Repetitive genomic regions and the inference of demographic history

Patil, Ajinkya Bharatraj; Vijay, Nagarjun

doi:10.1038/s41437-021-00443-8

Cited by 20 publications

(18 citation statements)

References 97 publications

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“…The estimates of historical effective population size (N e ) reflect evolutionary processes such as actual changes in population size, population structure, gene flow ( Mazet et al., 2015 , 2016 ), and linked selection ( Schrider et al., 2016 ) and/or regions of the genome used ( Patil and Vijay, 2021 ). Hence, we evaluated the effect of different genomic regions in estimating demographic histories.…”

Section: Resultsmentioning

confidence: 99%

Jack of all trades: Genome assembly of Wild Jack and comparative genomics of Artocarpus

et al. 2022

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Artocarpus (Moraceae), known as breadfruits for their diverse nutritious fruits, is prized for its high-quality timber, medicinal value, and economic importance. Breadfruits are native to Southeast Asia but have been introduced to other continents. The most commonly cultivated species are Artocarpus heterophyllus (Jackfruit) and Artocarpus altilis (Breadfruit). With numerous smaller but nutritionally comparable fruits on a larger tree, Artocarpus hirsutus, also called “Wild Jack” or “Ayani”, is an elusive forest species endemic to Indian Western Ghats. In this study, we sequenced and assembled the whole genome of Artocarpus hirsutus sampled from the sacred groves of Coorg, India. To decipher demographic and evolutionary history, we compared our Wild Jack genome with previously published Jackfruit and Breadfruit genomes. Demographic history reconstruction indicates a stronger effect of habitat rather than phylogeny on the population histories of these plants. Repetitive genomic regions, especially LTR Copia, strongly affected the demographic trajectory of A. heterophyllus. Upon further investigation, we found a recent lineage-specific accumulation of LTR Copia in A. heterophyllus, which had a major contribution to its larger genome size. Several genes from starch, sucrose metabolism, and plant hormone signal transduction pathways, in Artocarpus species had signatures of selection and gene family evolution. Our comparative genomic framework provides important insights by incorporating endemic species such as the Wild Jack.

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Section: Resultsmentioning

confidence: 99%

Jack of all trades: Genome assembly of Wild Jack and comparative genomics of Artocarpus

et al. 2022

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“…Using the assembled genome of B. sinensis generated in this study as a reference, we applied dDocent v2.7.6, 73 a bash pipeline, to call the SNPs in 154 individuals of the species. Within this pipeline, we used sickle v1.33 ( https://github.com/najoshi/sickle , last accessed 7 April 2021) to trim the paired-end reads of each individual by removing reads with lengths of <80 bp and base quality values <30.…”

Section: Methodsmentioning

confidence: 99%

The genome of the Paleogene relic treeBretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs

et al. 2022

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Among relic species, genomic information may provide the key to inferring their long-term survival. Therefore, in this study, we investigated the genome of the Paleogene relic tree species, Bretschneidera sinensis, which is a rare endemic species within southeastern Asia. Specifically, we assembled a high-quality genome for B. sinensis using PacBio high-fidelity and high-throughput chromosome conformation capture reads and annotated it with long and short RNA sequencing reads. Using the genome, we then detected a trade-off between active and passive disease defences among the gene families. Gene families involved in salicylic acid and MAPK signalling pathways expanded as active defence mechanisms against disease, but families involved in terpene synthase activity as passive defences contracted. When inferring the long evolutionary history of B. sinensis, we detected population declines corresponding to historical climate change around the Eocene–Oligocene transition and to climatic fluctuations in the Quaternary. Additionally, based on this genome, we identified 388 single nucleotide polymorphisms (SNPs) that were likely under selection, and showed diverse functions in growth and stress responses. Among them, we further found 41 climate-associated SNPs. The genome of B. sinensis and the SNP dataset will be important resources for understanding extinction/diversification processes using comparative genomics in different lineages.

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“…We masked the respective genomic region using BEDTOOLS maskfasta and followed similar steps mentioned above to get the demographic estimation. To assess the effect of each individual repeat family/type, we followed the published protocol/scripts (Patil and Vijay, 2021). We used filters like -C50, - Q30, -q 20 for bcftools mpileup to ensure quality bases and mapped reads to be considered in the variant calling.…”

Section: Methodsmentioning

confidence: 99%

“…We found that A. altilis underwent demographic contraction ~ 2 to 1 million years ago The estimates of historical effective population size (N e ) reflect evolutionary processes such as actual changes in population size, population structure, gene flow (Mazet et al, 2015(Mazet et al, , 2016, and linked selection (Schrider et al, 2016) and/or regions of the genome used (Patil and Vijay, 2021). Hence, we evaluated the effect of using different genomic regions in estimating demographic histories.…”

Section: Demography Rather Than Phylogeny Determines the Population H...mentioning

confidence: 99%

Jack of all trades: genome assembly of Wild Jack and comparative genomics of Artocarpus

Patil

Vajja

Raghavendra

et al. 2022

Preprint

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Known as breadfruits for their diverse nutritious fruits, the Artocarpus (Moraceae) genus is prized for its high-quality timber, medicinal value, and economic importance. Breadfruits are native to Southeast Asia but have been introduced to other continents. The most commonly cultivated species are Artocarpus heterophyllus (Jackfruit) and Artocarpus altilis (Breadfruit). With numerous smaller but nutritionally comparable fruits on a large tree, Artocarpus hirsutus, also called "Wild jack" or "Ayani" is an elusive forest species endemic to Indian Western Ghats. In this study, we sequenced and assembled the whole genome of Artocarpus hirsutus sampled from sacred groves of Coorg, India. We compared our Wild jack genome with previously published Jackfruit and Breadfruit genomes to decipher demography and evolution. Demographic history reconstruction indicates a stronger effect of habitat rather than phylogeny on the population histories of these plants. Repetitive genomic regions, especially LTR Copia, strongly affected the demographic trajectory of A. heterophyllus. Upon further investigation, we found a recent lineage-specific accumulation of LTR Copia in A. heterophyllus, which results in its larger genome size. Gene family evolution and signatures of selection identified multiple genes from starch, sucrose metabolism, plant hormone signal transduction, etc., in Artocarpus species. Our comparative genomic framework provides important insights by incorporating endemic species such as the Wild jack.

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Repetitive genomic regions and the inference of demographic history

Cited by 20 publications

References 97 publications

Jack of all trades: Genome assembly of Wild Jack and comparative genomics of Artocarpus

Jack of all trades: Genome assembly of Wild Jack and comparative genomics of Artocarpus

The genome of the Paleogene relic treeBretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs

Jack of all trades: genome assembly of Wild Jack and comparative genomics of Artocarpus

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