to genetic incompatibilities between species. Here, we used Illumina paired-end sequencing raw data and graph-based read-clustering with the TAREAN bioinformatic tool to study the satDNAs in two cactophilic neotropical cryptic species of Drosophila from the buzzatii cluster (repleta group), D. serido and D. antonietae, from five localities in Brazil. Both species share the same four families of satDNAs: pBuM, DBC-150, CDSTR138 and CDSTR230. They represent less than 4% of the genomic DNA and there are no large differences in the abundance of each satDNA between species. Despite not being the most abundant satDNA, CDSTR138 was found to be associated with most centromeres. All four satDNAs showed instances where repeats are more homogeneous within than between species, a phenomenon known as concerted evolution. On the other hand, there was no evidence for concerted evolution at the population level. Thus, these satDNAs may also be useful as potential markers for species identification. The low levels of satDNA differentiation (both quantitatively as qualitatively) between the two species might be among the reasons that allowed the establishment of a hybrid zone between the two species in the southern coast of Brazil.

EnseteChloroplasst

Ensete ventricosum is a morphologically gigantic, monocot, diploid sister to the banana plant species. It is commercially cultivated as a starch source, only in Ethiopia, where it feeds twenty million people. Here, the complete chloroplast (CP) genomes of 15 diverse landraces of E. ventricosum were assembled and annotated, for comparative genomics, genetic diversity analysis, and molecular marker development. The assembled E. ventricosum CP genomes ranged between 168,388 and 168,806 bp. The sampled CP genomes were quadripartite in structure and had two single-copy regions, a large single-copy region (LSC, average length 88,657 bp), and a small single-copy region (SSC, average length 11,098 bp) separated by inverted repeat regions (IR, average length 34,437 bp). The total number of annotated genes varies between 135 and 138, including 89–92 protein-coding genes, 38 tRNA genes, and 4 rRNA genes. All CP genes, including non-functional ones and intergenic regions, were transcribed with the transcriptome, covering almost 92% of the E. ventricosum CP genome. Codon usage, amino acid frequency, GC contents, and repeat nucleotides were similar among the 15 landraces. Mono- and tetranucleotide simple sequence repeats (SSRs) were found more frequently than other SSRs. An average of 71% of these SSRs were located in the LSC region, and the majority of the SSR motifs were composed of A/T nucleotides. A phylogenetic analysis of the 15 Ensete landraces indicated a common evolutionary origin, while the China sample was positioned separately, suggesting notable genetic differences. This study presents a comparative analysis of the chloroplast genomes of 15 E. ventricosum landraces, providing valuable insights into their genetic diversity and evolution. The identified SSR markers and conserved genomic features offer essential resources for future research and an improvement in Ensete conservation and breeding.

Keywords: 

plastid genome; comparative genomics; phylogenomic; molecular marker; genomic resource; RNA editing