Biology subjects

Kakrana, A.

Publications and source records attributed to Kakrana, A..

6 recordsLinked to original sources

bioRxiv2026

Phasis: a software tool for register-resolved discovery of plant phased small RNA loci

Plant PHAS locus discovery remains challenging because phasiRNA-producing loci must be distinguished from other sRNA-producing regions with high abundance or apparent periodicity. This problem is especially acute for reproductive 24-PHAS loci, which occur within genomes that also produce abundant 24-nt siRNAs from non-PHAS regions. We present Phasis, an open-source Python software tool for plant PHAS-locus discovery from small RNA sequencing data. Phasis combines statistical evidence for phased accumulation with locus-level features and a Register-Resolved Locus Interpretation Layer that evaluates whether candidate loci show coherent phased architecture. Across diverse plant datasets, Phasis recovered validated or annotated 21- and 24-PHAS loci with a strong balance between call-level precision and reference-locus recall, and generally outperformed PhaseTank and ShortStack in matched benchmark analyses. The register-resolved interpretation layer reduced unsupported calls by separating coherent phased loci from ambiguous sRNA-producing regions. In maize dcl5 mutant libraries, Phasis showed strong depletion of 24-PHAS recovery, supporting DCL5-dependent recovery of reproductive 24-PHAS signal. Together, these results support Phasis as a biologically interpretable tool for large-scale discovery of plant DCL-dependent phasiRNA loci.

plant biology↗

bioRxiv2026

A multi-omics approach to maize (Zea mays) tassel development

The development of the male inflorescence in maize (Zea mays L.) is a complex and highly regulated process that is essential for reproductive success and yield. To gain a comprehensive understanding of the regulatory programs involved in tassel formation, including the initial specification of anther cell types, the transcriptomes, small RNAs (sRNAs), and proteomes were profiled at four developmental stages (0.5-2.0 cm). The RNAseq analysis indicates dynamic shifts in gene expression underlying the transition from indeterminate meristems to organ initiation and germinal cell determination by 2.0 cm. Complementing these data, sRNA sequencing uncovered 182 microRNAs (miRNAs) with distinct temporal patterns. A core set of 126 miRNAs was expressed throughout tassel development, while others displayed strong stage-specific enrichment. Notably, families of miRNAs that target auxin signaling were dynamically regulated, suggesting fine-tuning of hormone signaling in relation to meristem activity. Later stages were enriched for miR2275 and miR11969, which previously have both been associated with meiocytes, indicating the onset of reproductive sRNA pathways during the early stages of anther differentiation. Together, these datasets provide a broad overview of tassel development and form a backbone to enrich existing RNAseq and single cell RNAseq data sets of specific steps in tassel and initial anther development, while also adding new data on sRNA expression.

plant biology↗

bioRxiv2023

Coffee microsporogenesis and related small interfering RNAs biosynthesis have a unique pattern among eudicots suggesting a sensitivity to climate changes.

Recently, the siRNAs pathways, and especially reproductive phasiRNAs, have attracted attention in eudicots since their biological roles are still unknown and their biogenesis took different evolutionary pathways compared to monocots. In this work, we used Coffea arabica L., a recently allotetraploid formed from the hybridization of C. canephora and C. eugenioides unreduced gametes, to explore microsporogenesis and small RNAs related pathways in a eudicot crop. First, we identified the microsporogenesis stages during anther development revealing that pre-meiosis occurs in anthers of 1.5 mm inside floral buds (FBs), whereas meiosis between 1.5 and 4.2 mm FBs, and post-meiosis in FBs larger than 4.2mm. These stages coincide with the Brazilian winter, a period of FBs reduced growth which suggests temperature sensitivity. Next, we identified and quantified the expression of reproductive 21- and 24-nt phasiRNAs during coffee anther development together with their canonical and novel miRNA triggers, and characterized the DCL and AGO families. Our results showed that the pattern of reproductive phasiRNA abundance in C. arabica is unique among described eudicots and the canonical trigger car-miR2275 is involved in the processing of both 21 and 24 nt phasiRNAs. Fourteen DCL genes were identified, but DCL5, related to phasiRNA biosynthesis in monocots, was not according to its specificity for monocots. Thus, our work explored the knowledge gap about microsporogenesis and related siRNAs pathways in coffee, contributing to the control of reproductive development and to the improvement of fertility in eudicots.

