Memorial lecture to University of Delhi HYM H.Y. Mohan Ram giving results about our molecular cytogenetics and cytogenomics research in University of Leicester and South China Botanical Garden

1. HY Mohan Ram Memorial Lecture
September 24, 1930 to June 18, 2018
Botany from Evolution and Phylogeny to
Biodiversity and Sustainability
“A passion for plant life - A specialist in general botany”
Pat Heslop Harrison
Institute for Environmental Futures, University of Leicester, UK
South China Botanical Garden SCBG, CAS, China
phh@molcyt.com
www.molcyt.com
Twitter Pathh1
H. Y. Mohan Ram (1930–2018)
From K. R. Shivanna Current Science

2. • Steward, Maheshwari,
Nitsch – memories
• HE Street – PHH is his
successor in University
of Leicester
A group photograph taken during the symposium shows, sitting from left to right: N S Rangaswamy (Convenor), B M Johri,
J Reinert, F C Steward, P Maheshwari, J Swarbrick, H E Street, J P Nitsch and B Sen. HYM is standing at the extreme left in
the last row.

3. • It is paradoxical that at a time when there is global concern for the
conservation of biodiversity, [India] should face an acute shortage of
experts who can study, evaluate and explain the role of the wide
variety of organisms that it has.
• We need trained persons who can quantify biodiversity and
determine the conservation status of species. More importantly, we
need to equip them with modern methods of studying, analysing,
storing and retrieving information ... There has been an over-
emphasis on areas such as molecular biology, biotechnology and
DOI: 10.1007/BF02708373 https://link.springer.com/article/10.1007/BF02708373

4. • My father, Jack Heslop-Harrison, came to Delhi University for two
months in 1973 and delivered a series of 10 lectures. HYM writes “I
have happy memories of accompanying him on a field trip to the
Southern Alps in New Zealand with several international experts on
reproductive biology.”
• PHH very first publication was 1. Shivanna KR, Heslop-Harrison Y, Heslop-Harrison JS.
1978. Inhibition of the pollen tube in the self-incompatibility response of grasses. Incompatibility
Newsletter 10: 5-7.
• A recent publication was 386. Rathore P, Schwarzacher T, Heslop-Harrison JP, Bhat V,
Tomaszewska P. 2022. Cenchrus ciliaris. Frontiers in Plant
Science 13: 952968. https://doi.org/10.3389/fpls.2022.952968.
• Maheshwari – memories in 1960s as young child
• Shiv Shivanna – first author of my first publication
• Vishnu Bhat – 2022 joint publication

5. Genes
DNA packaged in chromatin

6. Why chromosomes, repetitive DNA and
cytogenomics?
• Genome evolution
• Speciation, polyploidy and hybridization
• Phylogeny
• Biodiversity
• Impact:
–Conservation and biodiversity
–Genetic improvement and breeding
HMY Ram: Study, evaluate and explain the … wide variety of organisms
Theodore Dobzhansky: Nothing makes sense except in the light of evolution
Botany from Evolution and Phylogeny to Biodiversity and Sustainability Pat Heslop-Harrison

7. Organelle sequences
from chloroplasts or
mitochondria
Sequences from
viruses
Transgenes introduced
with molecular biology
methods
Genes, regulatory and non-
coding low-copy sequences
Dispersed repeats
Repetitive DNA sequences
Nuclear
Genome
Tandem repeats
Satellite sequences
DNA transposons
Retrotransposons
Centromeric
repeats
Structural
components of
chromosomes
Telomeric
repeats
Simple sequence
repeats or
microsatellites
Repeated genes
Subtelomeric
repeats
45S and 5S
rRNA genes
Blocks of tandem
repeats at discrete
chromosomal loci
DNA sequence components of the nuclear genome
After Biscotti, PHH et al. Chromosome Research 2015
Other genes
Transposable elements
Autonomous/
non-autonomous
Dispersed repeats
that we don’t know
about – except each is
significant proportion
of genome

8. Chromosomal sequence organization
Ziwei Wang, Qing Liu, PHH et al. GigaScience 2022, 11, giac027
Eleusine coracana
A chromosome-scale genome assembly of Ensete glaucum
Wild banana:
482Mb genome
Distribution of
b: genes
c,d,e: repeats
Centre:
Ancestral duplications