plant biology↗

bioRxiv2020

Reproductive phasiRNA loci and DICER-LIKE5, but not microRNA loci, diversified in monocotyledonous plants

In monocots other than maize and rice, the repertoire and diversity of microRNAs (miRNAs) and the populations of phased, secondary, small interfering RNAs (phasiRNAs) are poorly characterized. To remedy this, we sequenced small RNAs from vegetative and dissected inflorescence tissue in 28 phylogenetically diverse monocots and from several early-diverging angiosperm lineages, as well as publicly available data from 10 additional monocot species. We annotated miRNAs, siRNAs and phasiRNAs across the monocot phylogeny, identifying miRNAs apparently lost or gained in the grasses relative to other monocot families, as well as a number of tRNA fragments misannotated as miRNAs. Using our miRNA database cleaned of these misannotations, we identified conservation at the 8th, 9th, 19th and 3 end positions that we hypothesize are signatures of selection for processing, targeting, or Argonaute sorting. We show that 21-nt reproductive phasiRNAs are far more numerous in grass genomes than other monocots. Based on sequenced monocot genomes and transcriptomes, DICER-LIKE5 (DCL5), important to 24-nt phasiRNA biogenesis, likely originated via gene duplication before the diversification of the grasses. This curated database of phylogenetically diverse monocot miRNAs, siRNAs, and phasiRNAs represents a large collection of data that should facilitate continued exploration of small RNA diversification in flowering plants.

plant biology↗

bioRxiv2018

Reproductive phasiRNAs in grasses are compositionally distinct from other classes of small RNAs

Summary and keywordsO_LILittle is known about the characteristics and function of reproductive phased, secondary, small interfering RNAs (phasiRNAs) in the Poaceae, despite the availability of significant genomic resources, experimental data, and a growing number of computational tools. We utilized machine-learning methods to identify sequence-based and structural features that distinguish phasiRNAs in rice and maize from other small RNAs (sRNAs).\nC_LIO_LIWe developed Random Forest classifiers that can distinguish reproductive phasiRNAs from other sRNAs in complex sets of sequencing data, utilizing sequence-based (k-mers) and features describing position-specific sequence biases.\nC_LIO_LIThe classification performance attained is >80% in accuracy, sensitivity, specificity, and positive predicted value. Feature selection identified important features in both ends of phasiRNAs. We demonstrated that phasiRNAs have strand specificity and position-specific nucleotide biases potentially influencing AGO sorting; we also predicted targets to infer functions of phasiRNAs, and computationally-assessed their sequence characteristics relative to other sRNAs.\nC_LIO_LIOur results demonstrate that machine-learning methods effectively identify phasiRNAs despite the lack of characteristic features typically present in precursor loci of other small RNAs, such as sequence conservation or structural motifs. The 5-end features we identified provide insights into AGO-phasiRNA interactions; we describe a hypothetical model of competition for AGO loading between phasiRNAs of different nucleotide compositions.\nC_LI

plant biology↗

bioRxiv2017

PHASIS: A computational suite for de novo discovery and characterization of phased, siRNA-generating loci and their miRNA triggers

Phased, secondary siRNAs (phasiRNAs) are found widely in plants, from protein-coding transcripts and long, non-coding RNAs; animal piRNAs are also phased. Integrated methods characterizing \"PHAS\" loci are unavailable, and existing methods are quite limited and inefficient in handling large volumes of sequencing data. The PHASIS suite described here provides complete tools for the computational characterization of PHAS loci, with an emphasis on plants, in which these loci are numerous. Benchmarked comparisons demonstrate that PHASIS is sensitive, highly scalable and fast. Importantly, PHASIS eliminates the requirement of a sequenced genome and PARE/degradome data for discovery of phasiRNAs and their miRNA triggers.

bioinformatics↗