9. Sequence evolution: two banana genera
Wang et al. GigaScience, 2022, 11, giac027 using
RepeatExplorer by Macas, Novak et al.
Eleusine coracana
A chromosome-scale genome assembly of Ensete glaucum
Genus-specific repeats –
Dispersed retroelements
Localized tandem repeats
Together >70% of the DNA
Musa
Ensete/Musella
Copia
Gypsy
DNA
Trans-
posons

10. • Tandem repeats – one copy next to another
• Shown in dotplots

12. Sequence organization: centromeres
Wang et al. GigaScience, 2022, 11, giac027
Eleusine coracana
A chromosome-scale genome assembly of Ensete glaucum
Green / Pink : interspersed retroelements
Chromosome eg04 (nt 6,890,000- 6,990,400)
Single
Nanopore
read
(94kb)
Green / Pink : interspersed retroelements

13. 18S 5.8S ITS2
ITS1 NTSL
26S
STR
MuTR
NTSR
45S rDNA repeat unit in a banana species
ZiWei Wang, Qing Liu

14. Insertion of a retroelement in
the rDNA array with
characteristic LTRs (Long
Terminal Repeats)

16. • Measuring genetic differences with
molecular markers to trace both
species and varietal/genotypic
diversity
• Staple starchy food in Musaceae with
medicinal uses
Utility of GBS data: 1. Genetic Diversity

17. Utility of GBS data: 2. Population structure
K=3

18. From x=9 to x=11
Wang et al. GigaScience, 2022, 11, giac027
A chromosome-scale genome assembly of Ensete glaucum
eg01 eg02 eg03 eg04 eg05 eg06 eg07 eg08 eg09
ma01 ma02 ma03 ma04 ma05 ma06 ma07 ma08 ma09 ma10 ma11
45S
Musa acuminata x=11
Ensete glaucum x=9
Centromere regions
45S

19. Brassica genome
reorganization
with oligoprobes
Diploids:
Cabbage B.
oleracea
Turnip B. rapa
Black mustard B.
nigra
Tetraploids:
Oilseed B. napus
Indian oil B. juncea
African mustard B.
carinata
Neha Agrawal, Surinder Banga

20. B. rapa cv Purple Top
Milan Turnip
8 labelled chrs, one site
each
B. rapa Pak Choi
cv Chiffu -401
6 labelled chrs, one has 2 sites
Neha Agrawal, Surinder Banga

21. Introgression of wild Brassica fruticulosa chromosome segments into
Brassica juncea
(a) AD-101 and (b) AD-64 A01, A05, B02, B03 and B04 in AD-101 and
chromosomes A05, B02, B03 and B04 in AD-64
Surinder Banga, Neha Agrawal 2022

22. Qing Liu, PHH et al. bioRxiv 2022, 479819
3.85 Gb chromosome assembly for genome evolution
A chromosome-scale genome assembly of Avena longiglumis
1.6 cm long spikelet
of Avena longiglumis
a diploid oat
Density of
b Transposable element (TE, pink)
c LTR TE (purple) density
d LINE density (orange)
e Helitron density (cyan)
f-j Gene locations
k/l Expression profiling of genes
Centre Syntenic links

23. Qing Liu
Grass genome evolution
Genome expansion in diploid grasses:
from small, ancestral-type grasses (rice OS , Brachypodium BD) to Avena
Novel result:
Genome expansion to c. 10x larger Avena is relatively
uniform from telomere to sub-centromeric region
Not hypothesis of gene blocks interspersed with repeats and non-homologous
terminal region

24. Qing Liu
Grass genome evolution
Genome expansion in diploid grasses:
from small, ancestral-type grasses (rice OS , Brachypodium BD) to Avena
Novel result:
Genome expansion to c. 10x larger Avena is relatively
uniform from telomere to sub-centromeric region

25. Qing Liu
Grass
genome
evolution
Chromosomal evolution in blocks
includes nesting as well as translocations
OS06_AL05_
BD03
OS08_AL05_
BD03
AGK post ρ 14,241 genes
Oryza sativa Brachypodium
distachyon
Avena strigosa
Avena atlantica Avena longiglumis
Avena eriantha
ρ WGD

26. Qing Liu & PHH
Evolutionary chromosome translocations
Chromosome rearrangement in diploid Avena species
Multiple distal, inter-chromosome
translocations occur during evolution of
diploid species.
Not like translocations in wheats (Triticeae):
Not hypothesis of a few whole-arm rearrangements
A. strigosa
A. longiglumis
A. eriantha

27. Qing Liu & PHH
Annals Botany
2023
Evolutionary chromosome translocations
Chromosome rearrangement in hexaploid Avena species
Similar distal inter-genomic
translocations between
chromosomes in derived
hexaploid Avena

28. Speciation via polyploidy
Polyploidy and its role in diversification and evolution
Heslop-Harrison JS, Schwarzacher T, Liu Q. 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
Chromosome number, genome size, repetitive
DNA sequences, genes and regulatory
sequences and their expression evolve following
polyploidy – generating diversity and possible
novel traits and enabling species diversification.
6x Avena sativa, oats, showing translocations &
repetitive sequence homogenization in ancestral
diploid genome (labelled orange, blue, green)
Our other papers on Musaceae and Avena showed
chromosome evolution, genome rearrangement and
expansion in diploids with no recent polyploid events.

29. T2T genome assembly of
haplotypes of Musella lasiocarpa
A B C
Structural variation
Screen functional genes
Genomicresourcesmining
Genome Assembly Progress
2017: <1Gb genomes
2018: tens of thousands of fragmented contigs – 500x
coverage in 150bp reads N50=3Mb
2019: tens of contigs N50=20Mb ending in retroelements
2020: polyploid genomes assembled
2021: chromosome-scale assembly: N50=chromosome
length
2022: chromosomes assembled out to telomeres
[TT(T)AGGG]n; alternative configurations
2023: parental haplotypes assembled separately; polyploids
assembled
? 2024: methylation pattern of whole genome assembly

30. Complexity of mitochondrial genomes
Sorghum bicolor
Qing Liu et al. 2023
Gene exchange between the organelle genome and the
nuclear genome of A. longiglumis has undergone a
continuous and dynamic evolutionary process
Themitochondrialgenomelengthof A. longiglumis
was548kb,and39protein-codinggenesannotated:
Complex,repeat-mediatedstructure
PACMAD
BOP

32. We want to eat … we produce enough food but are using more resources than
available, degrade the planet, and want to feed more people better …
A cow emits the same greenhouse gas as a diesel car –
complex interaction of genetics of 1) feed, 2) cow and 3) rumen microbiota
Oligonucleotide pools, baits and tropical forage grasses
Digital Twins for Methane Reduction in Ruminants
Baihua Li, Paulina Tomaszewska, Lizo Masters, Hess Ekkeh; RGB Kew: Bat Vorontsova

33. Progress towards bringing together novel traits in hybrids
Understanding genome composition of 4x U. brizantha
BBDD
Paulina Tomaszewska pt186@leicester.ac.uk Urochloa polyploidy

34. Paulina Tomaszewska
pt186@le.ac.uk
Urochloa polyploidy
and breeding
Annals of Botany
131: 87–107,
2023
https://doi.org/10.

35. Genome
composition
of 6x U.
humidicola
Paulina Tomaszewska

36. • A key target is forage
quality: enhanced
digestibility decreases the
amount of land required,
and enhanced lipid
content decreases
methane emissions from
cattle.
• We found 953 genetic
polymorphisms, seven
putative LOF alleles
confering increased lipid
content and digestibility

38. A third of GHG emissions come
from Agriculture
•Nitrous oxide,
methane and
carbon dioxide
•Methane: 84
times greater
global warming
potential than
carbon dioxide
over 20 years
https://energy.ec.europa.eu/topics/oil-gas-and-coal/methane-emissions_en

40. • How do genomes evolve?
–Gene mutation very rarely
• (human: 10−8
/site/generation)
–Chromosome evolution
–Polyploidy and genome duplication
–Repetitive sequences: mobility & copy number
• (10−4
/generation in µsat)
–Recombination
–Epigenetic aspects: centromeres & expression

41. HMY: when there is global concern for the conservation of biodiversity [we need to] study, evaluate and
explain the role of the wide variety of organisms that the [world] has. We need trained persons who can
quantify biodiversity and determine the conservation status of species. More importantly, we need to equip
them with modern methods of studying, analysing, storing and retrieving information

42. HY Mohan Ram Memorial Lecture
September 24, 1930 to June 18, 2018
Botany from Evolution and Phylogeny to
Biodiversity and Sustainability
“A passion for plant life - A specialist in general botany”
Pat Heslop Harrison
phh@molcyt.com
www.pubs.molcyt.com
And many collaborators: from Shiv Shivanna to Vishnu Bhat/Priyanka
Rathore; and particularly Trude Schwarzacher, Qing Liu, Ziwei Wang,
Paulina Tomaszewska, Manosh Biswas, Bat Vorontsova, Lizo Masters,
Neha Agrawal …